WorldWideScience

Sample records for coarse graining rna

  1. Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Zonghui [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Luijten, Erik, E-mail: luijten@northwestern.edu [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208 (United States)

    2015-12-28

    All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.

  2. Predicting RNA 3D structure using a coarse-grain helix-centered model

    Science.gov (United States)

    Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2015-01-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

  3. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.

    Science.gov (United States)

    Jonikas, Magdalena A; Radmer, Randall J; Altman, Russ B

    2009-12-15

    The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications. We have developed a method for adding full atomic detail to coarse-grain models of RNA 3D structures. Our method [Coarse to Atomic (C2A)] uses geometries observed in known RNA crystal structures. Our method rebuilds full atomic detail from ideal coarse-grain backbones taken from crystal structures to within 1.87-3.31 A RMSD of the full atomic crystal structure. When starting from coarse-grain models generated by the modeling tool NAST, our method builds full atomic structures that are within 1.00 A RMSD of the starting structure. The resulting full atomic structures can be used as starting points for higher resolution modeling, thus bridging high- and low-resolution approaches to modeling RNA 3D structure. Code for the C2A method, as well as the examples discussed in this article, are freely available at www.simtk.org/home/c2a. russ.altman@stanford.edu

  4. Predicting RNA 3D structure using a coarse-grain helix-centered model.

    Science.gov (United States)

    Kerpedjiev, Peter; Höner Zu Siederdissen, Christian; Hofacker, Ivo L

    2015-06-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. © 2015 Kerpedjiev et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations

    Science.gov (United States)

    Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu

    2017-01-01

    We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861

  6. Coarse-graining complex dynamics

    DEFF Research Database (Denmark)

    Sibani, Paolo

    2013-01-01

    Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat-tailed distribu......Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat......-tailed distribution of the waiting time between consecutive jumps. We first argue that CTRW are inadequate to describe macroscopic relaxation processes for three reasons: macroscopic variables are not self-averaging, memory effects require an all-knowing observer,and different mechanisms whereby the jumps affect......: while CTRW make use of a renewal process involving identical traps of infinite size, RD embodies a dynamical entrenchment into a hierarchy of traps which are finite in size and possess different degrees of meta-stability. We show in particular how RD produces the stretched exponential, power...

  7. Spectral coarse grained controllability of complex networks

    Science.gov (United States)

    Wang, Pei; Xu, Shuang

    2017-07-01

    With the accumulation of interaction data from various systems, a fundamental question in network science is how to reduce the sizes while keeping certain properties of complex networks. Combined the spectral coarse graining theory and the structural controllability of complex networks, we explore the structural controllability of undirected complex networks during coarse graining processes. We evidence that the spectral coarse grained controllability (SCGC) properties for the Erdös-Rényi (ER) random networks, the scale-free (SF) random networks and the small-world (SW) random networks are distinct from each other. The SW networks are very robust, while the SF networks are sensitive during the coarse graining processes. As an emergent properties for the dense ER networks, during the coarse graining processes, there exists a threshold value of the coarse grained sizes, which separates the controllability of the reduced networks into robust and sensitive to coarse graining. Investigations on some real-world complex networks indicate that the SCGC properties are varied among different categories and different kinds of networks, some highly organized social or biological networks are more difficult to be controlled, while many man-made power networks and infrastructure networks can keep the controllability properties during the coarse graining processes. Furthermore, we speculate that the SCGC properties of complex networks may depend on their degree distributions. The associated investigations have potential implications in the control of large-scale complex networks, as well as in the understanding of the organization of complex networks.

  8. A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number

    Science.gov (United States)

    Tadmor, Arbel

    2009-03-01

    In this work a biophysical model of Escherichia coli is presented that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity.

  9. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

    Science.gov (United States)

    Zheng, Wenjun

    2017-02-01

    In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals

  10. Coarse grained model for semiquantitative lipid simulations

    NARCIS (Netherlands)

    Marrink, SJ; de Vries, AH; Mark, AE

    2004-01-01

    This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of

  11. Coarse-graining polymers as soft colloids

    OpenAIRE

    Louis, A.A.; Bolhuis, P. G.; Finken, R.; Krakoviack, V.; de Meijer, E. J.; Hansen, J. P.

    2001-01-01

    We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.

  12. Coarse-grained Simulations of Viral Assembly

    Science.gov (United States)

    Elrad, Oren M.

    2011-12-01

    The formation of viral capsids is a marvel of natural engineering and design. A large number (from 60 to thousands) of protein subunits assemble into complete, reproducible structures under a variety of conditions while avoiding kinetic and thermodynamic traps. Small single-stranded RNA viruses not only assemble their coat proteins in this fashion but also package their genome during the self-assembly process. Recent experiments have shown that the coat proteins are competent to assemble not merely around their own genomes but heterologous RNA, synthetic polyanions and even functionalized gold nanoparticles. Remarkably these viruses can even assemble around cargo not commensurate with their native state by adopting different morphologies. Understanding the properties that confer such exquisite precision and flexibility to the assembly process could aid biomedical research in the search for novel antiviral remedies, drug-delivery vehicles and contrast agents used in bioimaging. At the same time, viral assembly provides an excellent model system for the development of a statistical mechanical understanding of biological self-assembly, in the hopes of that we will identify some universal principles that underly such processes. This work consists of computational studies using coarse-grained representations of viral coat proteins and their cargoes. We find the relative strength of protein-cargo and protein-protein interactions has a profound effect on the assembly pathway, in some cases leading to assembly mechanisms that are markedly different from those found in previous work on the assembly of empty capsids. In the case of polymeric cargo, we find the first evidence for a previously theorized mechanism in which the polymer actively participates in recruiting free subunits to the assembly process through cooperative polymer-protein motions. We find that successful assembly is non-monotonic in protein-cargo affinity, such affinity can be detrimental to assembly if it

  13. Coarse graining flow of spin foam intertwiners

    CERN Document Server

    Dittrich, Bianca; Seth, Cameron J; Steinhaus, Sebastian

    2016-01-01

    Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behaviour on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group $\\text{SU}(2)_k \\times \\text{SU}(2)_k$, which implement the simplicity constraints analogous to 4D Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a 2D topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different ...

  14. Mineral Elements Content of some Coarse Grains used as staple ...

    African Journals Online (AJOL)

    In comparison with Recommended Dietary Allowances of essential and trace metals set by international standard organizations, the coarse grains analyzed in this work contribute little to the provision of essential and trace elements requirements. Keywords: Mineral Elements, Coarse Grains, Staple Food, Kano, Nigeria.

  15. Entropies from Coarse-graining: Convex Polytopes vs. Ellipsoids

    Directory of Open Access Journals (Sweden)

    Nikos Kalogeropoulos

    2015-09-01

    Full Text Available We examine the Boltzmann/Gibbs/Shannon SBGS and the non-additive Havrda-Charvát/Daróczy/Cressie-Read/Tsallis Sq and the Kaniadakis κ-entropy Sκ from the viewpoint of coarse-graining, symplectic capacities and convexity. We argue that the functional form of such entropies can be ascribed to a discordance in phase-space coarse-graining between two generally different approaches: the Euclidean/Riemannian metric one that reflects independence and picks cubes as the fundamental cells in coarse-graining and the symplectic/canonical one that picks spheres/ellipsoids for this role. Our discussion is motivated by and confined to the behaviour of Hamiltonian systems of many degrees of freedom. We see that Dvoretzky’s theorem provides asymptotic estimates for the minimal dimension beyond which these two approaches are close to each other. We state and speculate about the role that dualities may play in this viewpoint.

  16. Design of low-power coarse-grained reconfigurable architectures

    CERN Document Server

    Kim, Yoonjin

    2010-01-01

    Coarse-grained reconfigurable architecture (CGRA) has emerged as a solution for flexible, application-specific optimization of embedded systems. Helping you understand the issues involved in designing and constructing embedded systems, Design of Low-Power Coarse-Grained Reconfigurable Architectures offers new frameworks for optimizing the architecture of components in embedded systems in order to decrease area and save power. Real application benchmarks and gate-level simulations substantiate these frameworks.The first half of the book explains how to reduce power in the configuration cache. T

  17. Coarse graining and scaling in dissipative particle dynamics

    DEFF Research Database (Denmark)

    Füchslin, Rudolf M; Fellermann, Harold; Eriksson, Anders

    2009-01-01

    Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic...

  18. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

  19. Coarsegrained molecular dynamics simulation of cross – linking ...

    African Journals Online (AJOL)

    These three superatom structures are then allowed to crosslink (based on the attainment of a minimum distance of approach) with a coarse grained crosslinker ... Our predictions of the value of the work of separation, obtained from only a description of the molecular architecture of DGEBA and the crosslinker molecule, falls ...

  20. Martini Coarse-Grained Force Field : Extension to Carbohydrates

    NARCIS (Netherlands)

    Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

    2009-01-01

    We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

  1. Mapping Applications to a Coarse Grain Reconfigurable System

    NARCIS (Netherlands)

    Guo, Y.; Smit, Gerardus Johannes Maria; Broersma, Haitze J.; Rosien, M.A.J.; Heysters, P.M.; Omondi, A.; Sedukhin, S.

    This paper introduces a method which can be used to map applications written in a high level source language program, like C, to a coarse grain reconfigurable architecture, MONTIUM. The source code is first translated into a control data flow graph. Then after applying graph clustering, scheduling

  2. Coarse-Grained Potentials for Local Interactions in Unfolded Proteins

    NARCIS (Netherlands)

    Ghavami, Ali; van der Giessen, Erik; Onck, Patrick R.

    Recent studies have revealed the key role of natively unfolded proteins in many important biological processes. In order to study the conformational changes of these proteins, a one-bead-per-amino-acid coarse grained (CG) model is developed, and a method is proposed to extract the potential

  3. MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture

    DEFF Research Database (Denmark)

    Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

    2007-01-01

    The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi...

  4. Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory

    2008-01-01

    We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.

  5. Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E

    2001-12-21

    We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.

  6. Description and Specialization of Coarse-grained Reconfigurable Architectures

    OpenAIRE

    Oliveira Filho, Julio Alexandrino

    2010-01-01

    The functionality of electronic embedded systems, such as mobile phones and digital cameras, becomes more complex at each product generation. This increasing complexity implies great challenges at the design phase of these devices, as designers have to deal with high performance and low energy requirements at a low production budget. In the last years, coarse-grained, dynamically reconfigurable computer systems have increasingly gain in importance as an alternative to cope with these challe...

  7. High capacitance of coarse-grained carbide derived carbon electrodes

    Science.gov (United States)

    Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury

    2016-02-01

    We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.

  8. Coarse graining of force fields for metal-organic frameworks.

    Science.gov (United States)

    Dürholt, Johannes P; Galvelis, Raimondas; Schmid, Rochus

    2016-03-14

    We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four coordinated vertex, was developed as a proof of concept. By adding non-bonded interactions with a modified Buckingham potential, the resulting MOF-FF-CGNB is able to predict local deformation energies of the building blocks as well as bulk properties like the tbovs.pto energy difference or elastic constants in a semi-quantitative way. As expected, the negative thermal expansion of HKUST-1 is not reproduced by the maximally coarse grained model. At the expense of atomic resolution, substantially larger systems (up to tens of nanometers in size) can be simulated with respect to structural and mechanical properties, bridging the gap to the mesoscale. As an example the deformation of the [111] surface of HKUST-1 by a "tip" could be computed without artifacts from periodic images.

  9. Parametrizing coarse grained models for molecular systems at equilibrium

    KAUST Repository

    Kalligiannaki, Evangelia

    2016-10-18

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  10. Heterogeneous lamella structure unites ultrafine-grain strength with coarse-grain ductility.

    Science.gov (United States)

    Wu, Xiaolei; Yang, Muxin; Yuan, Fuping; Wu, Guilin; Wei, Yujie; Huang, Xiaoxu; Zhu, Yuntian

    2015-11-24

    Grain refinement can make conventional metals several times stronger, but this comes at dramatic loss of ductility. Here we report a heterogeneous lamella structure in Ti produced by asymmetric rolling and partial recrystallization that can produce an unprecedented property combination: as strong as ultrafine-grained metal and at the same time as ductile as conventional coarse-grained metal. It also has higher strain hardening than coarse-grained Ti, which was hitherto believed impossible. The heterogeneous lamella structure is characterized with soft micrograined lamellae embedded in hard ultrafine-grained lamella matrix. The unusual high strength is obtained with the assistance of high back stress developed from heterogeneous yielding, whereas the high ductility is attributed to back-stress hardening and dislocation hardening. The process discovered here is amenable to large-scale industrial production at low cost, and might be applicable to other metal systems.

  11. Coarse-grained incompressible magnetohydrodynamics: analyzing the turbulent cascades

    Science.gov (United States)

    Aluie, Hussein

    2017-02-01

    We formulate a coarse-graining approach to the dynamics of magnetohydrodynamic (MHD) fluids at a continuum of length-scales ℓ. In this methodology, effective equations are derived for the observable velocity and magnetic fields spatially-averaged at an arbitrary scale of resolution. The microscopic equations for the ‘bare’ velocity and magnetic fields are ‘renormalized’ by coarse-graining to yield macroscopic effective equations that contain both a subscale stress and a subscale electromotive force (EMF) generated by nonlinear interaction of eliminated fields and plasma motions. Particular attention is given to the effects of these subscale terms on the balances of the quadratic invariants of ideal incompressible MHD—energy, cross-helicity and magnetic helicity. At large coarse-graining length-scales, the direct dissipation of the invariants by microscopic mechanisms (such as molecular viscosity and Spitzer resistivity) is shown to be negligible. The balance at large scales is dominated instead by the subscale nonlinear terms, which can transfer invariants across scales, and are interpreted in terms of work concepts for energy and in terms of topological flux-linkage for the two helicities. An important application of this approach is to MHD turbulence, where the coarse-graining length ℓ lies in the inertial cascade range. We show that in the case of sufficiently rough velocity and/or magnetic fields, the nonlinear inter-scale transfer need not vanish and can persist to arbitrarily small scales. Although closed expressions are not available for subscale stress and subscale EMF, we derive rigorous upper bounds on the effective dissipation they produce in terms of scaling exponents of the velocity and magnetic fields. These bounds provide exact constraints on phenomenological theories of MHD turbulence in order to allow the nonlinear cascade of energy and cross-helicity. On the other hand, we prove a very strong version of the Woltjer-Taylor conjecture

  12. Transferability of coarse-grained force fields: the polymer case.

    Science.gov (United States)

    Carbone, Paola; Varzaneh, Hossein Ali Karimi; Chen, Xiaoyu; Müller-Plathe, Florian

    2008-02-14

    A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80 K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at

  13. Information Theoretic Tools for Parameter Fitting in Coarse Grained Models

    KAUST Repository

    Kalligiannaki, Evangelia

    2015-01-07

    We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics and finding the optimal parameter set for which the relative entropy rate with respect to the atomistic dynamics is minimized. The minimization problem leads to a generalization of the force matching methods to non equilibrium systems. A multiplicative noise example reveals the importance of the diffusion coefficient in the optimization problem.

  14. Subsurface Optical Microscopy of Coarse Grain Spinels. Phase 1

    Science.gov (United States)

    2013-12-01

    modules normally used by the life sciences using coarse grain magnesium aluminate (MgAl2O4), and aluminum oxy nitride (AlON). The microscope used is a...magnesium aluminate (MgAl2O4), and aluminum oxy nitride (AlON). Presently, the documentation of ceramic internal structures rely on specimen...Pressing LED light-emitting diode LSM Zeiss Pascal software MgAl2O4 magnesium aluminate NIH National Institutes of Health Z1m Zeiss Pascal 5

  15. Martini Coarse-Grained Force Field: Extension to Carbohydrates.

    Science.gov (United States)

    López, Cesar A; Rzepiela, Andrzej J; de Vries, Alex H; Dijkhuizen, Lubbert; Hünenberger, Philippe H; Marrink, Siewert J

    2009-12-08

    We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The carbohydrate building blocks considered are the monosaccharides glucose and fructose and the disaccharides sucrose, trehalose, maltose, cellobiose, nigerose, laminarabiose, kojibiose, and sophorose. Bonded parameters for these saccharides are optimized by comparison to conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated rotameric state for the glycosidic bond. Application of the new coarse-grained carbohydrate model to the oligosaccharides amylose and Curdlan shows a preservation of the main structural properties with 3 orders of magnitude more efficient sampling than the atomistic counterpart. Finally, we investigate the cryo- and anhydro-protective effect of glucose and trehalose on a lipid bilayer and find a strong decrease of the melting temperature, in good agreement with both experimental findings and atomistic simulation studies.

  16. Coarse-Grained Modeling of Colloid-Nanoparticle Mixtures

    Science.gov (United States)

    Denton, Alan R.; Chung, Jun Kyung

    2013-03-01

    Colloid-nanoparticle mixtures have attracted much recent attention for their rich phase behavior. The potential to independently vary size and charge ratios greatly expands the possibilities for tuning interparticle interactions and stabilizing unusual phases. Experiments have begun to explore the self-assembly and stability of colloid-nanoparticle mixtures, which are characterized by extreme size and charge asymmetries. In modeling such complex soft materials, coarse-grained methods often prove essential to surmount computational challenges posed by multiple length and time scales. We describe a hierarchical approach to modeling effective interactions in ultra-polydisperse mixtures. Using a sequential coarse-graining procedure, we show that a mixture of charged colloids and nanoparticles can be mapped onto a one-component model of pseudo-colloids interacting via a Yukawa effective pair potential and a one-body volume energy, which contributes to the free energy of the system. Nanoparticles are found to enhance electrostatic screening and to modify the volume energy. Taking the effective interactions as input to simulations and perturbation theory, we calculate structural properties and explore phase stability of highly asymmetric charged colloid-nanoparticle mixtures. This work was supported by the National Science Foundation under Grant No. DMR-1106331

  17. Coarse-grained rigid blob model for soft matter simulations.

    Science.gov (United States)

    Chao, Sheng D; Kress, Joel D; Redondo, Antonio

    2005-06-15

    We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above. We utilize a multipolar expansion to obtain the interblob potential-energy functions. The series, which contains controllable approximations that allow us to estimate the errors, approaches the original intermolecular potential as the number of terms increases. Using a novel numerical algorithm, we can calculate the interblob potentials very efficiently in terms of a few interaction moment tensors. This reduces the labor well beyond what is required in standard molecular-dynamics calculations and allows large-scale simulations for temporal scales commensurate with characteristic times of nano- and mesoscale systems. A detailed derivation of the formulas is presented, followed by illustrative applications to several systems showing that the method can effectively capture realistic microscopic details and can easily extend to large-scale simulations.

  18. A Bayesian statistics approach to multiscale coarse graining

    Science.gov (United States)

    Liu, Pu; Shi, Qiang; Daumé, Hal; Voth, Gregory A.

    2008-12-01

    Coarse-grained (CG) modeling provides a promising way to investigate many important physical and biological phenomena over large spatial and temporal scales. The multiscale coarse-graining (MS-CG) method has been proven to be a thermodynamically consistent way to systematically derive a CG model from atomistic force information, as shown in a variety of systems, ranging from simple liquids to proteins embedded in lipid bilayers. In the present work, Bayes' theorem, an advanced statistical tool widely used in signal processing and pattern recognition, is adopted to further improve the MS-CG force field obtained from the CG modeling. This approach can regularize the linear equation resulting from the underlying force-matching methodology, therefore substantially improving the quality of the MS-CG force field, especially for the regions with limited sampling. Moreover, this Bayesian approach can naturally provide an error estimation for each force field parameter, from which one can know the extent the results can be trusted. The robustness and accuracy of the Bayesian MS-CG algorithm is demonstrated for three different systems, including simple liquid methanol, polyalanine peptide solvated in explicit water, and a much more complicated peptide assembly with 32 NNQQNY hexapeptides.

  19. Minimizing memory as an objective for coarse-graining.

    Science.gov (United States)

    Guttenberg, Nicholas; Dama, James F; Saunders, Marissa G; Voth, Gregory A; Weare, Jonathan; Dinner, Aaron R

    2013-03-07

    Coarse-graining a molecular model is the process of integrating over degrees of freedom to obtain a reduced representation. This process typically involves two separate but related steps, selection of the coordinates comprising the reduced system and modeling their interactions. Both the coordinate selection and the modeling procedure present challenges. Here, we focus on the former. Typically, one seeks to integrate over the fast degrees of freedom and retain the slow degrees of freedom. Failure to separate timescales results in memory. With this motivation, we introduce a heuristic measure of memory and show that it can be used to compare competing coordinate selections for a given modeling procedure. We numerically explore the utility of this heuristic for three systems of increasing complexity. The first example is a four-particle linear model, which is exactly solvable. The second example is a sixteen-particle nonlinear model; this system has interactions that are characteristic of molecular force fields but is still sufficiently simple to permit exhaustive numerical treatment. The third example is an atomic-resolution representation of a protein, the class of models most often treated by relevant coarse-graining approaches; we specifically study an actin monomer. In all three cases, we find that the heuristic suggests coordinate selections that are physically intuitive and reflect molecular structure. The memory heuristic can thus serve as an objective codification of expert knowledge and a guide to sites within a model that requires further attention.

  20. Multiscale coarse-graining of the protein energy landscape.

    Directory of Open Access Journals (Sweden)

    Ronald D Hills

    2010-06-01

    Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.

  1. Data-driven coarse graining of large biomolecular structures.

    Science.gov (United States)

    Chen, Yi-Ling; Habeck, Michael

    2017-01-01

    Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements. Coarse graining (CG) allows us to understand biological structures from a hierarchical perspective and to gradually zoom into the adequate level of structural detail. This article introduces a Bayesian approach for coarse graining biomolecular structures. We develop a probabilistic model that aims to represent the shape of an experimental structure as a cloud of bead particles. The particles interact via a pairwise potential whose parameters are estimated along with the bead positions and the CG mapping between atoms and beads. Our model can also be applied to density maps obtained by cryo-electron microscopy. We illustrate our approach on various test systems.

  2. Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

    Science.gov (United States)

    Genheden, Samuel

    2017-10-01

    We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

  3. Unconstrained Structure Formation in Coarse-Grained Protein Simulations

    Science.gov (United States)

    Bereau, Tristan

    The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid

  4. Coarse-Grained Molecular Simulations of Allosteric Cooperativity

    CERN Document Server

    Nandigrami, Prithviraj

    2015-01-01

    Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two calcium ions to each domain of calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding is treated implicitly at the mean field level. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energy to the open and closed ensembles accurately describe...

  5. Variational coarse-graining procedure for dynamic homogenization

    Science.gov (United States)

    Liu, Chenchen; Reina, Celia

    2017-07-01

    We present a variational coarse-graining framework for heterogeneous media in the spirit of FE2 methods, that allows for a seamless transition from the traditional static scenario to dynamic loading conditions, while being applicable to general material behavior as well as to discrete or continuous representations of the material and its deformation, e.g., finite element discretizations or atomistic systems. The method automatically delivers the macroscopic equations of motion together with the generalization of Hill's averaging relations to the dynamic setting. These include the expression of the macroscopic stresses and linear momentum as a function of the microscopic fields. We further demonstrate with a proof of concept example, that the proposed theoretical framework can be used to perform multiscale numerical simulations. The results are compared with standard single-scale finite element simulations, showcasing the capability of the method to capture the dispersive nature of the medium in the range of frequencies permitted by the multiscale strategy.

  6. Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena

    CERN Document Server

    Gorban, Alexander N; Theodoropoulos, Constantinos; Kazantzis, Nikolaos K; Öttinger, Hans Christian

    2006-01-01

    Model reduction and coarse-graining are important in many areas of science and engineering. How does a system with many degrees of freedom become one with fewer? How can a reversible micro-description be adapted to the dissipative macroscopic model? These crucial questions, as well as many other related problems, are discussed in this book. Specific areas of study include dynamical systems, non-equilibrium statistical mechanics, kinetic theory, hydrodynamics and mechanics of continuous media, (bio)chemical kinetics, nonlinear dynamics, nonlinear control, nonlinear estimation, and particulate systems from various branches of engineering. The generic nature and the power of the pertinent conceptual, analytical and computational frameworks helps eliminate some of the traditional language barriers, which often unnecessarily impede scientific progress and the interaction of researchers between disciplines such as physics, chemistry, biology, applied mathematics and engineering. All contributions are authored by ex...

  7. MARTINI Coarse-Grained Models of Polyethylene and Polypropylene.

    Science.gov (United States)

    Panizon, Emanuele; Bochicchio, Davide; Monticelli, Luca; Rossi, Giulia

    2015-06-25

    The understanding of the interaction of nanoplastics with living organisms is crucial both to assess the health hazards of degraded plastics and to design functional polymer nanoparticles with biomedical applications. In this paper, we develop two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes. The models are compatible with the popular MARTINI force field for lipids, and they are developed using both structural and thermodynamic properties as targets in the parametrization. The models are then validated by showing their reliability at reproducing structural properties of the polymers, both linear and branched, in dilute conditions, in the melt, and in a PE-PP blend. PE and PP radius of gyration is correctly reproduced in all conditions, while PE-PP interactions in the blend are slightly overestimated. Partitioning of PP and PE oligomers in phosphatidylcholine membranes as obtained at CG level reproduces well atomistic data.

  8. Coarse-grained molecular dynamics simulations of biomolecules

    Directory of Open Access Journals (Sweden)

    Ken Takahashi

    2014-03-01

    Full Text Available Coarse-grained molecular dynamics (CGMD simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.

  9. Coarse-grained kinetic equations for quantum systems

    Science.gov (United States)

    Petrov, E. G.

    2013-01-01

    The nonequilibrium density matrix method is employed to derive a master equation for the averaged state populations of an open quantum system subjected to an external high frequency stochastic field. It is shown that if the characteristic time τstoch of the stochastic process is much lower than the characteristic time τsteady of the establishment of the system steady state populations, then on the time scale Δ t ˜ τsteady, the evolution of the system populations can be described by the coarse-grained kinetic equations with the averaged transition rates. As an example, the exact averaging is carried out for the dichotomous Markov process of the kangaroo type.

  10. Coarse-grain parallelism using remote method invocation

    Energy Technology Data Exchange (ETDEWEB)

    Hebert, A. [Ecole Polytechnique de Montreal, Qc. (Canada)

    2003-07-01

    The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)

  11. Coarse-grained DNA model capable of simulating ribose flexibility

    CERN Document Server

    Kovaleva, Natalya A; Mazo, Mikhail A; Zubova, Elena A

    2014-01-01

    We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA forms. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the sugar CG DNA model are: (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one non-harmonic potential and one three-particle potential, (2) explicit representation of sodium counterions and (3) implicit solvent approach. Effects of solvation and of partial charge screening at small distances are taken into account through the shape of potentials of interactions between charged particles. We obtain parameters of the sugar CG DNA model from the all-atom AMBER model. The suggested model allows adequate simulation of the transitions between A- and B-DNA forms, as well as of large deformations of long DNA molecules, for example, in binding with proteins. Small modifications of the model can provide th...

  12. A Column Arrangement Algorithm for a Coarse-grained Reconfigurable Architecture

    NARCIS (Netherlands)

    Guo, Y.; Hoede, C.; Plaks, T.P.; DeMara, R.; Gokhale, M.; Guccione, S.; Platzner, M.; Smit, Gerardus Johannes Maria; Wirthlin, M.

    In a coarse-grained reconfigurable architecture, the functions of resources such as Arithmetic Logic Units (ALUs) can be reconfigured. Unlike the programmability of a general purpose processor, the programmability of a coarse-grained reconfigurable architecture is limited. The limitation might be

  13. Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-09-01

    Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects the measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.

  14. Multi-blob coarse graining for ring polymer solutions.

    Science.gov (United States)

    Narros, Arturo; Likos, Christos N; Moreno, Angel J; Capone, Barbara

    2014-12-28

    We present a multi-scale molecular modeling of concentrated solutions of unknotted and non-concatenated ring polymers under good solvent conditions. The approach is based on a multi-blob representation of each ring polymer, which is capable of overcoming the shortcomings of single-blob approaches that lose their validity at concentrations exceeding the overlap density of the solution [A. Narros, A. J. Moreno, and C. N. Likos, Soft Matter, 2010, 6, 2435]. By means of a first principles coarse-graining strategy based on analytically determined effective pair potentials between the blobs, computed at zero density, we quantitatively reproduce the single molecule and solution properties of a system with well-defined topological constraints. Detailed comparisons with the underlying, monomer-resolved model demonstrate the validity of our approach, which employs fully transferable pair potentials between connected and unconnected blobs. We demonstrate that the pair structure between the centers of mass of the rings is accurately reproduced by the multi-blob approach, thus opening the way for simulation of arbitrarily long polymers. Finally, we show the importance of the topological constraint of non-concatenation on the structure of the concentrated solution and in particular on the size of the correlation hole and the shrinkage of the rings as melt concentrations are approached.

  15. Coarse-Grained Molecular Simulation of Lipid Self-Assembly

    Science.gov (United States)

    Shinoda, Wataru

    2013-03-01

    The talk will review our recent work on understanding the behavior of lipid self-assembly using a coarse-grained (CG) force field model developed recently. The CG model is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom (AA) molecular dynamics (MD) simulations. A series of MD simulations has elucidated that the CG model reproduces the phase diagram reasonably and produces the membranes with reasonable elastic moduli, surface and line tensions. With a help of technical development of free energy computation, we have evaluated the stability of liposome. A comparison of CG-MD and a simple continuum theory for the free energy barrier to the vesicle-to-bicelle transformation reveals that the internal structural relaxation in the bilayer membrane plays an important role in lowering the free energy barrier in case of a small unilamellar vesicle. The effects of lipid components and additives are also discussed in this talk. Especially the effect of fullerenes on the membrane properties will be discussed in details. The behavior of fullerenes in the bilayer membrane and the resultant membrane properties depend on the size of fullerene and bilayer thickness quite sensitively. To discuss these details, we need a chemically accurate CG model constructed based on extensive AA-MD results.

  16. Improving the treatment of coarse-grain electrostatics: CVCEL.

    Science.gov (United States)

    Ceres, N; Lavery, R

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

  17. Coarse graining of star-polymer - colloid nanocomposites

    Science.gov (United States)

    Marzi, Daniela; Likos, Christos N.; Capone, Barbara

    2012-07-01

    We consider mixtures of self-avoiding multiarm star polymers with hard colloids that are smaller than the star polymer size. By employing computer simulations, and by extending previous theoretical approaches, developed for the opposite limit of small star polymers [A. Jusufi et al., J. Phys.: Condens. Matter 13, 6177 (2001), 10.1088/0953-8984/13/28/303], we coarse-grain the mixture by deriving an effective cross-interaction between the unlike species. The excellent agreement between theory and simulation for all size ratios examined demonstrates that the theoretical approaches developed for the colloidal limit can be successfully modified to maintain their validity also for the present case of the protein limit, in contrast to the situation for mixtures of colloids and linear polymers. We further analyze, on the basis of the derived interactions, the non-additivity parameter of the mixture as a function of size ratio and star functionality and delineate the regions in which we expect mixing as opposed to demixing behavior. Our results are relevant for the study of star-colloid nanocomposites and pave the way for further investigations of the structure and thermodynamics of the same.

  18. Coarse graining of star-polymer--colloid nanocomposites.

    Science.gov (United States)

    Marzi, Daniela; Likos, Christos N; Capone, Barbara

    2012-07-07

    We consider mixtures of self-avoiding multiarm star polymers with hard colloids that are smaller than the star polymer size. By employing computer simulations, and by extending previous theoretical approaches, developed for the opposite limit of small star polymers [A. Jusufi et al., J. Phys.: Condens. Matter 13, 6177 (2001)], we coarse-grain the mixture by deriving an effective cross-interaction between the unlike species. The excellent agreement between theory and simulation for all size ratios examined demonstrates that the theoretical approaches developed for the colloidal limit can be successfully modified to maintain their validity also for the present case of the protein limit, in contrast to the situation for mixtures of colloids and linear polymers. We further analyze, on the basis of the derived interactions, the non-additivity parameter of the mixture as a function of size ratio and star functionality and delineate the regions in which we expect mixing as opposed to demixing behavior. Our results are relevant for the study of star-colloid nanocomposites and pave the way for further investigations of the structure and thermodynamics of the same.

  19. Thermodynamics of star polymer solutions: A coarse-grained study

    Science.gov (United States)

    Menichetti, Roberto; Pelissetto, Andrea; Randisi, Ferdinando

    2017-06-01

    We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality f. Each macromolecule is represented by a CG molecule with (f + 1) interaction sites, which captures the star topology. Potentials are obtained by requiring the CG model to reproduce a set of distribution functions computed in the microscopic model in the zero-density limit. Explicit results are given for f = 6, 12, and 40. We use the CG model to compute the osmotic equation of state of the solution for concentrations c such that Φp=c /c*≲1 , where c* is the overlap concentration. We also investigate in detail the phase diagram for f = 40, identifying the boundaries of the solid intermediate phase. Finally, we investigate how the polymer size changes with c. For Φp≲0.3 , polymers become harder as f increases at fixed reduced concentration c /c*. On the other hand, for Φp≳0.3 , polymers show the opposite behavior: At fixed Φp, the larger the value of f, the larger their size reduction is.

  20. Improving the treatment of coarse-grain electrostatics: CVCEL

    Energy Technology Data Exchange (ETDEWEB)

    Ceres, N.; Lavery, R., E-mail: richard.lavery@ibcp.fr [Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367 (France)

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

  1. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

    Science.gov (United States)

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-01

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  2. mineral elements content of some coarse grains used as staple food

    African Journals Online (AJOL)

    DR. AMINU

    2014-06-01

    Jun 1, 2014 ... potassium and calcium between the varieties of coarse grains whereas no significant differences. (p>0.05) ... maize, sorghum, wheat, cowpea and rice are the most ... adverse effect upon human and animals at excessively.

  3. Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion

    CERN Document Server

    Moore, Timothy C; McCabe, Clare

    2015-01-01

    A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.

  4. Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid.

    Science.gov (United States)

    Xia, Wenjie; Song, Jake; Hansoge, Nitin K; Phelan, Frederick R; Keten, Sinan; Douglas, Jack F

    2018-02-15

    Coarse-grained modeling achieves the enhanced computational efficiency required to model glass-forming materials by integrating out "unessential" molecular degrees of freedom, but no effective temperature transferable coarse-graining method currently exists to capture dynamics. We address this fundamental problem through an energy-renormalization scheme, in conjunction with the localization model of relaxation relating the Debye-Waller factor ⟨u 2 ⟩ to the structural relaxation time τ. Taking ortho-terphenyl as a model small-molecule glass-forming liquid, we show that preserving ⟨u 2 ⟩ (at picosecond time scale) under coarse-graining by renormalizing the cohesive interaction strength allows for quantitative prediction of both short- and long-time dynamics covering the entire temperature range of glass formation. Our findings provide physical insights into the dynamics of cooled liquids and make progress for building temperature-transferable coarse-grained models that predict key properties of glass-forming materials.

  5. Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

    Science.gov (United States)

    Li, Min; Zhang, John Zenghui; Xia, Fei

    2016-04-12

    Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

  6. Theory of wavelet-based coarse-graining hierarchies for molecular dynamics

    Science.gov (United States)

    Rinderspacher, Berend Christopher; Bardhan, Jaydeep P.; Ismail, Ahmed E.

    2017-07-01

    We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.

  7. Mechanical response of two polyimides through coarse-grained molecular dynamics simulations

    Science.gov (United States)

    Sudarkodi, V.; Sooraj, K.; Nair, Nisanth N.; Basu, Sumit; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Tsotsis, Tom

    2018-03-01

    Coarse-grained molecular dynamics (MD) simulations allow us to predict the mechanical responses of polymers, starting merely with a description of their molecular architectures. It is interesting to ask whether, given two competing molecular architectures, coarse-grained MD simulations can predict the differences that can be expected in their mechanical responses. We have studied two crosslinked polyimides PMR15 and HFPE52—both used in high- temperature applications—to assess whether the subtle differences in their uniaxial stress–strain responses, revealed by experiments, can be reproduced by carefully coarse-grained MD models. The coarse graining procedure for PMR15 is outlined in this work, while the coarse grain forcefields for HFPE52 are borrowed from an earlier one (Pandiyan et al 2015 Macromol. Theory Simul. 24 513–20). We show that the stress–strain responses of both these polyimides are qualitatively reproduced, and important insights into their deformation and failure mechanisms are obtained. More importantly, the differences in the molecular architecture between the polyimides carry over to the differences in the stress–strain responses in a manner that parallels the experimental results. A critical assessment of the successes and shortcomings of predicting mechanical responses through coarse-grained MD simulations has been made.

  8. Variant analysis in coarse grain heat affected zone of low carbon steel

    Science.gov (United States)

    Razab, Mohammad Khairul Azhar Abdul; Mamat, Sarizam; Ahmad, Muhammad Iqbal; Nasir, Nurul Syahida Mohd

    2017-09-01

    Coarse Grain Heat Affected Zone (CGHAZ) is a part of Heat Affected Zone (HAZ) that affected by heat during welding process. Application of different heat input dramatically varies CGHAZ microstructures without a noticeable changing in prior austenite grain size. The unique coarse microstructure and crack initiated at CGHAZ show there were possibility changes in crystallographic structure which may relate to the variant selection phenomenon. The aims of this study are to find the effects of heat input to the variant selection especially to the biggest grain at CGHAZ, hence correlate to the toughness and properties of the welded steel. The results show that heat input affected the variant selection at the biggest CGHAZ grain of low carbon steel. As heat input increase, grain area was increased and becomes coarser. Variant selection phenomenon present at low carbon steel due to the increase in grain diameter and high angle value. It was found that variant selections had occurred during the transformation.

  9. Behavior of coarse-grained soils under high stresses

    Energy Technology Data Exchange (ETDEWEB)

    Ramamurthy, T.; Kanitkar, V.K.; Prakash, K.

    1974-01-01

    This is a report on an experimental investigation of the volume change and shearing behavior of a weathered subrounded quartzite sand. The results indicated that the coarse sands are crushed more easily than fine and medium sands under high confining pressures; they also indicated that shearing would cause greater changes in gradation in a sample than the application of isotropic stresses. Due to the large magnitude of particle crushing, coarse sand mobilizes strength at a slower rate than fine and medium sands. However, when sufficient degradation has occurred at large axial strains, the strengths of all 4 fractions are almost the same, regardless of their initial differences in porosity, particle size, and particle strength. The importance of particle crushing under high confining pressure is stressed in examining the volume change and shearing behavior of sands, namely, the stress-strain relationship, mode of failure, dilatancy rate, coefficient of earth pressure at rest, and effective stress ratio at failure. (Longer abstract available)

  10. Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

    Energy Technology Data Exchange (ETDEWEB)

    Salerno, K. Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Agrawal, Anupriya [Washington Univ., St. Louis, MO (United States). Dept. of Mechanical Engineering and Materials Science; Clemson Univ., SC (United States). Dept. of Chemistry; Perahia, Dvora [Clemson Univ., SC (United States). Dept. of Chemistry; Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-02-05

    Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion is used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.

  11. Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles

    KAUST Repository

    Hong, Bingbing

    2012-01-01

    Coarse-grained models of poly(ethylene oxide) oligomer-grafted nanoparticles are established by matching their structural distribution functions to atomistic simulation data. Coarse-grained force fields for bulk oligomer chains show excellent transferability with respect to chain lengths and temperature, but structure and dynamics of grafted nanoparticle systems exhibit a strong dependence on the core-core interactions. This leads to poor transferability of the core potential to conditions different from the state point at which the potential was optimized. Remarkably, coarse graining of grafted nanoparticles can either accelerate or slowdown the core motions, depending on the length of the grafted chains. This stands in sharp contrast to linear polymer systems, for which coarse graining always accelerates the dynamics. Diffusivity data suggest that the grafting topology is one cause of slower motions of the cores for short-chain oligomer-grafted nanoparticles; an estimation based on transition-state theory shows the coarse-grained core-core potential also has a slowing-down effect on the nanoparticle organic hybrid materials motions; both effects diminish as grafted chains become longer. © 2012 American Institute of Physics.

  12. Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles.

    Science.gov (United States)

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.

  13. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

    Science.gov (United States)

    Munafò, A; Panesi, M; Magin, T E

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

  14. The Coarse-Grained/Fine-Grained Logic Interface in FPGAs with Embedded Floating-Point Arithmetic Units

    Directory of Open Access Journals (Sweden)

    Chi Wai Yu

    2008-01-01

    Full Text Available This paper examines the interface between fine-grained and coarse-grained programmable logic in FPGAs. Specifically, it presents an empirical study that covers the location, pin arrangement, and interconnect between embedded floating point units (FPUs and the fine-grained logic fabric in FPGAs. It also studies this interface in FPGAs which contain both FPUs and embedded memories. The results show that (1 FPUs should have a square aspect ratio; (2 they should be positioned near the center of the FPGA; (3 their I/O pins should be arranged around all four sides of the FPU; (4 embedded memory should be located between the FPUs; and (5 connecting higher I/O density coarse-grained blocks increases the demand for routing resources. The hybrid FPGAs with embedded memory required 12% wider channels than the case where embedded memory is not used.

  15. Bottom-up coarse-graining of a simple graphene model: the blob picture.

    Science.gov (United States)

    Kauzlarić, David; Meier, Julia T; Español, Pep; Succi, Sauro; Greiner, Andreas; Korvink, Jan G

    2011-02-14

    The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined.

  16. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Directory of Open Access Journals (Sweden)

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  17. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Science.gov (United States)

    2010-01-01

    ... Grains Crop Provisions If a conflict exists among the policy provisions, the order of priority is as..., including but not limited to protein and oil, will not be considered. Planted acreage—In addition to the... corn, and excluding: (i) High-amylose, high-oil, high-protein, flint, flour, Indian, or blue corn, or a...

  18. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    Science.gov (United States)

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-09

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths.

  19. Construction of ultra-coarse-grained model of protein with a Gō-like potential

    Science.gov (United States)

    Zhang, Yuwei; Cao, Zexing; Xia, Fei

    2017-08-01

    Ultra-Coarse-Grained (UCG) model whose resolution is less than residue-based coarse-grained model, is being developed in recent years. In this work, we attempt to construct a UCG model with a classical Gō-like potential. The heterogeneous parameters of local and nonlocal interactions in the energy potential function are derived by using fluctuation matching method. The simulated results with UCG models indicate that it could reproduce the root mean square fluctuations as accurate as that of long-time all-atom simulations. Therefore, the UCG model has great potential in the simulation of huge biological systems such as biomaterials.

  20. A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

    Science.gov (United States)

    Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

    2017-12-01

    We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

  1. Structural properties of thiophenes investigated with simulations of a coarse-grained model

    Science.gov (United States)

    Luettmer-Strathmann, Jutta; Almutairi, Amani

    Thiophenes have important applications in organic electronics, energy conversion, and storage. The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. In recent work, we developed a coarse-grained model for alpha-oligothiophenes in the bulk and near gold surfaces. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. In this work, we investigate structural properties of thiophenes with simulations of our coarse-grained model.

  2. Coarse-grained description of cosmic structure from Szekeres models

    Energy Technology Data Exchange (ETDEWEB)

    Sussman, Roberto A. [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, A.P. 70–543, 04510 México D.F., México (Mexico); Gaspar, I. Delgado [Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av Universidad 1002, 62210, Cuernavaca, Morelos, México (Mexico); Hidalgo, Juan Carlos, E-mail: sussman@nucleares.unam.mx, E-mail: ismael.delgadog@uaem.edu.mx, E-mail: hidalgo@fis.unam.mx [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, A.P. 48–3, 62251 Cuernavaca, Morelos, México (Mexico)

    2016-03-01

    We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ''pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10–20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.

  3. Capturing interdiffusion in polystyrene films using a coarse-grained model

    Science.gov (United States)

    Agrawal, Anupriya; Ge, Ting; Int Veld, Pieter J.; Perahia, Dvora; Grest, Gary S.

    Interdiffusion of polymers across interface underline self-healing processes and adhesion. Molecular simulations of interdiffusion must capture length scales comparable to the dimensions of the polymers and cover time scales up to the polymer diffusion times. This makes the use of coarse-grained models crucial. Here the interdiffusion of polystyrene films is simulated using a coarse-grained model. As the chain mobility in the coarse-grained model is intrinsically faster than that in the atomistic model, a dynamic scaling factor was first determined by comparing mobilities for short chains for the two models. The interpenetration of two polystyrene thin films were then followed for two films of equal molecular weight with N =500 and N =1760. Using this coarse-grained model, the temperature dependent interdiffusion was captured for time scale of hundreds of microseconds. The increases of mass uptake and interfacial width with time are faster for N =500 than for N =1760 and consistent with the predictions of reptation theory.

  4. Mesoscale simulation of entangled polymers: Part I. Coarse-Grained level Tunable DPD

    Science.gov (United States)

    Maia, Joao; Khani, Shagahyegh; Yamanoi, Mikio

    2014-03-01

    Dissipative Particle Dynamics (DPD) is a coarse-grained molecular dynamics based simulation method that has shown a very good potential in computational modeling of soft matter. However, it is associated with deficiencies in simulating the dynamics of entangled polymer systems. For instance, due to the upper limit of coarse-graining level the method could not be applicable to the whole mesoscopic range. Therefore, our group has proposed a new concept of DPD named Coarse-Grained level tunable DPD method in which the level of coarse graining can be tuned by adjusting the simulation parameters considering an energy balance in the system. The unphysical bond crossings that are artifacts of the soft potentials are prevented by applying an entanglement potential between the bonds. The performance of the method in capturing the entanglement effect is investigated by calculating the static and dynamic properties of polymers in entangled state. Linear and non-linear viscoelastic properties can also be predicted by the CG level tunable DPD method reasonably well. Moreover, this method is able to reproduce the 1.0 to 3.4 transition in power index of the zero shear viscosity with molecular weight which captures the Rouse to reptation behavior in entangled polymer systems.

  5. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices.

    Science.gov (United States)

    Lindsay, Richard J; Siess, Jan; Lohry, David P; McGee, Trevor S; Ritchie, Jordan S; Johnson, Quentin R; Shen, Tongye

    2018-01-14

    We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

  6. Polarizable Water Model for the Coarse-Grained MARTINI Force Field

    NARCIS (Netherlands)

    Yesylevskyy, Semen O.; Schafer, Lars V.; Sengupta, Durba; Marrink, Siewert J.

    Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent,

  7. A simple coarse-grained model for self-assembling silk-like protein fibers

    NARCIS (Netherlands)

    Schor, M.; Ensing, B.; Bolhuis, P.G.

    2010-01-01

    Collagen-silk-collagen triblock polypeptides can self-assemble at low pH into nanometer thin fibers with a length in the order of micrometers. Previously we predicted, via all-atom simulations, the structure of the folded silk domain to be a beta-roll. In this work we develop a simple coarse-grained

  8. Microscopic derivation of particle-based coarse-grained dynamics: Exact expression for memory function

    Science.gov (United States)

    Izvekov, Sergei

    2017-03-01

    We consider the generalized Langevin equations of motion describing exactly the particle-based coarse-grained dynamics in the classical microscopic ensemble that were derived recently within the Mori-Zwanzig formalism based on new projection operators [S. Izvekov, J. Chem. Phys. 138(13), 134106 (2013)]. The fundamental difference between the new family of projection operators and the standard Zwanzig projection operator used in the past to derive the coarse-grained equations of motion is that the new operators average out the explicit irrelevant trajectories leading to the possibility of solving the projected dynamics exactly. We clarify the definition of the projection operators and revisit the formalism to compute the projected dynamics exactly for the microscopic system in equilibrium. The resulting expression for the projected force is in the form of a "generalized additive fluctuating force" describing the departure of the generalized microscopic force associated with the coarse-grained coordinate from its projection. Starting with this key expression, we formulate a new exact formula for the memory function in terms of microscopic and coarse-grained conservative forces. We conclude by studying two independent limiting cases of practical importance: the Markov limit (vanishing correlations of projected force) and the limit of weak dependence of the memory function on the particle momenta. We present computationally affordable expressions which can be efficiently evaluated from standard molecular dynamics simulations.

  9. Molecular Dynamics Simulation of Coarse-Grain Model of Silicon Functionalized Graphene

    Directory of Open Access Journals (Sweden)

    Hui Zhixin

    2015-01-01

    Full Text Available The electronic transport, the storage capacity and the service life of the anode material for lithium ion batteries will be reduced seriously in the event of the material layering or cracking, so the anode material must have strong mechanical reliability. Firstly, in view of the traditional molecular dynamics (MD limited by the geometric scales of the model of Silicon functionalized graphenen (SFG as lithium ion batteries anode material, some full atomic models of SFG were established using Tersoff potential and Lennard-Jones potential, and used to calculate the modulus and the adhesion properties. What’s more, the assertion of mechanical equilibrium condition and energy conservation between full atomic and coarse-grain models through elastic strain energy were enforced to arrive at model parameters. The model of SFG coarse-grain bead-spring elements and its system energy function were obtained via full atomic simulations. Finally, the validity of the SFG coarse-grain model was verified by comparing the tensile property of coarse-grain model with full atoms model.

  10. Lessons Learned from Designing the Montium a Coarse-Grained Reconfigurable Processing Tile

    NARCIS (Netherlands)

    Smit, Gerardus Johannes Maria; Heysters, P.M.; Rosien, M.A.J.; Molenkamp, Egbert

    2004-01-01

    In this paper we describe in retrospective the main results of a four year project, called Chameleon. As part of this project we developed a coarse-grained reconfigurable core for DSP algorithms in wirelessdevices denoted MONTIUM. After presenting the main achievements within this project we present

  11. Clathrin Assembly Regulated by Adaptor Proteins in Coarse-Grained Models

    NARCIS (Netherlands)

    Giani, M.; den Otter, Wouter K.; Briels, Willem J.

    2016-01-01

    The assembly of clathrin triskelia into polyhedral cages during endocytosis is regulated by adaptor proteins (APs). We explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a Monte Carlo click interaction, to simulate their collective aggregation behavior.

  12. Establishment of the coarse grained parameters for epoxy-copper interfacial separation

    NARCIS (Netherlands)

    Wong, C.K.Y.; Leung, S.Y.Y.; Poelma, R.H.; Jansen, K.M.B.; Yuan, C.C.A.; Van Driel, W.D.; Zhang, G.

    2012-01-01

    Atomistic coarse grained parameters were calculated from a non-equilibrium molecular dynamics simulation of the separation of an epoxy-copper interface. The methodology to determine the interaction energy and the equilibrium distance between the interfacial materials at a minimum energy is

  13. Path-space variational inference for non-equilibrium coarse-grained systems

    Science.gov (United States)

    Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr

    2016-06-01

    In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.

  14. A Haskell-Based Programming Paradigm for Coarse-Grained Reconfigurable Arrays

    NARCIS (Netherlands)

    Niedermeier, A.; Kuper, Jan; Smit, Gerardus Johannes Maria

    2012-01-01

    Programming coarse-grain reconfigurable arrays (CGRAs) is a challenging task. In this work, we exploit the algebraic structure which is often present in the specification of a streaming application to distribute the different parts of a computation over a multi-core architecture. This architecture

  15. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

    DEFF Research Database (Denmark)

    Rossi, G.; Monticelli, L.; Puisto, S. R.

    2011-01-01

    in the parameterization. We refine the MARTINI procedure by including one additional target property related to the structure of the polymer, namely the radius of gyration. The force-field optimization is mainly based on experimental data. We test our procedure on polystyrene, a standard benchmark for coarse-grained (CG...

  16. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices

    Science.gov (United States)

    Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye

    2018-01-01

    We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

  17. Coarse-Graining Can Beat the Rotating Wave Approximation in Quantum Markovian Master Equations

    DEFF Research Database (Denmark)

    Majenz, Christian; Albash, Tameem; Breuer, Heinz-Peter

    2013-01-01

    We present a first-principles derivation of the Markovian semi-group master equation without invoking the rotating wave approximation (RWA). Instead we use a time coarse-graining approach which leaves us with a free timescale parameter, which we can optimize. Comparing this approach to the standard...

  18. MT-ADRES: multi-threading on coarse-grained reconfigurable architecture

    DEFF Research Database (Denmark)

    Wu, Kehuai; Kanstein, Andreas; Madsen, Jan

    2008-01-01

    The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi...

  19. Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes

    Energy Technology Data Exchange (ETDEWEB)

    Holm, Christian [Institut für Computerphysik, Universität Stuttgart, Allmandring 3, 70569 Stuttgart (Germany); Gompper, Gerhard [Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich (Germany); Dill, Ken A. [Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 (United States)

    2015-12-28

    This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

  20. Free vibration of super-graphene carbon nanotube networks via a beam element based coarse-grained method

    Science.gov (United States)

    Gu, Ruifeng; Wang, Lifeng; He, Xiaoqiao

    2017-08-01

    A new beam element based coarse-grained model is developed to investigate efficiently the mechanical behavior of a large system of super-graphene carbon nanotube (SGCNT) networks with all boundaries clamped supported. The natural frequencies and mode shapes of the SGCNT networks made of single-walled carbon nanotubes (SWCNTs) with different diameters and lengths are obtained via the proposed coarse-grained model. The applicability of the coarse-grained model for the SGCNT networks is verified by comparison with the molecular structural mechanics model. The natural frequencies and associated mode shapes obtained via the coarse-grained model agree well with the results obtained from the molecular structural mechanics method, indicating that the coarse-grained model developed in this study can be applied for the dynamic prediction of the SGCNT networks.

  1. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    Directory of Open Access Journals (Sweden)

    Hyuntae Na

    2015-10-01

    Full Text Available Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  2. Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins

    Science.gov (United States)

    Aina, A.; Wallin, S.

    2017-09-01

    We consider a generalized-ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are more shallow or absent. We test the method on an intermediate-resolution coarse-grained model for protein folding with 3 amino acid types and explore the potential for a large-scale coverage of sequence space by applying the method to sets of more than 1000 sequences. The resulting thermodynamic data are used to analyze the structures and stability properties of sequences covering the space between folds with different secondary structures.

  3. Scaling of transmission capacities in coarse-grained renewable electricity networks

    Science.gov (United States)

    Schäfer, M.; Bugge Siggaard, S.; Zhu, Kun; Risager Poulsen, C.; Greiner, M.

    2017-08-01

    Network models of large-scale electricity systems feature only a limited spatial resolution, either due to lack of data or in order to reduce the complexity of the problem with respect to numerical calculations. In such cases, both the network topology, the load and the generation patterns below a given spatial scale are aggregated into representative nodes. This coarse-graining affects power flows and thus the resulting transmission needs of the system. We derive analytical scaling laws for measures of network transmission capacity and cost in coarse-grained renewable electricity networks. For the cost measure only a very weak scaling with the spatial resolution of the system is found. The analytical results are shown to describe the scaling of the transmission infrastructure measures for a simplified, but data-driven and spatially detailed model of the European electricity system with a high share of fluctuating renewable generation.

  4. Lithologic data improve plant species distribution models based on coarse-grained occurrence data

    Energy Technology Data Exchange (ETDEWEB)

    Gaston, A.; Soriano, C.; Gomez-Miguel, V.

    2009-07-01

    The aim of this study was to assess the improvement of plant species distribution models based on coarse-grained occurrence data when adding lithologic data to climatic models. The distributions of 40 woody plant species from continental Spain were modelled. A logistic regression model with climatic predictors was fitted for each species and compared to a second model with climatic and lithologic predictors. Improvements on model likelihood and prediction accuracy on validation sub samples were assessed, as well as the effect of calcicole calcifuge habit on model improvement. Climatic models had reasonable mean prediction accuracy, but adding lithologic data improved model likelihood in most cases and increased mean prediction accuracy. Therefore, we recommend utilizing lithologic data for species distribution models based on coarse-grained occurrence data. Our data did not support the hypothesis that calcicole calcifuge habit may explain model improvement when adding lithologic data to climatic models, but further research is needed. (Author) 31 refs.

  5. Multiblob coarse-graining for mixtures of long polymers and soft colloids

    Science.gov (United States)

    Locatelli, Emanuele; Capone, Barbara; Likos, Christos N.

    2016-11-01

    Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems invokes a reduction of the degrees of freedom to be analysed, hence requiring the introduction of an efficient, quantitative, coarse-grained description. We here report on a novel coarse graining approach based on a set of transferable potentials that quantitatively reproduces properties of mixtures of linear and star-shaped homopolymeric nanocomposites. By renormalizing groups of monomers into a single effective potential between a f-functional star polymer and an homopolymer of length N0, and through a scaling argument, it will be shown how a substantial reduction of the to degrees of freedom allows for a full quantitative description of the system. Our methodology is tested upon full monomer simulations for systems of different molecular weight, proving its full predictive potential.

  6. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

    DEFF Research Database (Denmark)

    Stovgaard, Kasper; Andreetta, Christian; Ferkinghoff-Borg, Jesper

    2010-01-01

    CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, Torus......) is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function......, which is paramount for structure determination based on statistical inference. Results: We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids...

  7. Coarse-grained molecular dynamics simulations for giant protein-DNA complexes

    Science.gov (United States)

    Takada, Shoji

    Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.

  8. A simple coarse-grained model for self-assembling silk-like protein fibers.

    Science.gov (United States)

    Schor, Marieke; Ensing, Bernd; Bolhuis, Peter G

    2010-01-01

    Collagen-silk-collagen triblock polypeptides can self-assemble at low pH into nanometer thin fibers with a length in the order of micrometers. Previously we predicted, via all-atom simulations, the structure of the folded silk domain to be a beta-roll. In this work we develop a simple coarse-grained model of the silk domain to enable a numerical study of the fiber's properties and formation on a larger length and time scale. As an initial coarse-grained model for the fiber forming protein we chose the model of Brown et al., Proc. Natl. Acad Sci. U.S.A., 2003, 100, 10712-10717. We adapted this model, and optimized its parameters to reproduce the all-atom molecular dynamics simulation structural data. The unknown strength of the attraction between the beads representing the residues is optimized by computing the Potential of Mean Force for unfolding a strand of the beta-roll, using non-equilibrium steered MD simulations in combination with the Jarzynski relation. Using these optimized parameters we observed spontaneous folding of a short peptide. The coarse-grained beta-roll, as well as a much larger stack (a fiber) of beta-rolls, were found to be stable. Moreover, the predicted fiber persistence length is in agreement with experiment. The efficacy of the mapping of a coarse-grained system onto an all-atom simulation is discussed. The approach opens the way for large-scale simulations of fibers, based on molecular structure, and allows investigation of their nucleation, growth, cross-linking mechanism, network dynamics, and rheology.

  9. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

    DEFF Research Database (Denmark)

    Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen

    2012-01-01

    We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites c...... tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation....

  10. Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

    Directory of Open Access Journals (Sweden)

    Stovgaard Kasper

    2010-08-01

    Full Text Available Abstract Background Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. Results We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. Conclusion We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for

  11. Computational study on ice growth inhibition of Antarctic bacterium antifreeze protein using coarse grained simulation

    OpenAIRE

    Nguyen, Hung; Le, Ly; Ho, Tu Bao

    2014-01-01

    Antarctic bacterium antifreeze proteins (AFPs) protect and support the survival of cold-adapted organisms by binding and inhibiting the growth of ice crystals. The mechanism of the anti-freezing process in a water environment at low temperature of Antarctic bacterium AFPs remains unclear. In this research, we study the effects of Antarctic bacterium AFPs by coarse grained simulations solution at a temperature range from 262 to 273K. The results indicated that Antarctic bacterium AFPs were ful...

  12. Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces.

    Science.gov (United States)

    Ardham, Vikram Reddy; Leroy, Frédéric

    2017-08-21

    In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

  13. Model reduction for agent-based social simulation: Coarse-graining a civil violence model

    Science.gov (United States)

    Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

    2012-06-01

    Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

  14. Generalized coarse-grained model based on point multipole and Gay-Berne potentials.

    Science.gov (United States)

    Golubkov, Pavel A; Ren, Pengyu

    2006-08-14

    This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers.

  15. Markovian dissipative coarse grained molecular dynamics for a simple 2D graphene model.

    Science.gov (United States)

    Kauzlarić, David; Español, Pep; Greiner, Andreas; Succi, Sauro

    2012-12-21

    Based upon a finite-element "coarse-grained molecular dynamics" (CGMD) procedure, as applied to a simple atomistic 2D model of graphene, we formulate a new coarse-grained model for graphene mechanics explicitly accounting for dissipative effects. It is shown that, within the Mori-projection operator formalism, the reversible part of the dynamics is equivalent to the finite temperature CGMD-equations of motion, and that dissipative contributions to CGMD can also be included within the Mori formalism. The CGMD nodal momenta in the present graphene model display clear non-Markovian behavior, a property that can be ascribed to the fact that the CGMD-weighting function suppresses high-frequency modes more effectively than, e.g., a simple center of mass (COM) based CG procedure. The present coarse-grained graphene model is also shown to reproduce the short time behavior of the momentum correlation functions more accurately than COM-variables and it is less dissipative than COM-CG. Finally, we find that, while the intermediate time scale represented directly by the CGMD variables shows a clear non-Markovian dynamics, the macroscopic dynamics of normal modes can be approximated by a Markovian dissipation, with friction coefficients scaling like the square of the wave vector. This opens the way to the development of a CGMD model capable of describing the correct long time behavior of such macroscopic normal modes.

  16. Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials.

    Science.gov (United States)

    Xu, Peijun; Shen, Hujun; Yang, Lu; Ding, Yang; Li, Beibei; Shao, Ying; Mao, Yingchen; Li, Guohui

    2013-02-01

    Coarse-grained studies of CH(3)SH, CH(3)CHO and CHCl(3) liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

  17. Protein-DNA docking with a coarse-grained force field

    Directory of Open Access Journals (Sweden)

    Setny Piotr

    2012-09-01

    Full Text Available Abstract Background Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy. Results We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location. Conclusions We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.

  18. Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.

    Energy Technology Data Exchange (ETDEWEB)

    Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.

    2010-09-01

    This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and

  19. Coarse-grained and fine-grained parallel optimization for real-time en-face OCT imaging

    Science.gov (United States)

    Kapinchev, Konstantin; Bradu, Adrian; Barnes, Frederick; Podoleanu, Adrian

    2016-03-01

    This paper presents parallel optimizations in the en-face (C-scan) optical coherence tomography (OCT) display. Compared with the cross-sectional (B-scan) imagery, the production of en-face images is more computationally demanding, due to the increased size of the data handled by the digital signal processing (DSP) algorithms. A sequential implementation of the DSP leads to a limited number of real-time generated en-face images. There are OCT applications, where simultaneous production of large number of en-face images from multiple depths is required, such as real-time diagnostics and monitoring of surgery and ablation. In sequential computing, this requirement leads to a significant increase of the time to process the data and to generate the images. As a result, the processing time exceeds the acquisition time and the image generation is not in real-time. In these cases, not producing en-face images in real-time makes the OCT system ineffective. Parallel optimization of the DSP algorithms provides a solution to this problem. Coarse-grained central processing unit (CPU) based and fine-grained graphics processing unit (GPU) based parallel implementations of the conventional Fourier domain (CFD) OCT method and the Master-Slave Interferometry (MSI) OCT method are studied. In the coarse-grained CPU implementation, each parallel thread processes the whole OCT frame and generates a single en-face image. The corresponding fine-grained GPU implementation launches one parallel thread for every data point from the OCT frame and thus achieves maximum parallelism. The performance and scalability of the CPU-based and GPU-based parallel approaches are analyzed and compared. The quality and the resolution of the images generated by the CFD method and the MSI method are also discussed and compared.

  20. IMPORT PRICES AND HARD CURRENCY CONSTRAINTS IN EASTERN EUROPE: IMPLICATIONS FOR COARSE GRAIN IMPORTS AND PRODUCTION OF MEAT

    OpenAIRE

    Garcia, Roberto J.; Miljkovic, Dragan; Gomez, Miguel I.

    1998-01-01

    The objectives of this study were (a) to determine the degree to which hard currency earnings constrained overall imports and coarse grain imports in command economies; (b) to measure the importance of import prices on grain imports and to trace the link of grain availability to meat production; and (c) to determine how economic and political reforms in the selected countries may have affected the hard currency constraint, the importance of import prices, and grain imports and meat production...

  1. Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions

    Science.gov (United States)

    Wagner, Jacob W.; Dannenhoffer-Lafage, Thomas; Jin, Jaehyeok; Voth, Gregory A.

    2017-07-01

    Order parameters (i.e., collective variables) are often used to describe the behavior of systems as they capture different features of the free energy surface. Yet, most coarse-grained (CG) models only employ two- or three-body non-bonded interactions between the CG particles. In situations where these interactions are insufficient for the CG model to reproduce the structural distributions of the underlying fine-grained (FG) model, additional interactions must be included. In this paper, we introduce an approach to expand the basis sets available in the multiscale coarse-graining (MS-CG) methodology by including order parameters. Then, we investigate the ability of an additive local order parameter (e.g., density) and an additive global order parameter (i.e., distance from a hard wall) to improve the description of CG models in interfacial systems. Specifically, we study methanol liquid-vapor coexistence, acetonitrile liquid-vapor coexistence, and acetonitrile liquid confined by hard-wall plates, all using single site CG models. We find that the use of order parameters dramatically improves the reproduction of structural properties of interfacial CG systems relative to the FG reference as compared with pairwise CG interactions alone.

  2. An Impulse-C Hardware Accelerator for Packet Classification Based on Fine/Coarse Grain Optimization

    Directory of Open Access Journals (Sweden)

    O. Ahmed

    2013-01-01

    Full Text Available Current software-based packet classification algorithms exhibit relatively poor performance, prompting many researchers to concentrate on novel frameworks and architectures that employ both hardware and software components. The Packet Classification with Incremental Update (PCIU algorithm, Ahmed et al. (2010, is a novel and efficient packet classification algorithm with a unique incremental update capability that demonstrated excellent results and was shown to be scalable for many different tasks and clients. While a pure software implementation can generate powerful results on a server machine, an embedded solution may be more desirable for some applications and clients. Embedded, specialized hardware accelerator based solutions are typically much more efficient in speed, cost, and size than solutions that are implemented on general-purpose processor systems. This paper seeks to explore the design space of translating the PCIU algorithm into hardware by utilizing several optimization techniques, ranging from fine grain to coarse grain and parallel coarse grain approaches. The paper presents a detailed implementation of a hardware accelerator of the PCIU based on an Electronic System Level (ESL approach. Results obtained indicate that the hardware accelerator achieves on average 27x speedup over a state-of-the-art Xeon processor.

  3. Cratering efficiency on coarse-grain targets: Implications for the dynamical evolution of asteroid 25143 Itokawa

    Science.gov (United States)

    Tatsumi, Eri; Sugita, Seiji

    2018-01-01

    Remote sensing observations made by the spacecraft Hayabusa provided the first direct evidence of a rubble-pile asteroid: 25143 Itokawa. Itokawa was found to have a surface structure very different from other explored asteroids; covered with coarse pebbles and boulders ranging at least from cm to meter size. The cumulative size distribution of small circular depressions on Itokawa, most of which may be of impact origin, has a significantly shallower slope than that on the Moon; small craters are highly depleted on Itokawa compared to the Moon. This deficiency of small circular depressions and other features, such as clustered fragments and pits on boulders, suggest that the boulders on Itokawa might behave like armor, preventing crater formation: the ;armoring effect;. This might contribute to the low number density of small crater candidates. In this study, the cratering efficiency reduction due to coarse-grained targets was investigated based on impact experiments at velocities ranging from ∼ 70 m/s to ∼ 6 km/s using two vertical gas gun ranges. We propose a scaling law extended for cratering on coarse-grained targets (i.e., target grain size ≳ projectile size). We have found that the crater efficiency reduction is caused by energy dissipation at the collision site where momentum is transferred from the impactor to the first-contact target grain, and that the armoring effect can be classified into three regimes: (1) gravity scaled regime, (2) reduced size crater regime, or (3) no apparent crater regime, depending on the ratio of the impactor size to the target grain size and the ratio of the impactor kinetic energy to the disruption energy of a target grain. We found that the shallow slope of the circular depressions on Itokawa cannot be accounted for by this new scaling law, suggesting that obliteration processes, such as regolith convection and migration, play a greater role in the depletion of circular depressions on Itokawa. Based on the new extended

  4. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

    Science.gov (United States)

    Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P

    2016-09-01

    Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR).

  5. Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling

    Science.gov (United States)

    Fačkovec, B.; Vanden-Eijnden, E.; Wales, D. J.

    2015-07-01

    A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

  6. Autocorrelation study of the Θ transition for a coarse-grained polymer model.

    Science.gov (United States)

    Qi, Kai; Bachmann, Michael

    2014-08-21

    By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to critical slowing down, an extremal autocorrelation time can also be considered as an indicator for the collapse transition that helps to locate the transition point. This is particularly useful for finite systems, where response quantities such as the specific heat do not necessarily exhibit clear indications for pronounced thermal activity.

  7. Classical world arising out of quantum physics under the restriction of coarse-grained measurements.

    Science.gov (United States)

    Kofler, Johannes; Brukner, Caslav

    2007-11-02

    Conceptually different from the decoherence program, we present a novel theoretical approach to macroscopic realism and classical physics within quantum theory. It focuses on the limits of observability of quantum effects of macroscopic objects, i.e., on the required precision of our measurement apparatuses such that quantum phenomena can still be observed. First, we demonstrate that for unrestricted measurement accuracy, no classical description is possible for arbitrarily large systems. Then we show for a certain time evolution that under coarse-grained measurements, not only macrorealism but even classical Newtonian laws emerge out of the Schrödinger equation and the projection postulate.

  8. Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

    DEFF Research Database (Denmark)

    Murtola, Teemu; Karttunen, Mikko; Vattulainen, Ilpo

    2009-01-01

    We present a two-dimensional coarse-grained (CG) model for a lipid membrane composed of phospholipids and cholesterol. The effective CG interactions are determined using radial distribution functions (RDFs) from atom-scale molecular dynamics simulations using the inverse Monte Carlo (IMC) technique......, based on our earlier work [T. Murtola et al., J. Chem. Phys. 121, 9156 (2004); J. Chem. Phys. 126, 075101 (2007)]. Here, the original model is improved by including an internal discrete degree of freedom for the phospholipid tails to describe chain ordering. We also discuss the problem of RDF inversion...

  9. Characterization of mechanical unfolding intermediates of membrane proteins by coarse grained molecular dynamics simulation

    Science.gov (United States)

    Yamada, Tatsuya; Mitaku, Shigeki; Yamato, Takahisa

    2018-01-01

    Single-molecule force spectroscopy by atomic force microscopy allows us to get insight into the mechanical unfolding of membrane proteins, and a typical experiment exhibits characteristic patterns on the force distance curves. The origin of these patterns, however, has not been fully understood yet. We performed coarse-grained simulation of the forced unfolding of halorodopsin, reproduced the characteristic features of the experimental force distance curves. A further examination near the membrane-water interface indicated the existence of a motif for the force peak formation, i.e., the occurrence of hydrophobic residues in the upper interface region and hydrophilic residues below the lower interface region.

  10. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems.

    Science.gov (United States)

    Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A; Plecháč, Petr

    2015-08-28

    Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.

  11. Comparison of all-atom and coarse-grained normal mode analysis in the elastic network model

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Ming Wen; O' Riordan, Brian; Kim, Byung [University of Massachusetts Amherst, Amherst (United States); Kim, Moon Ki [Sungkyunkwan University, Suwon (Korea, Republic of)

    2013-11-15

    Elastic network-based normal mode analyses (EN-NMA) of four pairs of open-closed proteins (Lactoferrin, Maltodextrin-binding protein, LAO-binding protein, and Adenylate kinase) were conducted using both all-atom and coarse-grained models. The results indicated that the performance of the all-atom model was similar to that of the coarse-grained model in terms of predicting the conformational changes of backbones. Moreover, dynamic behavior was examined by studying relative atomic displacements and shapes of the dominant mode. For instance, for Maltodextrin-binding protein, the results from the all-atom model differed from those of the coarse-grained model, especially for residues that are biologically relevant. The coarse-grained model has better computational efficiency than the allatom model. However, the former may misrepresent the key dynamics of a protein related to biological functions as a consequence of excessive coarse approximation. Considering that the current power even in a high-end personal computer is sufficient to handle most of protein structures with up to 1,000 residues in a reasonable manner, which can only be used with supercomputers a few decades ago, an all-atom-based EN-NMA may deserve more attention as a reliable and powerful computational tool for protein dynamics study over the conventional coarse-graining approach.

  12. Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane.

    Science.gov (United States)

    Szklarczyk, Oliwia M; Arvaniti, Eirini; van Gunsteren, Wilfred F

    2015-06-30

    Force field parameters for polarizable coarse-grained (CG) supra-atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine-grained (FG) CH(2)r united atoms of the cyclohexane ring, and one representing three FG CH(2)r united atoms. Electronic polarizability is represented by a massless charge-on-spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self-diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.

  13. State refinements and coarse graining in a full theory embedding of loop quantum cosmology

    Science.gov (United States)

    Bodendorfer, N.

    2017-07-01

    Bridging between descriptions involving few large and many small quantum numbers is the main open problem in loop quantum gravity. In other words, one would like to be able to represent the same physical system in terms of a few ‘coarse’ quantum numbers, while the effective dynamics at the coarse level should agree with the one induced by a description involving many small quantum numbers. Efforts to understand this relationship face the problem of the enormous computational complexity involved in evolving a generic state containing many quanta. In a cosmological context however, certain symmetry assumptions on the quantum states allow one to simplify the problem. In this paper, we will show how quantum states describing a spatially flat homogeneous and isotropic universe can be refined and coarse grained. Invariance of the dynamics of the coarse observables is shown to require a certain scaling property (familiar from loop quantum cosmology) of the quantum states if no running of parameters is taken into account. The involved states are solutions to the Hamiltonian constraint when terms coming from spatial derivatives are neglected, i.e. one works in the approximation of non-interacting FRW patches. The technical means to arrive at this result are a version of loop quantum gravity based on variables inspired by loop quantum cosmology, as well as an exact solution to the quantum dynamics of loop quantum cosmology which extends to the full theory in the chosen approximation.

  14. Coupling a nano-particle with isothermal fluctuating hydrodynamics: Coarse-graining from microscopic to mesoscopic dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Español, Pep [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Donev, Aleksandar [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012 (United States)

    2015-12-21

    We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our “bottom-up” and previous “top-down” approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a “linear for spiky” weak approximation which replaces microscopic “fields” with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics

  15. Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

    Directory of Open Access Journals (Sweden)

    Lee-Wei Yang

    2008-01-01

    Full Text Available Molecular dynamics (MD simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.

  16. Distributions of experimental protein structures on coarse-grained free energy landscapes

    Science.gov (United States)

    Sankar, Kannan; Liu, Jie; Wang, Yuan; Jernigan, Robert L.

    2015-12-01

    Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.

  17. Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.

    Science.gov (United States)

    Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

    2011-10-21

    A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. © 2011 American Institute of Physics

  18. Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany)

    2015-11-07

    In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.

  19. A Coding Framework for Functional Adaptation of Coarse-Grained Components in Extensible EJB Servers

    Science.gov (United States)

    Caron, Olivier; Carré, Bernard; Muller, Alexis; Vanwormhoudt, Gilles

    Separation of functional concerns is a major step for managing the complexity of large scale component systems. It allows the identification of well defined functional or non-functional dimensions in order to facilitate their assembly, adaptation and finally their reuse. Current component-based middleware and application servers offer container services that much more facilitate the reuse of the functional core throughout technical concerns, such as persistence, components distribution, transactions, security management, and so on. But they rarely offer facilities for the separation of functional concerns within this core itself. This contribution is dedicated to this question, specifically within the field of ”coarse-grained view components”. In the Information System domain, these components are common and capture ”real-world semantics”, that is a structured set of entities related to a specific functional concern. Inspired by previous works on Subject-Oriented or View-Oriented Modeling, we retain model templates as good candidates for the definition of coarse-grained reusable view components. We propose a framework to provide such components onto the EJB technology. It takes advantages of extensible containers and exploits their Aspect-Oriented Programming facilities in order to inject specific view services compatible with standard J2EE/EJB ones.

  20. Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

    Science.gov (United States)

    Sinitskiy, Anton V; Voth, Gregory A

    2018-01-07

    Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

  1. Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments

    Science.gov (United States)

    Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.

    2016-03-01

    Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.

  2. An Integral Equation Method Coupling with Variational Approach for Studying Coarse-Grained Lipid Dynamics

    Science.gov (United States)

    Fu, Szu-Pei; Jiang, Shidong; Klöckner, Andreas; Ryham, Rolf; Wala, Matt; Young, Yuan-Nan

    2017-11-01

    In macroscopic model, the well-known Helfrich membrane model has been extensively utilized as it captures some macroscopic physical properties of a lipid bilayer membrane. However, some phenomena such as membrane fusion and micelle formation cannot be described in this macroscopic framework. Yet the immense molecular details of a lipid bilayer membrane are impossible to be included in a plausible physical model. Therefore, in order to include the salient molecular details, we study the dynamics of coarse-grained lipid bilayer membrane using Janus particle configurations to represent collections of lipids These coarse-grained lipid molecules interact with each other through an action field that describes their hydrophobic tail-tail interactions. For this action potential, we adopt the integral equation method on solving energy minimizer with specific boundary condition on each Janus particle. Both the QBX (quadrature by expansion) and fhe fast multipole method (FMM) are used to efficiently solve the integral equation. We also examine the numerical accuracy and qualitative observation from large system simulations.

  3. Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)

    Science.gov (United States)

    Sinitskiy, Anton V.; Voth, Gregory A.

    2018-01-01

    Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.

  4. Evaluation of ultrasonic array imaging algorithms for inspection of a coarse grained material

    Science.gov (United States)

    Van Pamel, A.; Lowe, M. J. S.; Brett, C. R.

    2014-02-01

    Improving the ultrasound inspection capability for coarse grain metals remains of longstanding interest to industry and the NDE research community and is expected to become increasingly important for next generation power plants. A test sample of coarse grained Inconel 625 which is representative of future power plant components has been manufactured to test the detectability of different inspection techniques. Conventional ultrasonic A, B, and C-scans showed the sample to be extraordinarily difficult to inspect due to its scattering behaviour. However, in recent years, array probes and Full Matrix Capture (FMC) imaging algorithms, which extract the maximum amount of information possible, have unlocked exciting possibilities for improvements. This article proposes a robust methodology to evaluate the detection performance of imaging algorithms, applying this to three FMC imaging algorithms; Total Focusing Method (TFM), Phase Coherent Imaging (PCI), and Decomposition of the Time Reversal Operator with Multiple Scattering (DORT MSF). The methodology considers the statistics of detection, presenting the detection performance as Probability of Detection (POD) and probability of False Alarm (PFA). The data is captured in pulse-echo mode using 64 element array probes at centre frequencies of 1MHz and 5MHz. All three algorithms are shown to perform very similarly when comparing their flaw detection capabilities on this particular case.

  5. The ELBA force field for coarse-grain modeling of lipid membranes.

    Directory of Open Access Journals (Sweden)

    Mario Orsi

    Full Text Available A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r = 1. Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC and dioleoylphosphatidylethanolamine (DOPE in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids; this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.

  6. A coarse-grained computational model of DNA from all-atom molecular dynamics simulations.

    Science.gov (United States)

    Papoian, Garegin; Savelyev, Alexey

    2007-03-01

    DNA folds into a highly compact chromatin structure in the eukariotic cells. Counterions and the aqueous solvent provide a stabilizing medium for the maintanence of the highly compact and organized DNA structures. Thus, detailed understanding of counterion condensation around DNA is required to build a coarse-grained computational model of a chromatin fiber. We carried out large-scale all-atom Molecular Dynamics simulations of a 16-mer DNA in explicit water with Na+ and K+ counterions to gain insight into generic aspects of monovalent counterion condensation around the whole DNA molecule, focusing on the discrete nature of water and ions. We found that the Na+ ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K+ ions. We have provided a microscopic explanation for the larger Na+ affinity towards DNA, that is based on a combination of steric, electrostatic, and hydration effects. Our simulations are consistent with the prior DNA compaction and electrophoretic mobility experiments. We developed a coarse-grained DNA model based on the results of these all-atom simulations.

  7. Coarse Graining to Investigate Membrane Induced Peptide Folding of Anticancer Peptides

    Science.gov (United States)

    Ganesan, Sai; Xu, Hongcheng; Matysiak, Silvina

    Information about membrane induced peptide folding mechanisms using all-atom molecular dynamics simulations is a challenge due to time and length scale issues.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model by adding oppositely charged dummy particles inside protein backbone beads.These two dummy particles represent a fluctuating dipole,thus introducing structural polarization into the coarse-grained model.With this model,we were able to achieve significant α- β secondary structure content de novo,without any added bias.We extended the model to zwitterionic and anionic lipids,by adding oppositely charged dummy particles inside polar beads, to capture the ability of the head group region to form hydrogen bonds.We use zwitterionic POPC and anionic POPS as our model lipids, and a cationic anticancer peptide,SVS1,as our model peptide.We have characterized the driving forces for SVS1 folding on lipid bilayers with varying anionic and zwitterionic lipid compositions.Based on our results, dipolar interactions between peptide backbone and lipid head groups contribute to stabilize folded conformations.Cooperativity in folding is induced by both intra peptide and membrane-peptide interaction.

  8. Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

    Energy Technology Data Exchange (ETDEWEB)

    Pantawane, Sanwardhini [Department of Physics, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina Campus, Mumbai 400098 (India); Choudhury, Niharendu, E-mail: nihcho@barc.gov.in [Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085 (India)

    2016-05-23

    In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degree of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.

  9. Coarse-graining for fast dynamics of order parameters in the phase-field model

    Science.gov (United States)

    Jou, D.; Galenko, P. K.

    2018-01-01

    In standard descriptions, the master equation can be obtained by coarse-graining with the application of the hypothesis of full local thermalization that is equivalent to the local thermodynamic equilibrium. By contrast, fast transformations proceed in the absence of local equilibrium and the master equation must be obtained with the absence of thermalization. In the present work, a non-Markovian master equation leading, in specific cases of relaxation to local thermodynamic equilibrium, to hyperbolic evolution equations for a binary alloy, is derived for a system with two order parameters. One of them is a conserved order parameter related to the atomistic composition, and the other one is a non-conserved order parameter, which is related to phase field. A microscopic basis for phenomenological phase-field models of fast phase transitions, when the transition is so fast that there is not sufficient time to achieve local thermalization between two successive elementary processes in the system, is provided. In a particular case, when the relaxation to local thermalization proceeds by the exponential law, the obtained coarse-grained equations are related to the hyperbolic phase-field model. The solution of the model equations is obtained to demonstrate non-equilibrium phenomenon of solute trapping which appears in rapid growth of dendritic crystals. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

  10. Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

    Science.gov (United States)

    Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta

    2016-11-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

  11. Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield.

    Science.gov (United States)

    Bhadra, Pratiti; Pal, Debnath

    2017-04-01

    Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Synthetic Aperture Focusing Technique in Ultrasonic Inspection of Coarse Grained Materials

    Energy Technology Data Exchange (ETDEWEB)

    Stepinski, Tadeusz (Uppsala Univ., Signals and Systems, Box 528, SE-751 20 Uppsala (Sweden))

    2007-12-15

    Experience from the ultrasonic inspection of nuclear power plants has shown that large focused transducers are relatively effective in suppressing grain (structure) noise. Operation of a large focused transducer can be thought of as an integration (coherent summation) of individual beams reflected from the target and received by individual points at the transducer surface. Synthetic aperture focusing technique (SAFT), in its simplest version mimics an acoustic lens used for focusing beams at a desired point in the region of interest. Thus, SAFT should be able to suppress the grain noise in the similar way as the focused transducer does. This report presents the results of investigation of SAFT algorithms applied for post-processing of ultrasonic data acquired in inspection of coarse grained metals. The performance of SAFT in terms of its spatial (cross-range) resolution and grain noise suppression is studied. The evaluation is made based on the experimental data obtained from the ultrasonic inspection of test specimens with artificial defects (side drilled holes). SAFT algorithms for both contact and immersion mode are introduced and experimentally verified

  13. Corrosion Inhibition of Sodium Phosphate for Coarse and Near Ultrafined-Grain Mild steel surface

    Directory of Open Access Journals (Sweden)

    Kazem Sabet Bokati

    2017-06-01

    Full Text Available An ultrafine grain surface layer with average crystallite size of 28 nm was produced on annealed mild steel through a wire brushing process. The effects of grain size reduction on the inhibition performance of sodium phosphate were investigated using polarization and electrochemical impedance spectroscopy (EIS measurements. The crystal grain size of wire brushed surface was analyzed by X-ray diffractometry (XRD and field emission scanning electron microscopy (FESEM. The electrochemical tests were conducted in artificial sea water (ASW in the presence and absence of 250 mg/lit sodium phosphate (SP. The wire brushed surface indicated considerable deformed plastic flows and high surface roughness. Due to the accumulated strains, a deformed layer with thickness of 20±5 μm was produced and the crystal grain size of severe deformed zone was about 28 nm. Wire brushed surface increased uniform corrosion rate of mild steel due to enhanced surface roughness and preferential sites to adsorption of corrosive ions. However, the wire brushed surface showed a positive effect on inhibition performance of sodium phosphate. The electrochemical results revealed that average inhibition efficiency increased from 65 to about 80 percent in ASW solution containing 1.5 mM Na3PO4 for coarse grained samples in comparison to that of ultra-fined grain samples respectively .The wire brushing process encouraged passivity on the surface in SP-containing solution due to a high density of nucleation sites which increased the adsorption of phosphate ions leading to a high fraction of passive layers and low corrosion rates.

  14. An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

    Science.gov (United States)

    Shen, Hujun; Li, Yan; Ren, Pengyu; Zhang, Dinglin; Li, Guohui

    2014-02-10

    Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

  15. Anomalously coarse-grained siliciclastic sediments on slope of Tiburon Rise, western Atlantic

    Energy Technology Data Exchange (ETDEWEB)

    Dolan, J.F.

    1987-05-01

    One surprising result of Ocean Drilling Project Leg 110 (Lesser Antilles forearc) was the discovery of extensive, anomalously coarse-grained Eocene-Oligocene siliciclastic deposits on the slope of the Tiburon Rise. These deposits are difficult to explain in terms of (1) mode of deposition and (2) timing of deposition with respect to sea level. These sands and silts occur at 1-150-cm thick planar-laminated beds within a 200-m thick sequences of hemipelagic clay. The siliciclastic layers locally exhibit graded bedding and partial Bouma sequences. Their quartz-rich composition and the rate occurrence of microcline and glaucophane suggest derivation from South America. Although these sediments probably reached the Tiburon Rise area as turbidites, their ultimate depositional mechanism is unclear. Despite local turbiditic textures, occurrence of the sediments on the slope of the rise, 400 m above the adjacent abyssal plain, suggests they are not predominantly turbidites. One possible explanation is transportation upslope by bottom currents. An alternative possibility is that during the Paleogene the rise was not a bathymetric high and that these are simply distal turbidites. However, interbedded calcilutite turbidites and small-scale slumps derived from higher on the rise demonstrate that paleoslopes existed during deposition of the siliciclastic sediments. The relationship between timing of deposition and sea level is also problematic. Deposition of the anomalously coarse-grained sediments occurred during a period of presumed high sea level, whereas sediments deposited during the subsequent late Oligocene sea level lowstand consist of fine-grained hemipelagic sediment. Exactly the opposite transition is predicted by traditional models of deep-sea siliciclastic sedimentation.

  16. Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?

    Science.gov (United States)

    Ardham, Vikram Reddy; Leroy, Frédéric

    2017-10-01

    Coarse-grained models have increasingly been used in large-scale particle-based simulations. However, due to their lack of degrees of freedom, it is a priori unlikely that they straightforwardly represent thermal properties with the same accuracy as their atomistic counterparts. We take a first step in addressing the impact of liquid coarse-graining on interfacial heat conduction by showing that an atomistic and a coarse-grained model of water may yield similar values of the Kapitza conductance on few-layer graphene with interactions ranging from hydrophobic to mildly hydrophilic. By design the water models employed yield similar liquid layer structures on the graphene surfaces. Moreover, they share common vibration properties close to the surfaces and thus couple with the vibrations of graphene in a similar way. These common properties explain why they yield similar Kapitza conductance values despite their bulk thermal conductivity differing by more than a factor of two.

  17. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.

    Science.gov (United States)

    Ruff, Kiersten M; Harmon, Tyler S; Pappu, Rohit V

    2015-12-28

    We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

  18. CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ruff, Kiersten M. [Computational and Systems Biology Program and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899 (United States); Harmon, Tyler S. [Department of Physics and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899 (United States); Pappu, Rohit V., E-mail: pappu@wustl.edu [Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, CB 1097, St. Louis, Missouri 63130-4899 (United States)

    2015-12-28

    We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

  19. Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations.

    Science.gov (United States)

    Grime, John M A; Voth, Gregory A

    2014-01-14

    The use of coarse-grained (CG) models can significantly increase the time and length scales accessible to computational molecular dynamics (MD) simulations. To address very large-scale phenomena, however, requires a careful consideration of memory requirements and parallel MD load balancing in order to make efficient use of current supercomputers. In this work, a CG-MD code is introduced which is specifically designed for very large, highly parallel simulations of systems with markedly non-uniform particle distributions, such as those found in highly CG models having an implicit solvent. The CG-MD code uses an unorthodox combination of sparse data representations with a Hilbert space-filling curve (SFC) to provide dynamic topological descriptions, reduced memory overhead, and advanced load-balancing characteristics. The results of representative large-scale simulations indicate that our approach can offer significant advantages over conventional MD techniques, and should enable new classes of CG-MD systems to be investigated.

  20. Aggregation of alpha-synuclein by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Farmer, Barry; Pandey, Ras

    Alpha-synuclein, an intrinsic protein abundant in neurons, is believed to be a major cause of neurodegenerative diseases (e.g. Alzheimer, Parkinson's disease). Abnormal aggregation of ASN leads to Lewy bodies with specific morphologies. We investigate the self-organizing structures in a crowded environment of ASN proteins by a coarse-grained Monte Carlo simulation. ASN is a chain of 140 residues. Structure detail of residues is neglected but its specificity is captured via unique knowledge-based residue-residue interactions. Large-scale simulations are performed to analyze a number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) as a function of temperature and protein concentration. Trend in multi-scale structural variations of the protein in a crowded environment is compared with that of a free protein chain.

  1. Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials.

    Science.gov (United States)

    John, S T; Csányi, Gábor

    2017-12-07

    We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations.

  2. Experimental study on waves propagation over a coarse-grained sloping beach

    Science.gov (United States)

    Hsu, Tai-Wen; Lai, Jian-Wu

    2013-04-01

    This study investigates velocity fields of wave propagation over a coarse-grained sloping beach using laboratory experiments. The experiment was conducted in a wave flume of 25 m long, 0.5 m wide and 0.6 m high in which a coarse-grained sloping 1:5 beach was placed with two layers ball. The glass ball is D=7.9 cm and the center to center distance of each ball is 8.0 cm. The test section for observing wave and flow fields is located at the middle part of the flume. A piston type wave maker driven by an electromechanical hydraulic serve system is installed at the end of the flume. The intrinsic permeability Kp and turbulent drag coefficient Cf were obtained from steady flow water-head experiments. The flow velocity was measured by the particle image velocimeter (PIV) and digital image process (DIP) techniques. Eleven fields of view (FOVS) were integrated into a complete representation including the outer, surf and swash zone. Details of the definition sketch of the coarse-grained sloping beach model as well as experimental setup are referred to Lai et al. (2008). A high resolution of CCD camera was used to capture the images which was calibrated by the direct linear transform (DCT) algorithm proposed by Abed El-Aziz and Kar-Ara (1971). The water surface between the interface of air and water at each time step are calculated by Otsu' (1978) detect algorithm. The comparison shows that the water surface elevation observed by integrated image agrees well with that of Otsu' detection results. For the flow field measurement, each image pair was cross correlated with 32X32 pixel inter rogation window and a half overlap between adjacent windows. The repeatability and synchronization are the key elements for both wave motion and PIV technique. The wave profiles and flow field were compared during several wave periods to ensure that they can be reproduced by the present system. The water depth is kept as a constant of h=32 cm. The incident wave conditions are set to be wave

  3. Structural investigation of MscL gating using experimental data and coarse grained MD simulations.

    Directory of Open Access Journals (Sweden)

    Evelyne Deplazes

    Full Text Available The mechanosensitive channel of large conductance (MscL has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation.

  4. Transformation and VHDL Code Generation from Coarse-grained Data flow Graph

    Energy Technology Data Exchange (ETDEWEB)

    Oh, M.W.; Ha, S.H. [Seoul National University, Seoul (Korea, Republic of)

    1998-12-01

    This paper discusses how we generate VHDL codes for DSP applications described in data flow graphs. Because the generated VHDL code implements the details of the control structure, we can easily transform it into a running circuit without any modifications, using logic synthesis tools. To improve the quality of the synthesized circuit we apply some graph transformation techniques to the original data flow graph. We mainly consider coarse-grained data flow graphs in which each node corresponds to an IP component of considerable size. The proposed facility is very useful for data flow graph based high level design tools, including our co design framework PeaCE (Ptolemy extension as Codesign Environment). (author). 12 refs., 7 figs., 1 tab.

  5. Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids.

    Science.gov (United States)

    DeVane, Russell; Jusufi, Arben; Shinoda, Wataru; Chiu, Chi-cheng; Nielsen, Steven O; Moore, Preston B; Klein, Michael L

    2010-12-16

    Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C(60) interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C(60) interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C(60) lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated.

  6. Macroscopic and large scale phenomena coarse graining, mean field limits and ergodicity

    CERN Document Server

    Rademacher, Jens; Zagaris, Antonios

    2016-01-01

    This book is the offspring of a summer school school “Macroscopic and large scale phenomena: coarse graining, mean field limits and ergodicity”, which was held in 2012 at the University of Twente, the Netherlands. The focus lies on mathematically rigorous methods for multiscale problems of physical origins. Each of the four book chapters is based on a set of lectures delivered at the school, yet all authors have expanded and refined their contributions. Francois Golse delivers a chapter on the dynamics of large particle systems in the mean field limit and surveys the most significant tools and methods to establish such limits with mathematical rigor. Golse discusses in depth a variety of examples, including Vlasov--Poisson and Vlasov--Maxwell systems. Lucia Scardia focuses on the rigorous derivation of macroscopic models using $\\Gamma$-convergence, a more recent variational method, which has proved very powerful for problems in material science. Scardia illustrates this by various basic examples and a mor...

  7. Early stages of clathrin aggregation at a membrane in coarse-grained simulations

    Science.gov (United States)

    Giani, M.; den Otter, W. K.; Briels, W. J.

    2017-04-01

    The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

  8. A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, Lauren J.; Stevens, Mark J., E-mail: msteve@sandia.gov [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

    2015-12-28

    A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

  9. Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study

    DEFF Research Database (Denmark)

    Telenius, J.; Koivuniemi, A.; Kulovesi, P.

    2012-01-01

    Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse...... system, we found drastic differences in both structural and dynamical properties that explain the prominent role of neutral lipids as stabilizers of the TFLL. Based on our results, we suggest that neutral lipids are able to increase the stability of the TFLL by modulating its dynamical and structural......-grained simulations of a lipid layer comprising phospholipids, free fatty acids, cholesteryl esters, and triglycerides at the air-water interface to shed light on the properties of TFLL. We consider structural as well as dynamical properties of the lipid layer as a function of surface pressure. Simulations revealed...

  10. Coarse graining of NN inelastic interactions up to 3 GeV: Repulsive versus structural core

    Science.gov (United States)

    Fernández-Soler, P.; Ruiz Arriola, E.

    2017-07-01

    The repulsive short-distance core is one of the main paradigms of nuclear physics which even seems confirmed by QCD lattice calculations. On the other hand nuclear potentials at short distances are motivated by high energy behavior where inelasticities play an important role. We analyze NN interactions up to 3 GeV in terms of simple coarse grained complex and energy dependent interactions. We discuss two possible and conflicting scenarios which share the common feature of a vanishing wave function at the core location in the particular case of S waves. We find that the optical potential with a repulsive core exhibits a strong energy dependence whereas the optical potential with the structural core is characterized by a rather adiabatic energy dependence which allows one to treat inelasticity perturbatively. We discuss the possible implications for nuclear structure calculations of both alternatives.

  11. Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles

    Science.gov (United States)

    Lopez, Hender; Lobaskin, Vladimir

    2015-12-01

    We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles (NPs). The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the aminoacids via a central force that depends on the nanoparticle size. The proposed methodology is used to predict the adsorption energies for six common human blood plasma proteins on hydrophobic charged or neutral nanoparticles of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the nanoparticle, which can be used for predicting the composition of the NP-protein corona. The predicted ranking is in good agreement with known experimental data for protein adsorption on surfaces.

  12. Bridging the Coarse-grained to Microscopic information gap: A numerical optimization method

    CERN Document Server

    Mansour, Andrew Abi

    2013-01-01

    Atom-resolved states must be constructed as part of a multiscale algorithm that coevolves the system at the atomic and coarse-grained (CG) scales. The CG description does not capture the constraints on distances and angles imposed by stiff bonded interactions. Thus, in isothermal simulations, using only CG information to construct the initial conditions yields microstates of negligible Boltzmann weight. In this paper, we present a reversible CG to all-atom mapping algorithm that overcomes this difficulty. The result is a scalable algorithm for simulating mesoscopic systems with atomic precision, over long periods of time, and with great efficiency over conventional MD. The mapping algorithm is implemented in parallel for distributed memory systems as part of the Deductive Multiscale Simulator software. It is demonstrated for Lactoferrin, an assembly of Nudaurelia Capensis Omega proteins, and Cowpea Chlorotic Mottle virus capsid.

  13. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  14. Reduced-order molecular-dynamics model for polystyrene by equivalent-structure coarse graining.

    Science.gov (United States)

    Srivastava, Anand; Ghosh, Somnath

    2012-02-01

    This paper develops a reduced-order equivalent-structure based model for polystyrene in a rigid body molecular dynamics framework. In general, a coarse-grained model for polymers is obtained by replacing a group of chemically connected atoms by an effective particle and deriving a coarse-grained interaction potential that reproduces the structure and dynamics at the desired length and time scale. In the current model, a detailed (~16 atoms) polystyrene monomer referred to as basic structural element (BSE) is replaced by an equivalent model with spherical backbone particles and an ellipsoidal particle that represents the styrene sidegroup. The governing principals of this homogenization is based on the mass, centroid, angular momentum, and energy equivalence between the detailed and the proposed reduced-order model. The bonded interactions parameters are readily obtained in the optimization of the equivalent structure from the detailed representation. The nonbonded interactions are treated separately. In order to capture the stereochemistry of the polystyrene molecule, an anisotropic biaxial nonbonded interaction potential function known as RE-squared (RE2) interaction has been used between pairs of ellipsoidal and/or spherical particles in the system. The required calibration of the nonbonded parameters is carried out by matching with the experimental density and the local structure using radial distribution function. This homogenization process scales up the modeling system size significantly as the higher frequency motions like -C-H- vibrations and sidegroup movements are suppressed. The accuracy of the model is established by comparing fine-scale simulation with explicit representations.

  15. Mapping the Energy Cascade in the North Atlantic Ocean: The Coarse-Graining Approach

    Science.gov (United States)

    Aluie, Hussein; Hecht, Matthew; Vallis, Geoffrey K.

    2018-02-01

    A coarse-graining framework is implemented to analyze nonlinear processes, measure energy transfer rates and map out the energy pathways from simulated global ocean data. Traditional tools to measure the energy cascade from turbulence theory, such as spectral flux or spectral transfer rely on the assumption of statistical homogeneity, or at least a large separation between the scales of motion and the scales of statistical inhomogeneity. The coarse-graining framework allows for probing the fully nonlinear dynamics simultaneously in scale and in space, and is not restricted by those assumptions. This paper describes how the framework can be applied to ocean flows. Energy transfer between scales is not unique due to a gauge freedom. Here, it is argued that a Galilean invariant subfilter scale (SFS) flux is a suitable quantity to properly measure energy scale-transfer in the Ocean. It is shown that the SFS definition can yield answers that are qualitatively different from traditional measures that conflate spatial transport with the scale-transfer of energy. The paper presents geographic maps of the energy scale-transfer that are both local in space and allow quasi-spectral, or scale-by-scale, dynamics to be diagnosed. Utilizing a strongly eddying simulation of flow in the North Atlantic Ocean, it is found that an upscale energy transfer does not hold everywhere. Indeed certain regions, near the Gulf Stream and in the Equatorial Counter Current have a marked downscale transfer. Nevertheless, on average an upscale transfer is a reasonable mean description of the extra-tropical energy scale-transfer over regions of O(10^3) kilometers in size.

  16. Polarizable water model for the coarse-grained MARTINI force field.

    Directory of Open Access Journals (Sweden)

    Semen O Yesylevskyy

    2010-06-01

    Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.

  17. A large coaxial reflection cell for broadband dielectric characterization of coarse-grained materials

    Science.gov (United States)

    Bore, Thierry; Bhuyan, Habibullah; Bittner, Tilman; Murgan, Vignesh; Wagner, Norman; Scheuermann, Alexander

    2018-01-01

    Knowledge of the frequency-dependent electromagnetic properties of coarse-grained materials is imperative for the successful application of high frequency electromagnetic measurement techniques for near and subsurface monitoring. This paper reports the design, calibration and application of a novel one-port large coaxial cell for broadband complex permittivity measurements of civil engineering materials. It was designed to allow the characterization of heterogeneous material with large aggregate dimensions (up to 28 mm) over a frequency range from 1 MHz–860 MHz. In the first step, the system parameters were calibrated using the measured scattering function in a perfectly known dielectric material in an optimization scheme. In the second step, the method was validated with measurements made on standard liquids. Then the performance of the cell was evaluated on a compacted coarse-grained soil. The dielectric spectra were obtained by means of fitting the measured scattering function using a transverse electromagnetic mode propagation model considering the frequency-dependent complex permittivity. Two scenarios were systematically analyzed and compared. The first scenario consisted of a broadband generalized dielectric relaxation model with two Cole–Cole type relaxation processes related to the interaction of the aqueous phase and the solid phase, a constant high frequency contribution as well as an apparent direct current conductivity term. The second scenario relied on a three-phase theoretical mixture equation which was used in a forward approach in order to calibrate the model. Both scenarios provide almost identical results for the broadband effective complex relative permittivity. The combination of both scenarios suggests the simultaneous estimation of water content, density, bulk and pore water conductivity for road base materials for in situ applications.

  18. Graph coarse-graining reveals differences in the module-level structure of functional brain networks.

    Science.gov (United States)

    Kujala, Rainer; Glerean, Enrico; Pan, Raj Kumar; Jääskeläinen, Iiro P; Sams, Mikko; Saramäki, Jari

    2016-11-01

    Networks have become a standard tool for analyzing functional magnetic resonance imaging (fMRI) data. In this approach, brain areas and their functional connections are mapped to the nodes and links of a network. Even though this mapping reduces the complexity of the underlying data, it remains challenging to understand the structure of the resulting networks due to the large number of nodes and links. One solution is to partition networks into modules and then investigate the modules' composition and relationship with brain functioning. While this approach works well for single networks, understanding differences between two networks by comparing their partitions is difficult and alternative approaches are thus necessary. To this end, we present a coarse-graining framework that uses a single set of data-driven modules as a frame of reference, enabling one to zoom out from the node- and link-level details. As a result, differences in the module-level connectivity can be understood in a transparent, statistically verifiable manner. We demonstrate the feasibility of the method by applying it to networks constructed from fMRI data recorded from 13 healthy subjects during rest and movie viewing. While independently partitioning the rest and movie networks is shown to yield little insight, the coarse-graining framework enables one to pinpoint differences in the module-level structure, such as the increased number of intra-module links within the visual cortex during movie viewing. In addition to quantifying differences due to external stimuli, the approach could also be applied in clinical settings, such as comparing patients with healthy controls. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  19. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.

    Science.gov (United States)

    Pickard, Frank C; Miller, Benjamin T; Schalk, Vinushka; Lerner, Michael G; Woodcock, H Lee; Brooks, Bernard R

    2014-07-01

    A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.

  20. A coarse-grained model for synergistic action of multiple enzymes on cellulose

    Directory of Open Access Journals (Sweden)

    Asztalos Andrea

    2012-08-01

    Full Text Available Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures

  1. Short- and medium-term response to storms on three Mediterranean coarse-grained beaches

    Science.gov (United States)

    Grottoli, Edoardo; Bertoni, Duccio; Ciavola, Paolo

    2017-10-01

    The storm response of three Italian coarse-grained beaches was investigated to better understand the morphodynamics of coarse-clastic beaches in a microtidal context. Two of the studied sites are located on the eastern side of the country (Portonovo and Sirolo) and the third one (Marina di Pisa) is on the western side. Portonovo and Sirolo are mixed sand and gravel beaches where the storms approach from two main directions, SE and NE. Marina di Pisa is a coarse-grained, gravel-dominated beach, exposed to storms driven by SW winds. Gravel nourishments were undertaken in recent years on the three sites. Beach topography was monitored measuring the same network of cross sections at a monthly (i.e. short-term) to seasonal frequency (i.e. medium-term). Geomorphic changes were examined before and after storm occurrences by means of profile analyses and shoreline position evaluations. The beach orientation and the influence of hard structures are the main factors controlling the transport and accumulation of significant amount of sediments and the consequent high variability of beach morphology over the medium-term. For Marina di Pisa, storms tend to accumulate material towards the upper part of the beach with no shoreline rotation and no chance to recover the initial configuration. Sirolo and Portonovo showed a similar behaviour that is more typical of pocket beaches. Both beaches show shoreline rotation after storms in a clockwise or counter-clockwise direction according to the incoming wave direction. The wider and longer beach at Sirolo allows the accumulation of a thin layer of sediment during storms, rather than at Portonovo where, given its longshore and landward boundaries, the beach material tends to accumulate in greater thickness. After storms, Sirolo and especially Portonovo can quickly recover the initial beach configuration, as soon as another storm of comparable energy approaches from the opposite direction of the previous one. Large morphological

  2. Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers.

    Science.gov (United States)

    Rahimi, Ali; Amjad-Iranagh, Sepideh; Modarress, Hamid

    2016-03-01

    Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

  3. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    NARCIS (Netherlands)

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  4. Determination of Mineral Elements of Some Coarse Grains by Microwave Digestion with Inductively Coupled Plasma Atomic Emission Spectrometry

    Directory of Open Access Journals (Sweden)

    Li Yang

    2012-01-01

    Full Text Available To determinate the mineral elements contents in millet,maise,oat,buckwheat,sorghum and purple rice, microwave digestion procedure optimized was applied for digesting six coarse grains. Nineteen mineral element concentrations were determined by inductively coupled plasma atomic emission spectrometry (ICP-AES. Results displayed the limits of detection (LODs and the limits of quantification (LOQs range from 0.0047 to 0.1250 μg/mL and 0.0155 to 0.4125 μg/mL. The relative standard deviations (RSDs range from 0.83% to 5.03%, which showed that this proposed method was accurate and precise to detect mineral elements in coarse grains simultaneously. Correlation coefficients (r were calculated in the range of 0.999096-0.999989. The sufficient dada obtained described that the coarse grains selected were abundant in mineral element contents in the human body on daily diet. The success of combining the microwave digestion technology with the ICP-AES was a simple and precise method to determine many mineral elements in coarse grains simultaneously.

  5. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

    NARCIS (Netherlands)

    Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF

    2006-01-01

    Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model

  6. Capturing the Large Scale Behavior of Many Particle Systems Through Coarse-Graining

    Science.gov (United States)

    Punshon-Smith, Samuel

    This dissertation is concerned with two areas of investigation: the first is understanding the mathematical structures behind the emergence of macroscopic laws and the effects of small scales fluctuations, the second involves the rigorous mathematical study of such laws and related questions of well-posedness. To address these areas of investigation the dissertation involves two parts: Part I concerns the theory of coarse-graining of many particle systems. We first investigate the mathematical structure behind the Mori-Zwanzig (projection operator) formalism by introducing two perturbative approaches to coarse-graining of systems that have an explicit scale separation. One concerns systems with little dissipation, while the other concerns systems with strong dissipation. In both settings we obtain an asymptotic series of `corrections' to the limiting description which are small with respect to the scaling parameter, these corrections represent the effects of small scales. We determine that only certain approximations give rise to dissipative effects in the resulting evolution. Next we apply this framework to the problem of coarse-graining the locally conserved quantities of a classical Hamiltonian system. By lumping conserved quantities into a collection of mesoscopic cells, we obtain, through a series of approximations, a stochastic particle system that resembles a discretization of the non-linear equations of fluctuating hydrodynamics. We study this system in the case that the transport coefficients are constant and prove well-posedness of the stochastic dynamics. Part II concerns the mathematical description of models where the underlying characteristics are stochastic. Such equations can model, for instance, the dynamics of a passive scalar in a random (turbulent) velocity field or the statistical behavior of a collection of particles subject to random environmental forces. First, we study general well-posedness properties of stochastic transport equation with

  7. Coarse-grained model of nanoscale segregation, water diffusion, and proton transport in Nafion membranes.

    Science.gov (United States)

    Vishnyakov, Aleksey; Mao, Runfang; Lee, Ming-Tsung; Neimark, Alexander V

    2018-01-14

    We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation. The simulation results qualitatively, and in many respects quantitatively, predict the specifics of nanoscale segregation in the hydrated Nafion membrane into hydrophobic and hydrophilic subphases, water diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from a collection of isolated water clusters to a 3D network of pores filled with water embedded in the hydrophobic matrix. The segregated morphology is characterized in terms of the pore size distribution with the average size growing with hydration from ∼1 to ∼4 nm. Comparison of the predicted water diffusivity with the experimental data taken from different sources shows good agreement at high and moderate hydration and substantial deviation at low hydration, around and below the percolation threshold. This discrepancy is attributed to the dynamic percolation effects of formation and rupture of merging bridges between the water clusters, which become progressively important at low hydration, when the coarse-grained model is unable to mimic the fine structure of water network that includes singe molecule bridges. Selected simulations of water diffusion are performed for the alkali metal substituted membrane which demonstrate the effects of the counter

  8. Multi-scale coarse-graining of non-conservative interactions in molecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)

    2014-03-14

    A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger

  9. Coarse-grained model of nanoscale segregation, water diffusion, and proton transport in Nafion membranes

    Science.gov (United States)

    Vishnyakov, Aleksey; Mao, Runfang; Lee, Ming-Tsung; Neimark, Alexander V.

    2018-01-01

    We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation. The simulation results qualitatively, and in many respects quantitatively, predict the specifics of nanoscale segregation in the hydrated Nafion membrane into hydrophobic and hydrophilic subphases, water diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from a collection of isolated water clusters to a 3D network of pores filled with water embedded in the hydrophobic matrix. The segregated morphology is characterized in terms of the pore size distribution with the average size growing with hydration from ˜1 to ˜4 nm. Comparison of the predicted water diffusivity with the experimental data taken from different sources shows good agreement at high and moderate hydration and substantial deviation at low hydration, around and below the percolation threshold. This discrepancy is attributed to the dynamic percolation effects of formation and rupture of merging bridges between the water clusters, which become progressively important at low hydration, when the coarse-grained model is unable to mimic the fine structure of water network that includes singe molecule bridges. Selected simulations of water diffusion are performed for the alkali metal substituted membrane which demonstrate the effects of the counter-ions on

  10. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

    Science.gov (United States)

    Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F

    2007-02-19

    Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.

  11. Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling.

    Science.gov (United States)

    Peng, Yuxing; Cao, Zhen; Zhou, Ruhong; Voth, Gregory A

    2014-09-09

    An enhanced conformational space sampling method is developed that utilizes replica exchange molecular dynamics between a set of imaginary time Feynman path integral replicas, each having an increasing degree of contraction (or coarse-graining) of the quasi-particle or "polymer beads" in the evaluation of the isomorphic ring-polymer potential energy terms. However, there is no contraction of beads in the effectively harmonic kinetic energy terms. The final replica in this procedure is the fully contracted one in which the potential energy is evaluated only at the centroid of the beads-and hence it is the classical distribution in the centroid variable-while the initial replica has the full degree (or even a heightened degree, if desired) of quantum delocalization and tunneling in the physical potential by the polymer necklace beads. The exchange between the different ring-polymer ensembles is governed by the Metropolis criteria to guarantee detailed balance. The method is applied successfully to several model systems, ranging from one-dimensional prototype rough energy landscape models having analytical solutions to the more realistic alanine dipeptide. A detailed comparison with the classical temperature-based replica exchange method shows an improved efficiency of this new method in the classical conformational space sampling due to coupling with the fictitious path integral (quantum) replicas.

  12. Coarse-Grain QoS-Aware Dynamic Instance Provisioning for Interactive Workload in the Cloud

    Directory of Open Access Journals (Sweden)

    Jianxiong Wan

    2014-01-01

    Full Text Available Cloud computing paradigm renders the Internet service providers (ISPs with a new approach to deliver their service with less cost. ISPs can rent virtual machines from the Infrastructure-as-a-Service (IaaS provided by the cloud rather than purchasing them. In addition, commercial cloud providers (CPs offer diverse VM instance rental services in various time granularities, which provide another opportunity for ISPs to reduce cost. We investigate a Coarse-grain QoS-aware Dynamic Instance Provisioning (CDIP problem for interactive workload in the cloud from the perspective of ISPs. We formulate the CDIP problem as an optimization problem where the objective is to minimize the VM instance rental cost and the constraint is the percentile delay bound. Since the Internet traffic shows a strong self-similar property, it is hard to get an analytical form of the percentile delay constraint. To address this issue, we purpose a lookup table structure together with a learning algorithm to estimate the performance of the instance provisioning policy. This approach is further extended with two function approximations to enhance the scalability of the learning algorithm. We also present an efficient dynamic instance provisioning algorithm, which takes full advantage of the rental service diversity, to determine the instance rental policy. Extensive simulations are conducted to validate the effectiveness of the proposed algorithms.

  13. Coarse-grain molecular dynamics study of fullerene transport across a cell membrane.

    Science.gov (United States)

    Sridhar, Akshay; Srikanth, Bharath; Kumar, Amit; Dasmahapatra, Ashok Kumar

    2015-07-14

    The study of the ability of drug molecules to enter cells through the membrane is of vital importance in the field of drug delivery. In cases where the transport of the drug molecules through the membrane is not easily accomplishable, other carrier molecules are used. Spherical fullerene molecules have been postulated as potential carriers of highly hydrophilic drugs across the plasma membrane. Here, we report the coarse-grain molecular dynamics study of the translocation of C60 fullerene and its derivatives across a cell membrane modeled as a 1,2-distearoyl-sn-glycero-3-phosphocholine bilayer. Simulation results indicate that pristine fullerene molecules enter the bilayer quickly and reside within it. The addition of polar functionalized groups makes the fullerenes less likely to reside within the bilayer but increases their residence time in bulk water. Addition of polar functional groups to one half of the fullerene surface, in effect creating a Janus particle, offers the most promise in developing fullerene models that can achieve complete translocation through the membrane bilayer.

  14. The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study.

    Directory of Open Access Journals (Sweden)

    William Hoiles

    Full Text Available Tethered bilayer lipid membranes (tBLMs provide a stable platform for modeling the dynamics and order of biological membranes where the tethers mimic the cytoskeletal supports present in biological cell membranes. In this paper coarse-grained molecular dynamics (CGMD is applied to study the effects of tethers on lipid membrane properties. Using results from the CGMD model and the overdamped Fokker-Planck equation, we show that the diffusion tensor and particle density of water in the tBLM is spatially dependent. Further, it is shown that the membrane thickness, lipid diffusion, defect density, free energy of lipid flip-flop, and membrane dielectric permittivity are all dependent on the tether density. The numerically computed results from the CGMD model are in agreement with the experimentally measured results from tBLMs containing different tether densities and lipids derived from Archaebacteria. Additionally, using experimental measurements from Escherichia coli bacteria and Saccharomyces Cerevisiae yeast tethered membranes, we illustrate how previous molecular dynamics results can be combined with the proposed model to estimate the dielectric permittivity and defect density of these membranes as a function of tether density.

  15. A new algorithm for construction of coarse-grained sites of large biomolecules.

    Science.gov (United States)

    Li, Min; Zhang, John Z H; Xia, Fei

    2016-04-05

    The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.

  16. Systematic methods for defining coarse-grained maps in large biomolecules.

    Science.gov (United States)

    Zhang, Zhiyong

    2015-01-01

    Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.

  17. Coarse-grained simulations of poly(propylene imine) dendrimers in solution

    Science.gov (United States)

    Smeijers, A. F.; Markvoort, A. J.; Pieterse, K.; Hilbers, P. A. J.

    2016-02-01

    The behavior of poly(propylene imine) (PPI) dendrimers in concentrated solutions has been investigated using molecular dynamics simulations containing up to a thousand PPI dendrimers of generation 4 or 5 in explicit water. To deal with large system sizes and time scales required to study the solutions over a wide range of dendrimer concentrations, a previously published coarse-grained model was applied. Simulation results on the radius of gyration, structure factor, intermolecular spacing, dendrimer interpenetration, and water penetration are compared with available experimental data, providing a clear concentration dependent molecular picture of PPI dendrimers. It is shown that with increasing concentration the dendrimer volume diminishes accompanied by a reduction of internalized water, ultimately resulting in solvent filled cavities between stacked dendrimers. Concurrently dendrimer interpenetration increases only slightly, leaving each dendrimer a separate entity also at high concentrations. Moreover, we compare apparent structure factors, as calculated in experimental studies relying on the decoupling approximation and the constant atomic form factor assumption, with directly computed structure factors. We demonstrate that these already diverge at rather low concentrations, not because of small changes in form factor, but rather because the decoupling approximation fails as monomer positions of separate dendrimers become correlated at concentrations well below the overlap concentration.

  18. Coarse-grained Brownian dynamics simulations of protein translocation through nanopores

    Science.gov (United States)

    Lee, Po-Hsien; Helms, Volkhard; Geyer, Tihamér

    2012-10-01

    A crucial process in biological cells is the translocation of newly synthesized proteins across cell membranes via integral membrane protein pores termed translocons. Recent improved techniques now allow producing artificial membranes with pores of similar dimensions of a few nm as the translocon system. For the translocon system, the protein has to be unfolded, whereas the artificial pores are wide enough so that small proteins can pass through even when folded. To study how proteins permeate through such membrane pores, we used coarse-grained Brownian dynamics simulations where the proteins were modeled as single beads or bead-spring polymers for both folded and unfolded states. The pores were modeled as cylindrical holes through the membrane with various radii and lengths. Diffusion was driven by a concentration gradient created across the porous membrane. Our results for both folded and unfolded configurations show the expected reciprocal relation between the flow rate and the pore length in agreement with an analytical solution derived by Brunn et al. [Q. J. Mech. Appl. Math. 37, 311 (1984)], 10.1093/qjmam/37.2.311. Furthermore, we find that the geometric constriction by the narrow pore leads to an accumulation of proteins at the pore entrance, which in turn compensates for the reduced diffusivity of the proteins inside the pore.

  19. Demixing by a Nematic Mean Field: Coarse-Grained Simulations of Liquid Crystalline Polymers

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez-Hernández, Abelardo; Hur, Su-Mi; Armas-Pérez, Julio; Cruz, Monica; de Pablo, Juan

    2017-03-01

    Liquid crystalline polymers exhibit a particular richness of behaviors that stems from their rigidity and their macromolecular nature. On the one hand, the orientational interaction between liquid-crystalline motifs promotes their alignment, thereby leading to the emergence of nematic phases. On the other hand, the large number of configurations associated with polymer chains favors formation of isotropic phases, with chain stiffness becoming the factor that tips the balance. In this work, a soft coarse-grained model is introduced to explore the interplay of chain stiffness, molecular weight and orientational coupling, and their role on the isotropic-nematic transition in homopolymer melts. We also study the structure of polymer mixtures composed of stiff and flexible polymeric molecules. We consider the effects of blend composition, persistence length, molecular weight and orientational coupling strength on the melt structure at the nano-and mesoscopic levels. Conditions are found where the systems separate into two phases, one isotropic and the other nematic. We confirm the existence of non-equilibrium states that exhibit sought-after percolating nematic domains, which are of interest for applications in organic photovoltaic and electronic devices.

  20. A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.

    Science.gov (United States)

    Sinitskiy, Anton V; Voth, Gregory A

    2015-09-07

    Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman's imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionist perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.

  1. Demixing by a Nematic Mean Field: Coarse-Grained Simulations of Liquid Crystalline Polymers

    Directory of Open Access Journals (Sweden)

    Abelardo Ramírez-Hernández

    2017-03-01

    Full Text Available Liquid crystalline polymers exhibit a particular richness of behaviors that stems from their rigidity and their macromolecular nature. On the one hand, the orientational interaction between liquid-crystalline motifs promotes their alignment, thereby leading to the emergence of nematic phases. On the other hand, the large number of configurations associated with polymer chains favors formation of isotropic phases, with chain stiffness becoming the factor that tips the balance. In this work, a soft coarse-grained model is introduced to explore the interplay of chain stiffness, molecular weight and orientational coupling, and their role on the isotropic-nematic transition in homopolymer melts. We also study the structure of polymer mixtures composed of stiff and flexible polymeric molecules. We consider the effects of blend composition, persistence length, molecular weight and orientational coupling strength on the melt structure at the nano- and mesoscopic levels. Conditions are found where the systems separate into two phases, one isotropic and the other nematic. We confirm the existence of non-equilibrium states that exhibit sought-after percolating nematic domains, which are of interest for applications in organic photovoltaic and electronic devices.

  2. Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

    Science.gov (United States)

    Sieradzan, Adam K; Jakubowski, Rafał

    2017-03-30

    In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  3. Multiscale crystal defect dynamics: A coarse-grained lattice defect model based on crystal microstructure

    Science.gov (United States)

    Lyu, Dandan; Li, Shaofan

    2017-10-01

    Crystal defects have microstructure, and this microstructure should be related to the microstructure of the original crystal. Hence each type of crystals may have similar defects due to the same failure mechanism originated from the same microstructure, if they are under the same loading conditions. In this work, we propose a multiscale crystal defect dynamics (MCDD) model that models defects by considering its intrinsic microstructure derived from the microstructure or material genome of the original perfect crystal. The main novelties of present work are: (1) the discrete exterior calculus and algebraic topology theory are used to construct a scale-up (coarse-grained) dual lattice model for crystal defects, which may represent all possible defect modes inside a crystal; (2) a higher order Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed constitutive relations for various defect process zones, and (3) an hierarchical strain gradient theory based finite element formulation is developed to support an hierarchical multiscale cohesive (process) zone model for various defects in a unified formulation. The efficiency of MCDD computational algorithm allows us to simulate dynamic defect evolution at large scale while taking into account atomistic interaction. The MCDD model has been validated by comparing of the results of MCDD simulations with that of molecular dynamics (MD) in the cases of nanoindentation and uniaxial tension. Numerical simulations have shown that MCDD model can predict dislocation nucleation induced instability and inelastic deformation, and thus it may provide an alternative solution to study crystal plasticity.

  4. Coarse-grained potential models for phenyl-based molecules: II. Application to fullerenes.

    Science.gov (United States)

    Chiu, Chi-cheng; DeVane, Russell; Klein, Michael L; Shinoda, Wataru; Moore, Preston B; Nielsen, Steven O

    2010-05-20

    The interaction of fullerenes with biological systems and the environment is a topic of current interest. Coarse-grained molecular dynamics (CGMD) simulations are well-suited to investigate some of the factors involved because they provide access to time and length scales that are not accessible using fully atomistic simulation methods. In the case of buckyballs (C(60)) and single-walled carbon nanotubes (SWNTs), it is necessary to parametrize a CG force field that accurately captures the balance between fullerene-fullerene and fullerene-solvent interactions. Herein, we derive CG force field parameters for C(60) and SWNTs by using the optimized benzene parameters from part I [DeVane, R.; Chiu, C.-c.; Nielsen, S. O.; Shinoda, W.; Moore, P. B.; Klein, M. L. J. Phys. Chem. B 2010, doi: 10.1021/jp9117369]. Solubility, transfer free energy, and dimerization free-energy data for C(60) and SWNTs obtained using the proposed models show excellent agreement with experimental and fully atomistic MD data. In particular, cluster analysis of C(60) aggregation in a hydrocarbon melt corroborates the force field parameters. The aggregation behavior of the present CG force field differs considerably from that of models currently in widespread use. The combined results provide a strong basis for applying this model for further large-scale MD studies involving C(60) and SWNTs.

  5. Coarse-grained molecular simulations of the melting kinetics of small unilamellar vesicles.

    Science.gov (United States)

    Patel, Lara A; Kindt, James T

    2016-02-14

    Simulations of small unilamellar lipid bilayer vesicles have been performed to model their response to an instantaneous rise in temperature, starting from an initial low-temperature structure, to temperatures near or above the main chain transition temperature. The MARTINI coarse-grained force-field was used to construct slabs of gel-phase DPPC bilayers, which were assembled into truncated icosahedral structures containing 13,165 or 31,021 lipids. Equilibration at 280 K produced structures with several (5-8) domains, characterized by facets of lipids packed in the gel phase connected by disordered ridges. Instantaneous heating to final temperatures ranging from 290 K to 310 K led to partial or total melting over 500 ns trajectories, accompanied by changes in vesicle shape and the sizes and arrangements of remaining gel-phase domains. At temperatures that produced partial melting, the gel-phase lipid content of the vesicles followed an exponential decay, similar in form and timescale to the sub-microsecond phase of melting kinetics observed in recent ultrafast IR temperature-jump experiments. The changing rate of melting appears to be the outcome of a number of competing contributions, but changes in curvature stress arising from the expansion of the bilayer area upon melting are a major factor. The simulations give a more detailed picture of the changes that occur in frozen vesicles following a temperature jump, which will be of use for the interpretation of temperature-jump experiments on vesicles.

  6. Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V., E-mail: aneimark@rutgers.edu [Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058 (United States)

    2016-01-07

    Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.

  7. In-medium Spectral Functions in a Coarse-Graining Approach

    Science.gov (United States)

    Endres, Stephan; van Hees, Hendrik; Weil, Janus; Bleicher, Marcus

    2015-04-01

    We use a coarse-graining approach to extract local thermodynamic properties from simulations with a microscopic transport model by averaging over a large ensemble of events. Setting up a grid of small space-time cells and going into each cell's rest frame allows to determine baryon and energy density. With help of an equation of state we get the corresponding temperature T and baryon-chemical potential μB. These results are used for the calculation of the thermal dilepton yield. We apply and compare two different spectral functions for the ρ meson, firstly a calculation from hadronic many-body theory and secondly a calculation from experimental scattering amplitudes. The results obtained with our approach are compared to measurements of the NA60 Collaboration. A relatively good description of the data is achieved with both spectral functions. However, the hadronic many-body calculation is found to be closer to the experimental data with regard to the in-medium broadening of the spectral shape.

  8. SmartCell: An Energy Efficient Coarse-Grained Reconfigurable Architecture for Stream-Based Applications

    Directory of Open Access Journals (Sweden)

    Liang Cao

    2009-01-01

    Full Text Available This paper presents SmartCell, a novel coarse-grained reconfigurable architecture, which tiles a large number of processor elements with reconfigurable interconnection fabrics on a single chip. SmartCell is able to provide high performance and energy efficient processing for stream-based applications. It can be configured to operate in various modes, such as SIMD, MIMD, and systolic array. This paper describes the SmartCell architecture design, including processing element, reconfigurable interconnection fabrics, instruction and control process, and configuration scheme. The SmartCell prototype with 64 PEs is implemented using 0.13  m CMOS standard cell technology. The core area is about 8.5  , and the power consumption is about 1.6 mW/MHz. The performance is evaluated through a set of benchmark applications, and then compared with FPGA, ASIC, and two well-known reconfigurable architectures including RaPiD and Montium. The results show that the SmartCell can bridge the performance and flexibility gap between ASIC and FPGA. It is also about 8% and 69% more energy efficient than Montium and RaPiD systems for evaluated benchmarks. Meanwhile, SmartCell can achieve 4 and 2 times more throughput gains when comparing with Montium and RaPiD, respectively. It is concluded that SmartCell system is a promising reconfigurable and energy efficient architecture for stream processing.

  9. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  10. Space Debris Detection on the HPDP, a Coarse-Grained Reconfigurable Array Architecture for Space

    Science.gov (United States)

    Suarez, Diego Andres; Bretz, Daniel; Helfers, Tim; Weidendorfer, Josef; Utzmann, Jens

    2016-08-01

    Stream processing, widely used in communications and digital signal processing applications, requires high- throughput data processing that is achieved in most cases using Application-Specific Integrated Circuit (ASIC) designs. Lack of programmability is an issue especially in space applications, which use on-board components with long life-cycles requiring applications updates. To this end, the High Performance Data Processor (HPDP) architecture integrates an array of coarse-grained reconfigurable elements to provide both flexible and efficient computational power suitable for stream-based data processing applications in space. In this work the capabilities of the HPDP architecture are demonstrated with the implementation of a real-time image processing algorithm for space debris detection in a space-based space surveillance system. The implementation challenges and alternatives are described making trade-offs to improve performance at the expense of negligible degradation of detection accuracy. The proposed implementation uses over 99% of the available computational resources. Performance estimations based on simulations show that the HPDP can amply match the application requirements.

  11. A multi-state coarse grained modeling approach for an intrinsically disordered peptide

    Science.gov (United States)

    Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

    2017-09-01

    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

  12. Characterization of unique small RNA populations from rice grain.

    Directory of Open Access Journals (Sweden)

    Sara E Heisel

    Full Text Available Small RNAs (approximately 20 to 24 nucleotides function as naturally occurring molecules critical in developmental pathways in plants and animals. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing. Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the genome. Hotspots here are defined as 1 kb regions within which small RNAs are significantly overproduced relative to the rest of the genome. Hotspots were identified to facilitate characterization of different categories of small RNA regulatory elements. Included in the hotspots, we found known members of 23 miRNA families representing 92 genes, one trans acting siRNA (ta-siRNA gene, novel siRNA-generating coding genes and phased siRNA generating genes. Interestingly, over 20% of the small RNA population in grain came from a single foldback structure, which generated eight phased 21-nt siRNAs. This is reminiscent of a newly arising miRNA derived from duplication of progenitor genes. Our results provide data identifying distinct populations of small RNAs, including phased small RNAs, in mature grain to facilitate characterization of small regulatory RNA expression in monocot species.

  13. cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.

    Science.gov (United States)

    Faustino, Ignacio; Marrink, S J

    2017-12-01

    We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models. This package works with Python 2.7 on MacOS and Linux. The program is freely available for download from https://github.com/ifaust83/cgheliparm. Together with the main script, the base reference files CG_X_std.lib, a number of examples and R scripts are also available from the same website. A tutorial on the use and application is also available at http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna. i.faustino@rug.nl. Supplementary data are available at Bioinformatics online.

  14. Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors

    Science.gov (United States)

    Li, Dechang; Liu, Ming S.; Ji, Baohua; Hwang, Kehchih; Huang, Yonggang

    2009-06-01

    Binding dynamics and pathways of ligands or inhibitors to target proteins are challenging both experimental and theoretical biologists. A dynamics understanding of inhibitors interacting with protein is essential for the design of novel potent drugs. In this work we applied a coarse-grained molecular dynamics method for simulating inhibitors entering the binding cavity of human immunodeficiency virus type 1 protease (PR). It shows that the coarse-grained dynamics, consistent with the experimental results, can capture the essential molecular dynamics of various inhibitors binding into PR. The primary driving force for the binding processes is the nonbond interaction between inhibitors and PR. The size and topology of inhibitors and the interacting strength between inhibitors and PR have great influence on the binding mode and processes. The interaction strength between the PR and various inhibitors is also analyzed by atomistic molecular mechanics and Poisson-Boltzmann solvation area method.

  15. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  16. Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

    Science.gov (United States)

    Flechsig, Holger

    2016-02-01

    ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

  17. Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Galo E. Balatti

    2017-10-01

    Full Text Available In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a peptides in water in the presence of a pre-equilibrated lipid bilayer; (b peptides inside the hydrophobic core of the membrane; and (c random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.

  18. Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling.

    Directory of Open Access Journals (Sweden)

    James T Macdonald

    Full Text Available Coarse-grained (CG methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using [Formula: see text]-carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific [Formula: see text]/[Formula: see text]-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational

  19. Fine-Grained, Local Maps and Coarse, Global Representations Support Human Spatial Working Memory

    Science.gov (United States)

    Katshu, Mohammad Zia Ul Haq; d'Avossa, Giovanni

    2014-01-01

    While sensory processes are tuned to particular features, such as an object's specific location, color or orientation, visual working memory (vWM) is assumed to store information using representations, which generalize over a feature dimension. Additionally, current vWM models presume that different features or objects are stored independently. On the other hand, configurational effects, when observed, are supposed to mainly reflect encoding strategies. We show that the location of the target, relative to the display center and boundaries, and overall memory load influenced recall precision, indicating that, like sensory processes, capacity limited vWM resources are spatially tuned. When recalling one of three memory items the target distance from the display center was overestimated, similar to the error when only one item was memorized, but its distance from the memory items' average position was underestimated, showing that not only individual memory items' position, but also the global configuration of the memory array may be stored. Finally, presenting the non-target items at recall, consequently providing landmarks and configurational information, improved precision and accuracy of target recall. Similarly, when the non-target items were translated at recall, relative to their position in the initial display, a parallel displacement of the recalled target was observed. These findings suggest that fine-grained spatial information in vWM is represented in local maps whose resolution varies with distance from landmarks, such as the display center, while coarse representations are used to store the memory array configuration. Both these representations are updated at the time of recall. PMID:25259601

  20. From Cooperative Self-Assembly to Water-Soluble Supramolecular Polymers Using Coarse-Grained Simulations.

    Science.gov (United States)

    Bochicchio, Davide; Pavan, Giovanni M

    2017-01-24

    Supramolecular polymers, formed via noncovalent self-assembly of elementary monomers, are extremely interesting for their dynamic bioinspired properties. In order to understand their behavior, it is necessary to access their dynamics while maintaining high resolution in the treatment of the monomer structure and monomer-monomer interactions, which is typically a difficult task, especially in aqueous solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble supramolecular polymers, we have developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers (hydrophobic, H-bonding, etc.), self-assembly cooperativity, and amplification of order into the growing fibers. This permitted us to monitor the amplification of the key interactions between the monomers (including H-bonding) in the BTA fibers during the dynamic polymerization process. Our molecular dynamics simulations provide a picture of a stepwise cooperative polymerization mechanism, where initial fast hydrophobic aggregation of the BTA monomers in water is followed by the slower reorganization of these disordered aggregates into ordered directional oligomers. Supramolecular polymer growth then proceeds on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect of temperature variations and subtle changes in the monomer structure on the polymerization and on the properties of the fibers seen in the real systems. This work provides a multiscale spatiotemporal characterization of BTA self-assembly in water and a useful platform to study a variety of BTA-based supramolecular polymers toward structure-property relationships.

  1. Pattern formation and coarse-graining in two-dimensional colloids driven by multiaxial magnetic fields.

    Science.gov (United States)

    Müller, Kathrin; Osterman, Natan; Babič, Dušan; Likos, Christos N; Dobnikar, Jure; Nikoubashman, Arash

    2014-05-13

    We study the pattern formation in a two-dimensional system of superparamagnetic colloids interacting via spatially coherent induced interactions driven by an external precessing magnetic field. On the pair level, upon changing the opening angle of the external field, the interactions smoothly vary from purely repulsive (opening angle equal to zero) to purely attractive (time-averaged pair interactions at an opening angle of 90°). In the experiments, we observed ordered hexagonal crystals at the repulsive end and coarsening frothlike structures for purely attractive interactions. In both of these limiting cases, the dense colloidal systems can be sufficiently accurately described by assuming pairwise additivity of the interaction potentials. However, for a range of intermediate angles, pronounced many-body depolarization effects compete with the direct induced interactions, resulting in inherently anisotropic effective interactions. Under such conditions, we observed the decay of hexagonal order with the concomitant formation of short chains and percolated networks of chains coexisting with free colloids. In order to describe and investigate these systems theoretically, we developed a coarse-grained model of a binary mixture of patchy and nonpatchy particles with the ratio of patchy and nonpatchy colloids as the order parameter. Combining genetic algorithms with Monte Carlo simulations, we optimized the model parameters and quantitatively reproduced the experimentally observed sequence of colloidal structures. The results offer new insight into the anisotropy induced by the many-body effects. At the same time, they allow for a very efficient description of the system by means of a pairwise-additive Hamiltonian, whereupon the original, one-component system features a two-component mixture of isotropic and patchy colloids.

  2. A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution.

    Science.gov (United States)

    Shelley, Mee Y; Selvan, Myvizhi Esai; Zhao, Jun; Babin, Volodymyr; Liao, Chenyi; Li, Jianing; Shelley, John C

    2017-08-08

    We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG), for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented, while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions. These characteristics fit well with the requirements for studying peptide association and aggregation, where the system sizes and time scales require considerable computational resources with all-atom models. In particular, AACG is well suited for biologics since changes in peptide shape and long-range electrostatics may play an important role. The application of AACG to melittin, a 26-residue peptide with a well-known propensity to aggregate in solution, serves as an initial demonstration of this technology for studying peptide aggregation. We observed the formation of melittin aggregates during our simulations and characterized the time-evolution of aggregate size distribution, buried surface areas, and residue contacts. Key interactions including π-cation and π-stacking involving TRP19 were also examined. Our AACG simulations demonstrated a clear salt effect and a moderate temperature effect on aggregation and support the molten globule model of melittin aggregates. As a showcase, this work illustrates the useful role for AACG in investigations of peptide aggregation and its potential to guide formulation and design of biologics.

  3. A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences.

    Science.gov (United States)

    Ruff, Kiersten M; Khan, Siddique J; Pappu, Rohit V

    2014-09-02

    The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington's disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. HIGH-FIDELITY SIMULATION-DRIVEN MODEL DEVELOPMENT FOR COARSE-GRAINED COMPUTATIONAL FLUID DYNAMICS

    Energy Technology Data Exchange (ETDEWEB)

    Hanna, Botros N.; Dinh, Nam T.; Bolotnov, Igor A.

    2016-06-01

    Nuclear reactor safety analysis requires identifying various credible accident scenarios and determining their consequences. For a full-scale nuclear power plant system behavior, it is impossible to obtain sufficient experimental data for a broad range of risk-significant accident scenarios. In single-phase flow convective problems, Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) can provide us with high fidelity results when physical data are unavailable. However, these methods are computationally expensive and cannot be afforded for simulation of long transient scenarios in nuclear accidents despite extraordinary advances in high performance scientific computing over the past decades. The major issue is the inability to make the transient computation parallel, thus making number of time steps required in high-fidelity methods unaffordable for long transients. In this work, we propose to apply a high fidelity simulation-driven approach to model sub-grid scale (SGS) effect in Coarse Grained Computational Fluid Dynamics CG-CFD. This approach aims to develop a statistical surrogate model instead of the deterministic SGS model. We chose to start with a turbulent natural convection case with volumetric heating in a horizontal fluid layer with a rigid, insulated lower boundary and isothermal (cold) upper boundary. This scenario of unstable stratification is relevant to turbulent natural convection in a molten corium pool during a severe nuclear reactor accident, as well as in containment mixing and passive cooling. The presented approach demonstrates how to create a correction for the CG-CFD solution by modifying the energy balance equation. A global correction for the temperature equation proves to achieve a significant improvement to the prediction of steady state temperature distribution through the fluid layer.

  5. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

    Science.gov (United States)

    Hu, Jie; Chen, Tao; Wang, Moye; Chan, Hue Sun; Zhang, Zhuqing

    2017-05-31

    Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.

  6. Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models.

    Science.gov (United States)

    Lemke, Tobias; Peter, Christine

    2017-12-12

    Coarse-grained (CG) simulation models have become very popular tools to study complex molecular systems with great computational efficiency on length and time scales that are inaccessible to simulations at atomistic resolution. In so-called bottom-up coarse-graining strategies, the interactions in the CG model are devised such that an accurate representation of an atomistic sampling of configurational phase space is achieved. This means the coarse-graining methods use the underlying multibody potential of mean force (i.e., free-energy surface) derived from the atomistic simulation as parametrization target. Here, we present a new method where a neural network (NN) is used to extract high-dimensional free energy surfaces (FES) from molecular dynamics (MD) simulation trajectories. These FES are used for simulations on a CG level of resolution. The method is applied to simulating homo-oligo-peptides (oligo-glutamic-acid (oligo-glu) and oligo-aspartic-acid (oligo-asp)) of different lengths. We show that the NN not only is able to correctly describe the free-energy surface for oligomer lengths that it was trained on but also is able to predict the conformational sampling of longer chains.

  7. Development of a Coarse-Grained Model of Collagen-Like Peptide (CLP) for Studies of CLP Triple Helix Melting.

    Science.gov (United States)

    Condon, Joshua E; Jayaraman, Arthi

    2018-02-15

    In this paper, we present the development of a phenomenological coarse-grained model that represents single strands of collagen-like peptides (CLPs) as well as CLP triple helices. The goal of this model development is to enable coarse-grained molecular simulations of solutions of CLPs and conjugates of CLPs with other macromolecules and to predict trends in the CLP melting temperature with varying CLP design, namely CLP length and composition. Since the CLP triple helix is stabilized primarily by hydrogen bonds between amino acids in adjacent strands, for modeling CLP melting we get inspiration from a recent coarse-grained (CG) model that was used to capture specific and directional hydrogen-bonding interactions in base-pair hybridization within oligonucleotides and reproduced known DNA melting trends with DNA sequence and composition in implicit water. In this paper, we systematically describe the changes we make to this original CG model and then show that these improvements reproduce the known melting trends of CLPs seen in past experiments. Specifically, the CG simulations of CLP solutions at experimentally relevant concentrations show increasing melting temperature with increasing CLP length and decreasing melting temperature with incorporation of charged residues in place of uncharged residues in the CLP, in agreement with past experimental observations. Finally, results from simulations of CLP triple helices conjugated with elastin like peptides (ELPs), using this new CG model of CLP, reproduce the same trends in ELP aggregation as seen in past experiments.

  8. A comparison study on stages of sleep: Quantifying multiscale complexity using higher moments on coarse-graining

    Science.gov (United States)

    Shi, Wenbin; Shang, Pengjian; Ma, Yan; Sun, Shuchen; Yeh, Chien-Hung

    2017-03-01

    It is of great interests in identifying dynamical properties of human sleep signals using electroencephalographic (EEG) measures. Multiscale entropy (MSE) is effective in quantifying the degree of unpredictability of time series in different time scales. To understand the superior coarse-graining approach for the EEG analysis, we therefor use different moments to coarse-grain a time series, and examine their volatility as well as the effectiveness in quantifying the complexities of sleep EEG in different sleep stages. Both the simulated signals (logistic map) and the EEGs with different sleep stages are calculated and compared using three types of coarse-graining procedure: including MSEμ (mean), MSEσ2 (variance) and MSEskew (skewness). The simulated results show that the generalized MSE (including MSEσ2 and MSEskew) can identify the differences in chaotic more easily with less fluctuation of entropy values in different time scales. As for the analysis of human sleep EEG, we find: (1) at small scales (sleep and lower with increasing time scales.

  9. Towards a thorough use of the Mori-Zwanzig formalism for statistical coarse-graining of turbulent flows

    Science.gov (United States)

    Gouasmi, Ayoub; Parish, Eric; Duraisamy, Karthik; Computational Aerosciences Laboratory Team

    2016-11-01

    The Mori-Zwanzig formalism provides a mathematically-consistent framework to represent the unresolved physics in coarse-grained simulations. The closure terms that arise can be formally represented as memory or non-Markovian effects. However, the general procedure to compute these memory effects is not tractable in fluid flow problems. Accordingly, existing Mori-Zwanzig closure models only scratch the surface of the framework: they simplify the memory effect by making assumptions that cannot be numerically assessed. We propose a more tractable procedure to approximate memory effects with a good level of accuracy. This approach is demonstrated on the Viscous Burgers Equation and the Kuramoto-Sivanshinsky Equation. Building on these results, we provide perspectives in the development of Mori-Zwanzig-based coarse-grained models for turbulent flows. This work was supported in part by AFOSR under the project "LES Modeling of Non-local effects using Statistical Coarse-graining" with Dr. Jean-Luc Cambier as the technical monitor.

  10. Crystallographic Analysis of Fatigue Crack Initiation Behavior in Coarse-Grained Magnesium Alloy Under Tension-Tension Loading Cycles

    Science.gov (United States)

    Tamada, Kazuhiro; Kakiuchi, Toshifumi; Uematsu, Yoshihiko

    2017-07-01

    Plane bending fatigue tests are conducted to investigate fatigue crack initiation mechanisms in coarse-grained magnesium alloy, AZ31, under the stress ratios R = -1 and 0.1. The initial crystallographic structures are analyzed by an electron backscatter diffraction method. The slip or twin operation during fatigue tests is identified from the line angle analyses based on Euler angles of the grains. Under the stress ratio R = -1, relatively thick tension twin bands are formed in coarse grains. Subsequently, compression twin or secondary pyramidal slip operates within the tension twin band, resulting in the fatigue crack initiation. On the other hand, under R = 0.1 with tension-tension loading cycles, twin bands are formed on the specimen surface, but the angles of those bands do not correspond to tension twins. Misorientation analyses of c-axes in the matrix grain and twin band reveal that double twins are activated. Under R = 0.1, fatigue crack initiates along the double twin boundaries. The different manners of fatigue crack initiation at R = -1 and 0.1 are related to the asymmetricity of twining under tension and compression loadings. The fatigue strengths under different stress ratios cannot be estimated by the modified Goodman diagram due to the effect of stress ratio on crack initiation mechanisms.

  11. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    Science.gov (United States)

    Garrido, J. M.; Algaba, J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.; Blas, F. J.

    2016-04-01

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  12. Derivation of free energy expressions for tube models from coarse-grained slip-link models.

    Science.gov (United States)

    Steenbakkers, Rudi J A; Schieber, Jay D

    2012-07-21

    We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)] by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)] can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)] starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)]. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)]. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical formulation of tube models. The next step will be to formulate the dynamics of the primitive

  13. Transferability of coarse-grained force field for nCB liquid crystal systems.

    Science.gov (United States)

    Zhang, Jianguo; Guo, Hongxia

    2014-05-01

    In this paper, the transferability of the coarse-grained (CG) force field originally developed for the liquid crystal (LC) molecule 5CB ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 2075 - 2089 ) was investigated by its homologues 6CB and 8CB molecules. Note that, to construct the 5CB CG force field, we combined the structure-based and thermodynamic quantities-based methods and at the same time attempted to use several fragment molecular systems to derive the CG nonbonded interaction parameters. The resultant 5CB CG force field exhibits a good transferability to some extent. For example, not only the experimental densities, the local packing of atom groups, and the antiparallel arrangements of nearest neighboring molecules, but also the unique LC mesophases as well as the nematic-isotropic phase transition temperatures of 6CB and 8CB were reproduced. Meanwhile, the limitations of this 5CB CG force field were also observed, such as the phase transition from nematic to smectic was postponed to the lower temperature and the resulting smectic phase structure is single-layer-like instead of partially interdigitated bilayer-like as observed in underlying atomistic model. Apparently, more attention should be paid when applying a CG force field to the state point which is quite different from which the force field is explicitly parametrized for. The origin of the above limitations can be potentially traced back to the inherent simplifications and some approximations often adopted in the creation process of CG force field, for example, choosing symmetric CG potentials which do not explicitly include electrostatic interactions and are parametrized by reproducing the target properties of the specific nematic 5CB phase at 300 K and 1 atm, as well as using soft nonbonded potential and excluding torsion barriers. Moreover, although by construction this CG force field could inevitably incorporate both thermodynamic and local structural information on the nematic 5CB phase, the

  14. Concurrent Multiscale Simulation at Finite Temperature: Coarse-Grained Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, R E

    2004-01-22

    With the advent of nanotechnology, predictive simulations of nanoscale systems have become in great demand. In some cases nanoscale systems can be simulated directly at the level of atoms. The atomistic techniques used range from models based on a quantum mechanical treatment of the electronic bonds to those based on more empirical descriptions of the interatomic forces. In many cases, however, even nanoscale systems are too big for a purely atomistic approach, typically because the nanoscale device is coupled to its surroundings, and it is necessary to simulate the entire system comprising billions of atoms. A well-known example is the growth of nanoscale epitaxial quantum dots in which the size, shape and location of the dot is affected by the elastic strain developed in a large volume of the substrate as well as the local atomic bonding. The natural solution is to model the surroundings with a more coarse-grained description, suitable for the intrinsically longer length scale. The challenge then is to develop the computational methodology suitable for this kind of concurrent multiscale modeling, one in which the simulated length scale can be changed smoothly and seamlessly from one region of the simulation to another while maintaining the fidelity of the relevant mechanics, dynamics and thermodynamics. The realization that Nature has different relevant length scales goes back at least as far as Democritus. Some 24 centuries ago he put forward the idea that solid matter is comprised ultimately at small scales by a fundamental constituent that he termed an atom. Implicit in his philosophy was the idea that an understanding of the atom would lead to a more robust understanding of the macroscopic world around us. In the intervening period, of course, not only has the science of this atomistic picture been put on a sound footing through the inventions of chemistry, the discovery of the nucleus and the development of quantum mechanics and modern condensed matter

  15. Thinning Approximation for Two-Dimensional Scattering Patterns from Coarse-Grained Polymer Melts under Shear Flow

    Science.gov (United States)

    Hagita, Katsumi; Murashima, Takahiro; Takano, Hiroshi; Kawakatsu, Toshihiro

    2017-12-01

    We proposed a thinning approximation (TA) for estimation of the two-dimensional (2D) wide-angle scattering patterns from Kremer-Grest polymer melts under shear. In the TA, extra particles are inserted at the middle of bonds for fine-graining of the coarse-grained polymers. For the case without the TA, spots corresponding to the orientation of bonds at a high shear rate are difficult to observe because the bond length of successive particles is comparable to the distance between neighboring particles. With the insertion of the extra particles, a ring pattern originating from the neighboring particles can be moved to a wide-angle region. Thus, we can observe the spots at high shear rates. We also examined the relationship between 2D scattering patterns and the Weissenberg number, which is defined as the product of the shear rate and the longest relaxation time. It is confirmed that the relationship for coarse-grained polymers with the TA is consistent with that of the all-atomistic model of polyethylene.

  16. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    Science.gov (United States)

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. © 2014 Wiley Periodicals, Inc.

  17. Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

    Science.gov (United States)

    de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás

    2017-12-01

    The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of

  18. A coarse-grained analysis of the functional brain connectivity from EEG recordings of a visuo-perceptual discrimination task

    Science.gov (United States)

    Protopapa, Foteini; Mylonas, Dimitris; Smyrnis, Nikolaos; Siettos, Constantinos

    2013-10-01

    We report the emergent functional connectivity of cortical areas during a visuo-perceptual discrimination task with or without the retention in memory of the location of visual targets using EEG. The networks were computed using multivariate Granger causality on groups of electrodes reflecting coarse-grained brain areas. The analysis showed that at alpha band (8-12Hz) there are no significant differences. In contrast, in beta and gamma band, we identified a top-down information flow pattern which was evident for the task that required the activation of the working memory mechanism.

  19. Cyclic steps and superimposed antidune deposits: important elements of coarse-grained deepwater channel-levée complexes

    Science.gov (United States)

    Lang, Joerg; Brandes, Christian; Winsemann, Jutta

    2017-04-01

    The facies distribution and architecture of submarine fans can be strongly impacted by erosion and deposition by supercritical density flows. We present field examples from the Sandino Forearc Basin (southern Central America), where cyclic-step and antidune deposits represent important sedimentary facies of coarse-grained channel-levée complexes. These bedforms occur in all sub-environments of the depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. Large-scale scours (18 to 29 m deep, 18 to 25 m wide, 60 to >120 m long) with an amalgamated infill, comprising massive, normally coarse-tail graded or spaced subhorizontally stratified conglomerates and pebbly sandstones, are interpreted as deposits of the hydraulic-jump zone of cyclic steps. These cyclic steps probably formed during avulsion, when high-density flows were routed into the evolving channel. The large-scale scour fills can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump deposits. Channel fills include repetitive successions deposited by cyclic steps with superimposed antidunes. The hydraulic-jump zone of cyclic-step deposits comprises regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m wide), which are infilled by intraclast-rich conglomerates or pebbly sandstones and display normal coarse-tail grading or backsets. Laterally and vertically these deposits are associated with subhorizontally stratified, low-angle cross-stratified or sinusoidal stratified pebbly sandstones and sandstones (wavelength 0.5 to 18 m), interpreted as representing antidune deposits formed on the stoss-side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called crudely or spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation

  20. raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

    Science.gov (United States)

    Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

    2017-03-01

    We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

  1. Fast Calculation of Protein-Protein Binding Free Energies using Umbrella Sampling with a Coarse-Grained Model.

    Science.gov (United States)

    Patel, Jagdish Suresh; Ytreberg, F Marty

    2017-12-29

    Determination of protein-protein binding affinity values is key to understanding various underlying biological phenomena, such as how mutations change protein-protein binding. Most existing non-rigorous (fast) and rigorous (slow) methods that rely on all-atom representation of the proteins force the user to choose between speed and accuracy. In an attempt to achieve balance between speed and accuracy, we have combined rigorous umbrella sampling molecular dynamics simulation with a coarse-grained protein model. We predicted the effect of mutations on binding affinity by selecting three protein-protein systems and comparing results to empirical relative binding affinity values, and to non-rigorous modeling approaches. We obtained significant improvement both in our ability to discern stabilizing from destabilizing mutations and in the correlation between predicted and experimental values compared to non-rigorous approaches. Overall our results suggest that using a rigorous affinity calculation method with coarse-grained protein models could offer fast and reliable predictions of protein-protein binding free energies.

  2. Relationship Between Bake Hardening, Snoek-Köster and Dislocation-Enhanced Snoek Peaks in Coarse Grained Low Carbon Steel

    Directory of Open Access Journals (Sweden)

    Li Weijuan

    2016-09-01

    Full Text Available In the present work, specimens prepared from coarse grained low carbon steel with different prestrains were baked and then, their bake hardening (BH property and internal friction were determined. TEM was used to characterize the dislocation structure in BH treated samples. The measurements of internal friction in prestrained samples and baked samples were carried out using a multifunctional internal friction apparatus. The results indicate that, in coarse grained low carbon steel, the bake hardening properties (BH values were negative, which were increased by increasing the prestrain from 2 to 5%, and then were decreased by increasing the prestrain from 5 to 10%. In the specimen with prestrain 5%, the BH value reached the maximum value and the height of Snoek-Köster peak was observed to be the maximum alike. With increasing the prestrain, both of the BH value and Snoek-Köster peak heights are similarly varied. It is concluded that Snoek-Köster and dislocation-enhanced Snoek peaks, caused by the interactions between interstitial solute carbon atoms and dislocations, can be used in further development of the bake hardening steels.

  3. Coarse and nano emulsions for effective delivery of natural pest control agent pulegone for stored grain protection.

    Science.gov (United States)

    Golden, Gilad; Quinn, Elazar; Shaaya, Eli; Kostyukovsky, Moshe; Poverenov, Elena

    2017-11-09

    One of the most significant contributors to the global food crisis is grain loss during storage mainly caused by pest insects. Currently, there are two main methods used for insect pest control: fumigation and grain protection by contact insecticides. Since some chemical insecticides can harm humans and environment, there is a global tendency to reduce their use by finding alternative eco-friendly approaches. In this paper, a natural pest-managing agent pulegone was encapsulated into coarse and nano emulsions. The emulsions were characterized by spectroscopic and microscopic methods and their stability and pulegone release ability were examined. The insecticidal activity of the prepared formulations against two stored product insects, rice weevil (Sitophilus oryzae L.) and red flour beetle (Tribolium castaneum Herbst) was demonstrated. The nano emulsion-based formulation offered significant advantages and provided powerful bioactivity, with high (> 90%) mortality rates for as long as 5 weeks for both insects, in comparison with coarse emulsions showing high efficacy for only one week. The developed pulegone-based nano emulsions could serve as a model for an effective alternative method for pest control. Though being of a natural source, toxicological studies should be done before the widespread application of pulegone or pulegone-containing essential oils on dry food products. This article is protected by copyright. All rights reserved.

  4. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    Science.gov (United States)

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-08

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.

  5. Metallurgical characteristics and failure mode transition for dissimilar resistance spot welds between ultra-fine grained and coarse-grained low carbon steel sheets

    Energy Technology Data Exchange (ETDEWEB)

    Khodabakhshi, F.; Kazeminezhad, M., E-mail: mkazemi@sharif.edu; Kokabi, A.H.

    2015-06-18

    We studied the microstructure and mechanical characteristics of spot welded specimens, fabricated from low carbon steel sheets with different microstructures. Both ultra-fine grained (UFG) steel sheet and coarse grained (CG) steel sheet were used. The refined microstructure of the UFG steel has been produced by severe plastic deformation (SPD) using the constrained groove pressing (CGP) method. The grain size of the base metals was approximately 260 nm and 30 µm in diameter, respectively, in the UFG and CG steels. Examining the microstructure of a cross section cut through the spot weld reveals a similar grain size and phase distribution in the nugget on both the sides of the initial interface between sheets. Some recrystallization is observed in the heat affected zone on the UFG side as previously reported after the welding of symmetrical UFG–UFG spot welded specimens. The same energy deposit produces larger nuggets after the spot welding of UFG steels. Moreover, the hardness distribution across the nugget changes after welding on both sides of the initial (UFG/CG) interface. This effect is presently attributed to a change in the solidification, cooling rate and tempering after welding, likely because the higher resistance of UFG steel sheets increases the heat release by the Joule effect during spot welding. These changes in the mechanical behavior modify the transition between the interfacial failure (IF) and pull out failure (PF) mode with respect to energy deposit.

  6. Coarse-Grained Tsunami Deposits in the Canary Islands: Evidence of the Tsunamigenic Potential of Volcanic Flank Failures

    Science.gov (United States)

    Austin-Giddings, W. D.; Tappin, D. R.; McGuire, W. J.

    2008-12-01

    Coarse-grained, polymict deposits draping hillslopes at high elevations on ocean island volcanoes have been variously interpreted as sourced from sea-level high-stands and tsunamis, their origin is thus controversial. Here, we present a detailed facies analysis of coarse-grained, fossiliferous sediments located at Agaete, on the north-west coast of Gran Canaria. Previously interpreted as the result of a sea-level high-stand, these deposits have recently been re-interpreted as sourced from a tsunami resulting from a volcano flank collapse. The tsunami deposit occurs at several locations in the Agaete valley, up to 188 m a.s.l. and two kilometres inland from the coast. The sediments comprise two reverse graded units, separated by a soil horizon with calcrete. The units are up to 2 m in thickness and contain a diverse assemblage of volcanic clasts, large beachrock boulders and a marine fauna that includes planktic, shallow and deep-water benthic foraminifera. The base of the lower unit is erosional and truncates plant roots and contains large soil clasts up to 1.5m in diameter. The upper unit is finer grained and is more extensive. At one location the lower unit comprises prograding beds that are interpreted as alluvial. The alternative 'high-stand' interpretation of the coarse-grained deposit is here discounted because of the absence of supporting geomorphological features such as a marine terrace and/or a wave cut platform, the composition of the sediments and their altitude. A tsunami origin is therefore proposed. Gran Canaria is in its post-shield erosional stage of development and has experienced limited vertical uplift of ~40-50 m over the past 1.75 Ma. Thus uplift cannot account for the occurrence of the sediments at elevations of 188 m a.s.l. The Güimar lateral collapse on the neighbouring island of Tenerife (~800ka) has been cited as a possible source. U/Pb dating of the deposits is currently being undertaken.

  7. Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

    Energy Technology Data Exchange (ETDEWEB)

    Cipcigan, Flaviu S., E-mail: flaviu.cipcigan@ed.ac.uk [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Sokhan, Vlad P. [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Crain, Jason [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Martyna, Glenn J. [IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 (United States)

    2016-12-01

    One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a

  8. Loss of ductility due to the decarburation and Mn depletion of a coarse-grained TWIP steel

    Directory of Open Access Journals (Sweden)

    Fernando de las Cuevas

    2017-12-01

    Full Text Available A clear transition in the tensile ductility behavior has been observed for grain sizes D in the range of 15 μm - 20 μm (1.50 μm ≤ D < 50 μm in a 22% Mn, 0.6% C (in mass % TWIP steel. This behavior is a combination of the intrinsic effect of grain size D on strength and work hardening rate of the material, with an extrinsic effect, superficial decarburization and Mn depletion processes occurred during annealing treatments at T ≥ 1000 ºC. In the present work, this extrinsic effect happened in TWIP steel has been studied in depth. GDOES (Glow Discharge Optical Emission Spectrometry analyses have been carried out in order to study quantitatively the C and Mn concentration profiles. The depth of surface decarburization has been modeled by using Birks-Jackson theory. Two micro-constituents have been observed via Ferritoscope into decarburized volume: α’-martensite and α-austenite. The ductility of coarse-grained TWIP steel, subjected for high annealing temperatures and long annealing times, declines as a consequence of the formation of α’-martensite and less stable α-austenite with lower stacking fault energy, SFE, due to the Mn depletion in the decarburized volume.

  9. Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme.

    Directory of Open Access Journals (Sweden)

    Xiaoxu Li

    Full Text Available In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD force field is developed for phospholipids. The coarse-grained (CG models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop.

  10. Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, Ras; Farmer, Barry

    Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

  11. Four-dimensional quantitative analysis of the gait of mutant mice using coarse-grained motion capture.

    Science.gov (United States)

    Oota, S; Mekada, K; Fujita, Y; Humphries, J; Fukami-Kobayashi, K; Obata, Y; Rowe, T; Yoshiki, A

    2009-01-01

    To analyze an abnormal gait pattern in mutant mice (Hugger), we conducted coarse-grained motion capture. Using a simple retroreflective marker-based approach, we could detect high-resolution mutant-specific gait patterns. The phenotypic gait patterns are caused by extreme vertical motion of limbs, revealing inefficient motor functions. To elucidate the inefficiency, we developed a musculoskeletal computer model of the mouse hindlimb based on X-ray CT data. By integrating motion data with the model, we determined mutant-specific musculotendon lengths, suggesting that three major muscles were involved in the abnormal gait. This approach worked well on laboratory mice, which were putatively too small to be motion capture subjects. Motion capture technology was originally developed for human study, and our approach may help fill neuroscience gaps between mouse and human behavioral phenotypes.

  12. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

    Science.gov (United States)

    Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

    2015-02-10

    Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

  13. Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

    Science.gov (United States)

    Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

    2012-04-01

    Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

  14. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...... in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable...... to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A...

  15. The Effects of Hydration on Protein of Azurin using Coarse-Grained Method and The Free-Energy Analysis

    Science.gov (United States)

    Fitrasari, Dian; Purqon, Acep

    2017-07-01

    Proteins play important roles in body metabolism. However, to reveal hydration effects, it is cost computing especially for all-atom calculation. Coarse-grained method is one of potential solution to reduce the calculation and computable in longer timescale. Furthermore, the protein of Azurin is interesting protein and potentially applicable to cancer medicine for the stability property reason. We investigate the effects of hydration on Azurin, the conformation and the stabilities. Furthermore, we analyze the free-energy of the conformation system to find the favorable structure using free energy perturbation (FEP) calculation. Our calculation results show that free energy value of azurin is -136.9 kJ/mol. It shows a good agreement with experimental results with relative error index remained at 0.07%.

  16. The Effect of Cold Plastic Straining of Submicrocrystalline and Coarse-Grained Titanium on the Temperature Behavior of Flow Stress in the Stage of Microplastic Deformation

    Science.gov (United States)

    Dudarev, E. F.; Pochivalova, G. P.; Kolobov, Yu. R.; Bakach, G. P.; Skosyrskii, A. B.; Zhorovkov, M. F.; Goraynov, А. А.

    2013-10-01

    The results of an experimental investigation of the effect of mechanical-thermal treatment of submicrocrystalline and coarse-grained titanium on the deformation behavior in the stage of microplastic deformation at room and elevated temperatures are reported. The structural factors giving rise to the flowstress changes in the stage of microplastic deformation as a result of mechanical-thermal treatment are discussed. The general tendencies and special features of the effect of annealing and testing temperatures on the deformation behavior and flow stress in the first and second stages of microplastic deformation of submicrocrystalline and coarse-grained titanium subjected to large plastic deformation at 295 K are clarified.

  17. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Vakser Ilya A

    2011-07-01

    Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

  18. Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study.

    Science.gov (United States)

    Condon, Joshua E; Martin, Tyler B; Jayaraman, Arthi

    2017-04-19

    Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state". In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase separation observed in experiments of ELPs. Therefore, we utilize phenomenological coarse-grained (CG) MD simulations to probe how conjugating a block of generic-LCST polymer to another rigid unresponsive macromolecular block impacts the transition temperatures at concentrations and length scales larger than atomistic simulations. We find that when multiple LCST polymer chains are conjugated to a rigid unresponsive polymer block, the increased local crowding of the LCST polymers shifts the transition marked by onset of chain aggregation to smaller effective polymer-polymer attraction energies compared to the free LCST polymer chains. The driving force needed for aggregation is reduced in the conjugates compared to free LCST polymer due to reduction in the loss of polymer configurational entropy upon aggregation.

  19. Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

    Science.gov (United States)

    Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

    2016-12-01

    One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230-233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeller through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO_MD.

  20. Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations.

    Science.gov (United States)

    Jewel, Yead; Dutta, Prashanta; Liu, Jin

    2017-10-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H(+) symport process. Lactose/H(+) symport is a highly complex process that involves sugar translocation, H(+) transfer, and large-scale protein conformational changes. The complete picture of lactose/H(+) symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition. © 2017 Wiley Periodicals, Inc.

  1. Methane Hydrate Fformation in a Coarse-Grained, Brine-Saturated Sample Through the Induction of a Propagating Gas Front

    Science.gov (United States)

    Meyer, D.

    2016-12-01

    We generate methane hydrate in a coarse-grained, brine-saturated, vertically-oriented sample through gas injection. From 0 - 80 hours, we estimate a hydrate saturation of 0.56 behind the formation front, using mass balance, indicating that hydrate formation is limited by locally-elevated salinity creating three-phase equilibrium conditions. After 80 hours, the hydrate phase saturation drops to 0.50 and the magnitude of the pressure drop-rebound cycles increases, suggesting temporary reductions in permeability and the development of heterogeneous distributions of free gas in the sample. The sample consists of an industrial, fine sand mixed with a 0.5 wt% fraction of natural, smectitic clay from the Eugene Island region in the Gulf of Mexico (5.08cm diameter, 11.79cm length). The sample is initially saturated with a 7 wt% sodium chloride brine, pressurized to 12.24 MPa, and cooled to 1 degree Celsius, to bring the sample into the hydrate stability zone. Syringe pumps filled with methane gas and brine are connected to the top and bottom of the sample, respectively, to control fluid flow. We withdraw from the base of the sample at a rate of 0.0005 mL/min and inject methane to maintain a constant pressure, initiating hydrate formation. We analyze this experiment, as well as a gas flood experiment executed under the same conditions, using computed-tomography scans and an analytical solution to investigate the formation behavior and thermodynamic state of hydrate in gas-rich, coarse-grained reservoirs.

  2. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O 1 →4 -bonded polyglucose chains

    Science.gov (United States)

    Lubecka, Emilia A.; Liwo, Adam

    2017-09-01

    Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all

  3. Application of physical and numerical simulations for interpretation of peripheral coarse grain structure during hot extrusion of AA7020 aluminum alloy

    NARCIS (Netherlands)

    Eivani, A.R.; Zhou, J.

    2017-01-01

    In this research, hot compression test is used to simulate the metallurgical phenomena occurring in the peripheral part of AA7020 aluminum alloy extrudates during hot extrusion and leading to the formation of the peripheral coarse grain (PCG) structure. The temperature profiles at a tracking

  4. Coarse-grained molecular simulation of epidermal growth factor receptor protein tyrosine kinase multi-site self-phosphorylation.

    Directory of Open Access Journals (Sweden)

    John G Koland

    2014-01-01

    Full Text Available Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR, the intrinsic protein tyrosine kinase (PTK activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites in either of the two C-terminal (CT domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in

  5. Dissociation of Laboratory-Synthesized Methane Hydrate in Coarse-Grained Sediments by Slow Depressurization

    Science.gov (United States)

    Phillips, S. C.; You, K.; Borgfeldt, T.; Meyer, D.; Dong, T.; Flemings, P. B.

    2016-12-01

    We performed four dissociation experiments in which experimentally-formed methane hydrate was dissociated via slow, stepwise depressurization, revealing in situ salinity conditions. Overall, these results suggest the occurrence of local pore water freshening around dissociating hydrate in which bulk equilibrium behavior is limited by salt diffusion. Depressurization was performed at a constant confining temperature over 1 to 3 weeks by releasing small volumes of methane gas from the top of a vertically-oriented sample into an inverted graduated cylinder. We identify three distinct regimes of depressurization based on pressure drop behavior: (1) release of free gas down to initial hydrate dissociation at 3.3 MPa in NaBr or 4.64 MPa in NaCl, (2) dissociation of methane hydrate characterized by a slow, logarithmic increase in pressure after each gas release and (3) residual free gas release. Initial hydrate dissociation in NaCl brine at 4.64 MPa corresponds to the phase boundary for hydrate in 9.6 wt% NaCl. In the NaCl experiment, pressure increases of 0.16 MPa while the sample was shut in over 3 days likely correspond to a recovery in salinity of 0.7 wt. %. Salt ions likely diffuse from brine ahead of the hydrate front, based on a length scale for diffusion of NaCl of 6.3 cm for 3 days. In this experiment dissociation at bulk equilibrium is expected to decline from 4.54 to 4.04 MPa; however actual dissociation during 73 gas releases over 15 days, results in a pressure drop from 4.64 to 3.25 MPa. Hydrate samples were formed by injection of methane gas at 1 ºC and 12.24 MPa within a cylinder packed with medium-grained quartz sand and initially saturated in a 7 wt% NaBr or NaCl solution. In two experiments in which the system was thoroughly leak tested, total methane consumed during formation and recovered during depressurization match within 7% indicating this approach to be relatively accurate for determining total methane in experimental or pressure core samples.

  6. A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method.

    Science.gov (United States)

    Naômé, Aymeric; Laaksonen, Aatto; Vercauteren, Daniel P

    2014-08-12

    We present a new class of coarse-grained (CG) force fields (FFs) for B-DNA with explicit ions suited for large-scale mesoscale simulations at microsecond-micrometer scale using a wide spectrum of particle simulation methods from molecular dynamics to dissipative particle dynamics. The effective solvent-mediated pairwise interactions making up the FFs are obtained by inverting radial distribution functions and other particle-particle distributions obtained from all-atom simulations of numbers of octadecamer DNA fragments from the Ascona B-DNA library. The inverse Monte Carlo (IMC) method, later known as Newton inversion (NI) (Lyubartsev, A. P.; Laaksonen, A. Phys. Rev. E, 1995, 52, 3730-3737), was used together with the iterative Boltzmann inversion (IBI) scheme to compute the effective CG potentials. We show that this systematic structure-based approach is capable of providing converged potentials that accurately reproduce the structural features of the underlying atomistic system within a few percents of relative difference. We also show that a simple one-site-per-nucleotide model with 10 intramolecular pair interaction potentials is able to reproduce key features of DNA, for example, the persistence length and its dependence on the ionic concentration, experimentally determined around 50 nm at physiological salt concentration.

  7. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Kawamoto, Shuhei; Shinoda, Wataru, E-mail: w.shinoda@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Klein, Michael L. [Institute for Computational Molecular Science, Temple University, SERC Building 1925 North 12th Street, Philadelphia, Pennsylvania 19122 (United States)

    2015-12-28

    The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle–vesicle, vesicle–planar, and planar–planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.

  8. Interaction of menthol with mixed-lipid bilayer of stratum corneum: A coarse-grained simulation study.

    Science.gov (United States)

    Wan, Guang; Dai, Xingxing; Yin, Qianqian; Shi, Xinyuan; Qiao, Yanjiang

    2015-07-01

    Menthol is a widely used penetration enhancer in clinical medicine due to its high efficiency and relative safety. Although there are many studies focused on the penetration-enhancing activity of menthol, the details of molecular mechanism are rarely involved in the discussion. In this study, we present a series of coarse-grained molecular dynamics simulations to investigate the interaction of menthol with a mixed-lipid bilayer model consisting of ceramides, cholesterol and free fatty acids in a 2:2:1 molar ratio. Taking both the concentration of menthol and temperature into consideration, it was found that a rise in temperature and concentration within a specific range (1-20%) could improve the penetration-enhancing property of menthol and the floppiness of the bilayer. However, at high concentrations (30% and more), menthol completely mixed with the lipids and the membrane can no longer maintain a bilayer structure. Our results elucidates some of the molecular basis for menthol's penetration enhancing effects and may provide some assistance for the development and applications of menthol as a penetration enhancer. Furthermore, we establish a method to investigate the penetration enhancement mechanism of traditional Chinese medicine using the mixed-lipid bilayer model of stratum corneum by molecular dynamics simulations. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. A Snapshot of Present Research at AAU and DTU on Large-Diameter Piles in Coarse-Grained Materials

    DEFF Research Database (Denmark)

    Leth, C. T.; Sørensen, Søren Peder Hyldal; Klinkvort, Rasmus Tofte

    2012-01-01

    are developed for piles with diameters up to approximately 2.0 m and are based on a very limited number of tests. Hence, the method has not been validated for piles with diameters of 4 to 6 m. During the last six years extensive studies on non-slender large-diameter piles in coarse-grained material have been...... conducted at Aalborg University (AAU) and at the Technical University of Denmark (DTU). The piles have been investigated by means of physical and numerical modelling. The former consists of both centrifuge tests and tests in a so-called pressure tank (1G tests but with an applied overburden pressure......). The goal of the work has been to investigate the general behaviour of monopiles for nowadays offshore wind turbines and to revise the p-y curves for piles in sand in order to account for diameter on the response of monopiles subjected to both static and cyclic loads. The paper summarizes and compares...

  10. Computational Calculation Of The Ionization Energies Of The Human Prion Protein By The Coarse-grain Method

    Science.gov (United States)

    Lyu, Justin; Andrianarijaona, V. M.

    2016-05-01

    The causes of the misfolding of prion protein -i.e. the transformation of PrPC to PrPSc - have not been clearly elucidated. Many studies have focused on identifying possible chemical conditions, such as pH, temperature and chemical denaturation, that may trigger the pathological transformation of prion proteins (Weiwei Tao, Gwonchan Yoon, Penghui Cao, `` β-sheet-like formation during the mechanical unfolding of prion protein'', The Journal of Chemical Physics, 2015, 143, 125101). Here, we attempt to calculate the ionization energies of the prion protein, which will be able to shed light onto the possible causes of the misfolding. We plan on using the coarse-grain method which allows for a more feasible calculation time by means of approximation. We believe that by being able to approximate the ionization potential, particularly that of the regions known to form stable β-strands of the PrPSc form, the possible sources of denaturation, be it chemical or mechanical, may be narrowed down.

  11. A coarse-grained simulation to study the digestion and bioaccessibility of lipophilic nutrients and micronutrients in emulsion.

    Science.gov (United States)

    Marze, Sébastien

    2014-01-01

    The digestion of lipophilic nutrients and micronutrients requires numerous and simultaneous processes of chemical, physical and biological nature. Studying these processes experimentally is challenging, explaining why there is only little information about the mechanisms and interactions involved. Nevertheless, the bioaccessibility of lipophilic micronutrients is poorly understood so new investigation approaches are needed, all the more when digestion of lipophilic nutrients is also involved. In this article, the development of a coarse-grained simulation with no adjustable parameter is reported, enabling the study of the chemical and physical processes controlling bioaccessibility in such systems. The intestinal digestion of a droplet of a pure triglyceride containing a lipophilic vitamin was simulated to obtain their bioaccessibility kinetics (via lipolysis and/or solubilization in bile salt). The parameters examined here were the type of triglyceride, the type of vitamin, the digestive fluid amount, the droplet size, and different digestion conditions reflecting the in vitro or in vivo cases. Among these structure and composition parameters, the type of triglyceride and the digestion conditions had the greatest effects on bioaccessibility. An interplay between triglyceride digestion and micronutrient bioaccessibility kinetics was evidenced, highlighting the roles of the different parameters, in agreement with the experimental literature. This new approach is shown to be relevant to both nutrition and pharmacology.

  12. Construction of non-Markovian coarse-grained models employing the Mori-Zwanzig formalism and iterative Boltzmann inversion.

    Science.gov (United States)

    Yoshimoto, Yuta; Li, Zhen; Kinefuchi, Ikuya; Karniadakis, George Em

    2017-12-28

    We propose a new coarse-grained (CG) molecular simulation technique based on the Mori-Zwanzig (MZ) formalism along with the iterative Boltzmann inversion (IBI). Non-Markovian dissipative particle dynamics (NMDPD) taking into account memory effects is derived in a pairwise interaction form from the MZ-guided generalized Langevin equation. It is based on the introduction of auxiliary variables that allow for the replacement of a non-Markovian equation with a Markovian one in a higher dimensional space. We demonstrate that the NMDPD model exploiting MZ-guided memory kernels can successfully reproduce the dynamic properties such as the mean square displacement and velocity autocorrelation function of a Lennard-Jones system, as long as the memory kernels are appropriately evaluated based on the Volterra integral equation using the force-velocity and velocity-velocity correlations. Furthermore, we find that the IBI correction of a pair CG potential significantly improves the representation of static properties characterized by a radial distribution function and pressure, while it has little influence on the dynamic processes. Our findings suggest that combining the advantages of both the MZ formalism and IBI leads to an accurate representation of both the static and dynamic properties of microscopic systems that exhibit non-Markovian behavior.

  13. Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field.

    Science.gov (United States)

    Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio

    2015-01-01

    We present the first investigation of the kinetic and thermodynamic stability of two homologous thermophilic and mesophilic proteins based on the coarse-grained model OPEP. The object of our investigation is a pair of G-domains of relatively large size, 200 amino acids each, with an experimental stability gap of about 40 K. The OPEP force field is able to maintain stable the fold of these relatively large proteins within the hundrend-nanosecond time scale without including external constraints. This makes possible to characterize the conformational landscape of the folded protein as well as to explore the unfolding. In agreement with all-atom simulations used as a reference, we show that the conformational landscape of the thermophilic protein is characterized by a larger number of substates with slower dynamics on the network of states and more resilient to temperature increase. Moreover, we verify the stability gap between the two proteins using replica-exchange simulations and estimate a difference between the melting temperatures of about 23 K, in fair agreement with experiment. The detailed investigation of the unfolding thermodynamics, allows to gain insight into the mechanism underlying the enhanced stability of the thermophile relating it to a smaller heat capacity of unfolding.

  14. Coarse-grained modeling of the titration and conductance behavior of aqueous fullerene hexa malonic acid (FHMA) solutions.

    Science.gov (United States)

    Allison, Stuart A; Wu, Hengfu; Moyher, Avery; Soegiarto, Linda; Truong, Bi; Nguyen, Duy; Nguyen, Tam; Park, Donghyun

    2014-03-20

    The coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa malonic acid (FHMA). The spherical FHMA molecule, a highly charged electrolyte with an absolute valence charge as large as 12, is modeled as a dielectric sphere in Newtonian fluid, and electrostatics are treated numerically at the level of the non-linear Poisson-Boltzmann equation. Transport properties (electrophoretic mobilities and conductances) of the various charge states of FHMA are numerically computed using established numerical algorithms. For reasonable choices of the model parameters, good agreement between experiment (published literature) and modeling is achieved. In order to accomplish this, however, a moderate degree of specific binding of principal counterion and FHMA must be included in the modeling. It should be emphasized, however, that alternative explanations are possible. This comparison is made at 25 °C for both Na(+) and Ca(2+) principal counterions. The model is also used to characterize the different charge states and degree of counterion binding to those charge states as a function of pH.

  15. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    Energy Technology Data Exchange (ETDEWEB)

    MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  16. Coarse-Grained Langevin Equation for Protein Dynamics: Global Anisotropy and a Mode Approach to Local Complexity.

    Science.gov (United States)

    Copperman, J; Guenza, M G

    2015-07-23

    We utilize a multiscale approach where molecular dynamic simulations are performed to obtain quantitative structural averages used as input to a coarse-grained Langevin equation for protein dynamics, which can be solved analytically. The approach describes proteins as fundamentally semiflexible objects collapsed into the free energy well representing the folded state. The normal-mode analytical solution to this Langevin equation naturally separates into global modes describing the fully anisotropic tumbling of the macromolecule as a whole and internal modes which describe local fluctuations about the folded structure. Complexity in the configurational free-energy landscape of the macromolecule leads to a renormalization of the internal modes, while the global modes provide a basis set in which the dipolar orientation and global anisotropy can be accounted for when comparing to experiments. This simple approach predicts the dynamics of both global rotational diffusion and internal motion from the picosecond to the nanosecond regime and is quantitative when compared to time correlation functions calculated from molecular dynamic simulations and in good agreement with nuclear magnetic resonance relaxation experiments. Fundamental to this approach is the inclusion of internal dissipation, which is absent in any rigid-body hydrodynamical modeling scheme.

  17. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism.

    Science.gov (United States)

    Kawamoto, Shuhei; Klein, Michael L; Shinoda, Wataru

    2015-12-28

    The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.

  18. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

    2015-12-28

    We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  19. Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

    Science.gov (United States)

    Kapoor, Abhijeet; Travesset, Alex

    2014-03-01

    We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

  20. Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water.

    Science.gov (United States)

    Haji-Akbari, Amir; DeFever, Ryan S; Sarupria, Sapna; Debenedetti, Pablo G

    2014-12-21

    Freezing in the vicinity of water-vapor interfaces is of considerable interest to a wide range of disciplines, most notably the atmospheric sciences. In this work, we use molecular dynamics and two advanced sampling techniques, forward flux sampling and umbrella sampling, to study homogeneous nucleation of ice in free-standing thin films of supercooled water. We use a coarse-grained monoatomic model of water, known as mW, and we find that in this model a vapor-liquid interface suppresses crystallization in its vicinity. This suppression occurs in the vicinity of flat interfaces where no net Laplace pressure in induced. Our free energy calculations reveal that the pre-critical crystalline nuclei that emerge near the interface are thermodynamically less stable than those that emerge in the bulk. We investigate the origin of this instability by computing the average asphericity of nuclei that form in different regions of the film, and observe that average asphericity increases closer to the interface, which is consistent with an increase in the free energy due to increased surface-to-volume ratios.

  1. Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations.

    Science.gov (United States)

    Lee, Myungjin; Kolev, Vesselin; Warshel, Arieh

    2017-12-21

    Simulating the nature of voltage-activated systems is a problem of major current interest, ranging from the action of voltage-gated ion channels to energy storage batteries. However, fully microscopic converging molecular simulations of external voltage effects present a major challenge, and macroscopic models are associated with major uncertainties about the dielectric treatment and the underlying physical basis. Recently we developed a coarse-grained (CG) model that represents explicitly the electrodes, the electrolytes, and the membrane/protein system. The CG model provides a semimacroscopic way of capturing the microscopic physics of voltage-activated systems. Our method was originally validated by reproducing macroscopic and analytical results for key test cases and then used in modeling voltage-activated ion channels and related problems. In this work, we further establish the reliability of the CG voltage model by comparing it to the results of Monte Carlo (MC) simulations with a microscopic electrolyte model. The comparison explores different aspects of membrane, electrolyte, and electrode systems ranging from the Gouy-Chapman model to the determination of the electrolyte charge distribution in the solution between two electrodes (without and with a separating membrane), as well as the evaluation of gating charges. Overall the agreement is very impressive. This provides confidence in the CG model and also shows that the MC model can be used in realistic simulation of voltage activation of membrane proteins with sufficient computer time.

  2. Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism

    Science.gov (United States)

    Kawamoto, Shuhei; Klein, Michael L.; Shinoda, Wataru

    2015-12-01

    The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle-vesicle, vesicle-planar, and planar-planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion.

  3. Formation Mechanism and Properties of Polyelectrolyte Multilayer-Supported Lipid Bilayers: A Coarse-Grained Molecular Dynamics Study

    Directory of Open Access Journals (Sweden)

    Caixia Wen

    2017-03-01

    Full Text Available Polyelectrolyte multilayer (PEM-supported lipid bilayers (SLBs that connect with functional proteins are popular models for cell membranes and are usually obtained via vesicle adsorption and spreading. However, the exact mechanism by which SLBs are formed is not fully understood. In this study, we employ coarse-grained molecular dynamics simulations to investigate the pathways by which vesicles undergo spreading upon the deposition on PEM-cushioned substrates. The substrates consist of positive chitosan (CHI/negative alginate (ALG multilayers. We find that an isolated vesicle tends to completely disintegrate upon deposition, forming a well-ordered lipid bilayer at appropriate polymer ionic strengths by a mechanism described as “parachute” model. Lipids from the vesicle’s outer leaflet are predominantly oriented toward the bulk after the formation of the SLB. The PEM cushion provides adsorption energy of 26.9 kJ mol–1 per lipid for the SLBs. The process by which SLBs are formed is almost independent of the number of layers of CHI/ALG in the PEM cushion. Additional simulations on vesicle clusters also demonstrate that the formation of SLBs can be catalyzed by either neighboring vesicles or preexisting bilayer edges on the support. Moreover, our simulations show that SLBs created on PEM supports preserve the lateral mobility and the symmetric density profile of the phospholipids, as in a freestanding bilayer.

  4. Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide.

    Science.gov (United States)

    Cao, Fenglei; Deetz, Joshua D; Sun, Huai

    2017-01-23

    The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.

  5. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Hang; Ma, Wen [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Han, Wei [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-12-28

    Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

  6. Critical mechanical properties and FEA simulation for crashworthiness assessment of a coarse-grained cast AM50 alloy

    Directory of Open Access Journals (Sweden)

    S. Xu

    2015-09-01

    Full Text Available A coarse-grained AM50 alloy was used as a model alloy for investigation of constitutive behaviour, Charpy toughness and effect of stress state on deformation and failure of cast Mg alloys. The results provide critical mechanical properties of a cast AM50 alloy for crashworthiness assessment and development of finite element simulation techniques. For cast Mg alloys, the effect of strain rate and temperature is larger on tensile strength than on compressive strength because twinning is more extensive in compression than in tension. The effect of strain rate on compressive strength is negligible because twinning activity of the cast Mg alloy is dominant. The load vs. deflection of Charpy specimens were measured for modelling, and the effect of loading rate and temperature on load of Charpy specimens is very small because part of the specimen is in compression. The equivalent strain to fracture of the cylindrical round notched tension specimen decreases with increasing stress triaxiality; though for the flat-grooved plane strain specimen, the equivalent fracture strain remains constant over the range of stress triaxiality investigated. Because the two different specimen geometries give rise to different Lode angle values, the test results show that the Lode angle parameter is an important parameter for deformation and fracture of Mg alloys. Finite element simulations of loading of the cylindrical notched-tension and Charpy specimens were carried out using a Lode-angle dependent von Mises model, and were found to provide a reasonable description of the load–displacement curves measured in the tests. For the flat-grooved plane strain specimens, the computations under-predicted the force–displacement response measured.

  7. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

    Science.gov (United States)

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

    2015-04-14

    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  8. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.

    Directory of Open Access Journals (Sweden)

    Qingzhen Hou

    Full Text Available Large-scale identification of native binding orientations is crucial for understanding the role of protein-protein interactions in their biological context. Measuring binding free energy is the method of choice to estimate binding strength and reveal the relevance of particular conformations in which proteins interact. In a recent study, we successfully applied coarse-grained molecular dynamics simulations to measure binding free energy for two protein complexes with similar accuracy to full-atomistic simulation, but 500-fold less time consuming. Here, we investigate the efficacy of this approach as a scoring method to identify stable binding conformations from thousands of docking decoys produced by protein docking programs. To test our method, we first applied it to calculate binding free energies of all protein conformations in a CAPRI (Critical Assessment of PRedicted Interactions benchmark dataset, which included over 19000 protein docking solutions for 15 benchmark targets. Based on the binding free energies, we ranked all docking solutions to select the near-native binding modes under the assumption that the native-solutions have lowest binding free energies. In our top 100 ranked structures, for the 'easy' targets that have many near-native conformations, we obtain a strong enrichment of acceptable or better quality structures; for the 'hard' targets without near-native decoys, our method is still able to retain structures which have native binding contacts. Moreover, in our top 10 selections, CLUB-MARTINI shows a comparable performance when compared with other state-of-the-art docking scoring functions. As a proof of concept, CLUB-MARTINI performs remarkably well for many targets and is able to pinpoint near-native binding modes in the top selections. To the best of our knowledge, this is the first time interaction free energy calculated from MD simulations have been used to rank docking solutions at a large scale.

  9. Structural variation of alpha-synuclein with temperature by a coarse-grained approach with knowledge-based interactions

    Directory of Open Access Journals (Sweden)

    Peter Mirau

    2015-09-01

    Full Text Available Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN, a disordered protein (that plays a key role in neurodegenerative disease is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal (1-60 and C-terminal (96-140 regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component (NAC (61-95. Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation (clumping in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration (Rg of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. (JACS, 2009. Our analysis of the structure function provides an insight into the mass (N distribution of ASN, and the dimensionality (D of the structure as a function of temperature. We find that the globular structure with D ≈ 3 at low T, a random coil, D ≈ 2 at high T and in between (2 ≤ D ≤ 3 at the intermediate temperatures. The magnitudes of D are in agreement with experimental estimates (J. Biological Chem 2002.

  10. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer

    Energy Technology Data Exchange (ETDEWEB)

    Mustafa, Ghulam, E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org; Nandekar, Prajwal P.; Yu, Xiaofeng [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Wade, Rebecca C., E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120 Heidelberg (Germany); Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120 Heidelberg (Germany)

    2015-12-28

    An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.

  11. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

  12. Response formulae for n-point correlations in statistical mechanical systems and application to a problem of coarse graining

    Science.gov (United States)

    Lucarini, Valerio; Wouters, Jeroen

    2017-09-01

    Predicting the response of a system to perturbations is a key challenge in mathematical and natural sciences. Under suitable conditions on the nature of the system, of the perturbation, and of the observables of interest, response theories allow to construct operators describing the smooth change of the invariant measure of the system of interest as a function of the small parameter controlling the intensity of the perturbation. In particular, response theories can be developed both for stochastic and chaotic deterministic dynamical systems, where in the latter case stricter conditions imposing some degree of structural stability are required. In this paper we extend previous findings and derive general response formulae describing how n- point correlations are affected by perturbations to the vector flow. We also show how to compute the response of the spectral properties of the system to perturbations. We then apply our results to the seemingly unrelated problem of coarse graining in multiscale systems: we find explicit formulae describing the change in the terms describing the parameterisation of the neglected degrees of freedom resulting from applying perturbations to the full system. All the terms envisioned by the Mori-Zwanzig theory—the deterministic, stochastic, and non-Markovian terms—are affected at first order in the perturbation. The obtained results provide a more comprehensive understanding of the response of statistical mechanical systems to perturbations. They also contribute to the goal of constructing accurate and robust parameterisations and are of potential relevance for fields like molecular dynamics, condensed matter, and geophysical fluid dynamics. We envision possible applications of our general results to the study of the response of climate variability to anthropogenic and natural forcing and to the study of the equivalence of thermostatted statistical mechanical systems.

  13. Peculiar Spatiotemporal Behavior of Unstable Plastic Flow in an AlMgMnScZr Alloy with Coarse and Ultrafine Grains

    Directory of Open Access Journals (Sweden)

    Daria Zhemchuzhnikova

    2017-08-01

    Full Text Available The work addresses the effects of nanosize particles and grain refinement on the patterns of stress serrations and kinematics of deformation bands associated with the Portevin–Le Chatelier instability of plastic flow. Ultra-fine-grained microstructure was obtained using equal-channel angular pressing of the initial coarse-grained alloy. Tensile tests were carried out on flat specimens at strain rates in the range from 3 × 10−5 to 1.4 × 10−2 s−1. Using local extensometry techniques, it was found that the presence of nanoscale precipitates promotes quasi-continuous propagation of deformation bands in the entire strain-rate range. The grain refinement leads to a transition to relay-race propagation at high strain rates and static strain localization at low rates. The results are discussed from the viewpoint of competition between various dynamical modes of plastic deformation associated with collective dynamics of dislocations.

  14. Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment

    OpenAIRE

    Mognetti, B. M.; Virnau, P.; Yelash, L.; Paul, W.; Binder, K.; Mueller, M.; MacDowell, L. G.

    2008-01-01

    The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on thermodynamic perturbation theory is discussed. Molecules are described by coarse grained (CG) models, where either the whole molecule (carbon dioxide, benzene, methane) or a group of a few successive CH_2 groups (in the case of alkanes) are lumped into an ...

  15. Conformational Properties of a Polymer in an Ionic Liquid: Computer Simulations and Integral Equation Theory of a Coarse-Grained Model.

    Science.gov (United States)

    Choi, Eunsong; Yethiraj, Arun

    2015-07-23

    We study the conformational properties of polymers in room temperature ionic liquids using theory and simulations of a coarse-grained model. Atomistic simulations have shown that single poly(ethylene oxide) (PEO) molecules in the ionic liquid 1-butyl 3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) are expanded at room temperature (i.e., the radius of gyration, Rg), scales with molecular weight, Mw, as Rg ∼ Mw(0.9), instead of the expected self-avoiding walk behavior. The simulations were restricted to fairly short chains, however, which might not be in the true scaling regime. In this work, we investigate a coarse-grained model for the behavior of PEO in [BMIM][BF4]. We use existing force fields for PEO and [BMIM][BF4] and Lorentz–Berthelot mixing rules for the cross interactions. The coarse-grained model predicts that PEO collapses in the ionic liquid. We also present an integral equation theory for the structure of the ionic liquid and the conformation properties of the polymer. The theory is in excellent agreement with the simulation results. We conclude that the properties of polymers in ionic liquids are unusually sensitive to the details of the intermolecular interactions. The integral equation theory is sufficiently accurate to be a useful guide to computational work.

  16. Computing the non-Markovian coarse-grained interactions derived from the Mori-Zwanzig formalism in molecular systems: Application to polymer melts

    Science.gov (United States)

    Li, Zhen; Lee, Hee Sun; Darve, Eric; Karniadakis, George Em

    2017-01-01

    Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.

  17. Construction of a coarse-grain quasi-classical trajectory method. II. Comparison against the direct molecular simulation method.

    Science.gov (United States)

    Macdonald, R L; Grover, M S; Schwartzentruber, T E; Panesi, M

    2018-02-07

    This work presents the analysis of non-equilibrium energy transfer and dissociation of nitrogen molecules (N2(Σg+1)) using two different approaches: the direct molecular simulation (DMS) method and the coarse-grain quasi-classical trajectory (CG-QCT) method. The two methods are used to study thermochemical relaxation in a zero-dimensional isochoric and isothermal reactor in which the nitrogen molecules are heated to several thousand degrees Kelvin, forcing the system into strong non-equilibrium. The analysis considers thermochemical relaxation for temperatures ranging from 10 000 to 25 000 K. Both methods make use of the same potential energy surface for the N2(Σg+1)-N2(Σg+1) system taken from the NASA Ames quantum chemistry database. Within the CG-QCT method, the rovibrational energy levels of the electronic ground state of the nitrogen molecule are lumped into a reduced number of bins. Two different grouping strategies are used: the more conventional vibrational-based grouping, widely used in the literature, and energy-based grouping. The analysis of both the internal state populations and concentration profiles show excellent agreement between the energy-based grouping and the DMS solutions. During the energy transfer process, discrepancies arise between the energy-based grouping and DMS solution due to the increased importance of mode separation for low energy states. By contrast, the vibrational grouping, traditionally considered state-of-the-art, captures well the behavior of the energy relaxation but fails to consistently predict the dissociation process. The deficiency of the vibrational grouping model is due to the assumption of strict mode separation and equilibrium of rotational energy states. These assumptions result in errors predicting the energy contribution to dissociation from the rotational and vibrational modes, with rotational energy actually contributing 30%-40% of the energy required to dissociate a molecule. This work confirms the findings

  18. Toward decrypting the allosteric mechanism of the ryanodine receptor based on coarse-grained structural and dynamic modeling.

    Science.gov (United States)

    Zheng, Wenjun

    2015-12-01

    The ryanodine receptors (RyRs) are a family of calcium (Ca) channels that regulate Ca release by undergoing a closed-to-open gating transition in response to action potential or Ca binding. The allosteric mechanism of RyRs gating, which is activated/regulated by ligand/protein binding >200 Å away from the channel gate, remains elusive for the lack of high-resolution structures. Recent solution of the closed-form structures of the RyR1 isoform by cryo-electron microscopy has paved the way for detailed structure-driven studies of RyRs functions. Toward elucidating the allosteric mechanism of RyRs gating, we performed coarse-grained modeling based on the newly solved closed-form structures of RyR1. Our normal mode analysis captured a key mode of collective motions dominating the observed structural variations in RyR1, which features large outward and downward movements of the peripheral domains with the channel remaining closed, and involves hotspot residues that overlap well with key functional sites and disease mutations. In particular, we found a key interaction between a peripheral domain and the Ca-binding EF hand domain, which may allow for direct coupling of Ca binding to the collective motions as captured by the above mode. This key mode was robustly reproduced by the normal mode analysis of the other two closed-form structures of RyR1 solved independently. To elucidate the closed-to-open conformational changes in RyR1 with amino-acid level of details, we flexibly fitted the closed-form structures of RyR1 into a 10-Å cryo-electron microscopy map of the open state. We observed extensive structural changes involving the peripheral domains and the central domains, resulting in the channel pore opening. In sum, our findings have offered unprecedented structural and dynamic insights to the allosteric mechanism of RyR1 via modulation of the key collective motions involved in RyR1 gating. The predicted hotspot residues and open-form conformation of RyR1 will guide

  19. Efficient and flexible memory architecture to alleviate data and context bandwidth bottlenecks of coarse-grained reconfigurable arrays

    Science.gov (United States)

    Yang, Chen; Liu, LeiBo; Yin, ShouYi; Wei, ShaoJun

    2014-12-01

    The computational capability of a coarse-grained reconfigurable array (CGRA) can be significantly restrained due to data and context memory bandwidth bottlenecks. Traditionally, two methods have been used to resolve this problem. One method loads the context into the CGRA at run time. This method occupies very small on-chip memory but induces very large latency, which leads to low computational efficiency. The other method adopts a multi-context structure. This method loads the context into the on-chip context memory at the boot phase. Broadcasting the pointer of a set of contexts changes the hardware configuration on a cycle-by-cycle basis. The size of the context memory induces a large area overhead in multi-context structures, which results in major restrictions on application complexity. This paper proposes a Predictable Context Cache (PCC) architecture to address the above context issues by buffering the context inside a CGRA. In this architecture, context is dynamically transferred into the CGRA. Utilizing a PCC significantly reduces the on-chip context memory and the complexity of the applications running on the CGRA is no longer restricted by the size of the on-chip context memory. Data preloading is the most frequently used approach to hide input data latency and speed up the data transmission process for the data bandwidth issue. Rather than fundamentally reducing the amount of input data, the transferred data and computations are processed in parallel. However, the data preloading method cannot work efficiently because data transmission becomes the critical path as the reconfigurable array scale increases. This paper also presents a Hierarchical Data Memory (HDM) architecture as a solution to the efficiency problem. In this architecture, high internal bandwidth is provided to buffer both reused input data and intermediate data. The HDM architecture relieves the external memory from the data transfer burden so that the performance is significantly

  20. A Tri-modal 2024 Al -B4C composites with super-high strength and ductility: Effect of coarse-grained aluminum fraction on mechanical behavior

    Directory of Open Access Journals (Sweden)

    Alireza Abdollahi

    2014-12-01

    Full Text Available In this study, ultrafine grained 2024 Al alloy based B4C particles reinforced composite was produced by mechanical milling and hot extrusion. Mechanical milling was used to synthesize the nanostructured Al2024 in attrition mill under argon atmosphere up to 50h. A similar process was used to produce Al2024-5%wt. B4C composite powder. To produce trimodal composites, milled powders were combined with coarse grained aluminum in 30 and 50 wt% and then were exposed to hot extrusion at 570°C. The microstructure of hot extruded samples were studied by optical microscope, Transmission electron microscope (TEM and scanning electron microscope (SEM equipped with EDS spectroscopy. The mechanical properties of samples were compared by using tensile, compression and hardness tests. The results showed that the strength, after 50 h milling and addition of 5wt% B4C, increased from 340 to 582 MPa and the hardness increased from 87 HBN to 173 HBN, but the elongation decreased from 14 to 0.5%. By adding the coarse-grained aluminum powder, the strength and hardness decreased slightly, but the increases in return. Ductility increase is the result of increase in dislocation movements and strength increase is the result of restriction in plastic deformation by nanostructured regions. Furthermore, the strength and hardness of trimodal composites were higher, but their ductility was lower.

  1. The Effect of Chemical Composition on Microstructure and Properties of Intercritically Reheated Coarse-Grained Heat-Affected Zone in X70 Steels

    Science.gov (United States)

    Zhu, Zhixiong; Kuzmikova, Lenka; Li, Huijun; Barbaro, Frank

    2013-12-01

    The current study investigates the effect of different levels of Ti, N, and Ti/N ratios on microstructure and properties in the intercritically reheated coarse-grained heat-affected zone (ICCGHAZ) of two-pass submerged arc welds in API 5L grade X70 pipe. Gleeble simulation was employed to reproduce the ICCGHAZ of actual welds. Hardness and Charpy V-notch (CVN) tests were performed on the simulated samples. The microstructure of simulated ICCGHAZ was characterized by optical microscopy and scanning electron microscopy (SEM). LePera color etching technique was employed to identify and quantify the martensitic-austenitic (M-A) constituent. Results show that the simulated ICCGHAZ exhibited extremely low toughness, but in the studied range of Ti and N, there was no correlation with Ti/N ratio. The beneficial effect of near-stoichiometric Ti/N ratio observed in coarse-grained heat-affected zone (CGHAZ) did not translate to ICCGHAZ. This was because of the negative effect of the blocky M-A constituent formed on prior austenite grain boundaries.

  2. Striped domains of coarse-grained magnetite observed by X-ray photoemission electron microscopy as a source of the high remanence of granites in the Vredefort dome

    Directory of Open Access Journals (Sweden)

    Hiroto eKubo

    2015-06-01

    Full Text Available The characteristics of a coarse-grained high-remanence magnetite obtained from shocked Vredefort granite were investigated by X-ray magnetic circular dichroism (XMCD analysis and X-ray absorption spectroscopy (XAS. The study utilized a spectroscopic photoelectron low-energy electron emission microscope (SPELEEM and was conducted in the SPring-8 large-synchrotron radiation facility. It is generally believed that the strong and stable bulk remanence of Vredefort granites is due to the presence of minerals that have been strongly magnetized by either an impact-generated magnetic field or terrestrial lightning strikes. Although coarse-grained magnetite is traditionally characterized by weak coercivity and remanence, the specimen used in the present study exhibited high coercivity and an intense remanent magnetization. The presence of hematite lamellae observed on the partially oxidized magnetite specimen indicated an array of striped domains, intensifying a remanence and coercivity. We also conducted XAS and XMCD analyses on a natural lodestone permanent magnet produced by lightning strikes; while maghemite was found to be present, no magnetic domain structures were observed. Considering that the nucleation of hematite lamellae on magnetite/maghemite grains is due to high-temperature oxidation, we attribute the intense remanent magnetization and magnetic hardening of Vredefort granites to post-impact hydrothermal activity.

  3. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  4. Transferability of Polymer Chain Properties between Coarse-Grained and Atomistic Models of Natural Rubber Molecule Validated by Molecular Dynamics Simulations

    Science.gov (United States)

    Kitjanon, Jiramate; Khuntawee, Wasinee; Sutthibutpong, Thana; Boonnoy, Phansiri; Phongphanphanee, Saree; Wong-ekkabut, Jirasak

    2017-09-01

    In this study, we have successfully parameterized the coarse-grained (CG) model of cis-1,4-polyisoprene (main component of natural rubber) based on the MARTINI force field. An isoprene monomer is mapped into one bead of CG model. The structure, bulk and thermodynamics properties of cis-1,4-polyisoprene with new CG model are well comparable to the atomistic simulation model and experiment. Our CG model of cis-1,4-polyisoprene will be helpful to study in the advanced rubber nanocomposite materials.

  5. Matching conditions in the quasicontinuum method: Removal of the error introduced at the interface between the coarse-grained and fully atomistic region

    DEFF Research Database (Denmark)

    Shimokawa, T.; Mortensen, Jens Jørgen; Schiøtz, Jakob

    2004-01-01

    The quasicontinuum method is a way of reducing the number of degrees of freedom in an atomistic simulation by removing the majority of the atoms in regions of slowly varying strain fields. Due to the different ways the energy of the atoms is calculated in the coarse-grained regions and the regions...... the quasicontinuum method without these problems by introducing a buffer layer between the two regions of space. The method is applicable to short-ranged potentials in the face-centered cubic, body-centered cubic, and hexagonal close-packed crystal structures....

  6. Numerical simulation of the mechanical behavior of ultrafine- and coarse-grained Zr-Nb alloys over a wide range of strain rates

    Science.gov (United States)

    Serbenta, V. A.; Skripnyak, N. V.; Skripnyak, V. A.; Skripnyak, E. G.

    2017-12-01

    This paper presents the results on the development of theoretical methods of evaluation and prediction of mechanical properties of Zr-Nb alloys over a range of strain rates from 10-3 to 103 s-1. The mechanical behavior of coarse- and ultrafine-grained Zr-1Nb (E110) was investigated numerically. The ranges of strain rates and temperatures in which the mechanical behavior of Zr-1Nb alloy can be described using modified models of Johnson-Cook and Zerilli-Armstrong were defined. The results can be used in engineering analysis of designed technical systems for nuclear reactors.

  7. Subglacial conditions and Scandinavian Ice Sheet dynamics at the coarse-grained substratum of the fore-mountain area of southern Poland

    Science.gov (United States)

    Salamon, Tomasz

    2016-11-01

    The fore-mountain areas of southern Poland are locally composed of the coarse-grained sediments of alluvial fans, which created unusual conditions under the advancing Scandinavian Ice Sheet during the Elsterian glaciation. This highly permeable substratum potentially enabled rapid outflow of meltwater from the ice sheet base, thereby reducing the water pressure and strongly influencing the ice sheet dynamics. The subglacial conditions and the relationship between the ice sheet behaviour and its coarse-grained substratum were studied at the foreland of the western Carpathian Mountains. The sedimentological and structural analysis of the till and related sediments that were deposited above the alluvial gravel of the fore-mountain fans are presented. The study indicates that despite the high permeability of the coarse-grained substratum, it did not slow the ice sheet movement. Conversely, the ice sheet moved mainly due to basal slip and locally shallow deformations. This was a consequence of very high basal water pressure, which resulted largely from the presence of permafrost that restricted subglacial groundwater outflow. In addition, the ice sheet substratum was inclined opposite to the direction of its movement, increasing the pressure of the subglacial water. Numerous subhorizontal sandy laminae within the till indicate that the meltwater from the ice sheet base was drained by a water film along the ice/bed interface. The water escape structures within the till and subtill sediments indicate the occasional instability of the ice sheet hydrological system and suggest that the meltwater was periodically stored in the ice sheet base. Temporal changes occurring in the ice sheet hydrological system might indicate variations in the ice sheet behaviour; i.e. phases of relatively fast ice flow and phases of ice stagnation. The latter were probably correlated with the freezing of the ice margin to its base. The study shows how the coarse-grained substratum could

  8. Effect of thermal and thermo-mechanical cycling on the boron segregation behavior in the coarse-grained heat-affected zone of low-alloy steel

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sanghoon; Kang, Yongjoon; Lee, Changhee, E-mail: chlee@hanyang.ac.kr

    2016-06-15

    The boron segregation behavior in the coarse-grained heat-affected zone (CGHAZ) of 10 ppm boron-added low-alloy steel during the welding cycle was investigated by taking the changes in the microstructure and hardness into account. Various CGHAZs were simulated with a Gleeble system as a function of the heat input and external stress, and the boron segregation behavior was analyzed by secondary ion mass spectrometry (SIMS) and particle tracking autoradiography (PTA). The segregation of boron was found to initially increase, and then decrease with an increase in the heat input. This is believed to be due to the back-diffusion of boron with an increase in the exposure time at high temperature after non-equilibrium grain boundary segregation. The grain boundary segregation of boron could be decreased by an external stress applied during the welding cycle. Such behavior may be due to an increase in the grain boundary area as a result of the grain size reduction induced by the external stress. - Highlights: • Boron segregation behavior in the CGHAZ of low-alloy steel during a welding cycle was investigated. • Various CGHAZs were simulated with a Gleeble system as a function of the heat input and external stress. • Boron segregation behavior was analyzed using SIMS and PTA techniques.

  9. Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories.

    Science.gov (United States)

    Ozmaian, Masoumeh; Jasnow, David; Eskandari Nasrabad, Afshin; Zilman, Anton; Coalson, Rob D

    2018-01-14

    The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT cross-link strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations. Coarse grained molecular dynamics simulations confirm this prediction, for both small nanoparticles (nanoparticle volume = monomer volume) and large nanoparticles (nanoparticle volume = 27 × monomer volume). Simulation results for these cross-linked systems are compared with analogous results for systems with no cross-linking. At the same solution phase nanoparticle concentration, strong cross-linking results in additional compression of the brush relative to the non-crosslinked analog and, at all but the lowest concentrations, to a lesser degree of infiltration by nanoparticles. For large nanoparticles, the monomer density profiles show clear oscillations moving outwards from the grafting surface, corresponding to a degree of layering of the absorbed nanoparticles in the brush as they pack against the grafting surface.

  10. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

    Science.gov (United States)

    Stadlbauer, Petr; Mazzanti, Liuba; Cragnolini, Tristan; Wales, David J; Derreumaux, Philippe; Pasquali, Samuela; Šponer, Jiří

    2016-12-13

    G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse-grained force field.

  11. Effects of cross-linking on partitioning of nanoparticles into a polymer brush: Coarse-grained simulations test simple approximate theories

    Science.gov (United States)

    Ozmaian, Masoumeh; Jasnow, David; Eskandari Nasrabad, Afshin; Zilman, Anton; Coalson, Rob D.

    2018-01-01

    The effect of cohesive contacts or, equivalently, dynamical cross-linking on the equilibrium morphology of a polymer brush infiltrated by nanoparticles that are attracted to the polymer strands is studied for plane-grafted brushes using coarse-grained molecular dynamics and approximate statistical mechanical models. In particular, the Alexander-de Gennes (AdG) and Strong Stretching Theory (SST) mean-field theory (MFT) models are considered. It is found that for values of the MFT cross-link strength interaction parameter beyond a certain threshold, both AdG and SST models predict that the polymer brush will be in a compact state of nearly uniform density packed next to the grafting surface over a wide range of solution phase nanoparticle concentrations. Coarse grained molecular dynamics simulations confirm this prediction, for both small nanoparticles (nanoparticle volume = monomer volume) and large nanoparticles (nanoparticle volume = 27 × monomer volume). Simulation results for these cross-linked systems are compared with analogous results for systems with no cross-linking. At the same solution phase nanoparticle concentration, strong cross-linking results in additional compression of the brush relative to the non-crosslinked analog and, at all but the lowest concentrations, to a lesser degree of infiltration by nanoparticles. For large nanoparticles, the monomer density profiles show clear oscillations moving outwards from the grafting surface, corresponding to a degree of layering of the absorbed nanoparticles in the brush as they pack against the grafting surface.

  12. Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

    Science.gov (United States)

    Richter, Martin; Fingerhut, Benjamin P.

    2017-06-01

    The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.

  13. The effect of coarse second-phase particles on the rate of grain refinement during severe deformation processing

    DEFF Research Database (Denmark)

    Apps, P.J.; Bowen, Jacob R.; Prangnell, P.B.

    2003-01-01

    The effect of second-phase particles on the rate of grain refinement during severe deformation processing has been investigated, by comparing the microstructure evolution in an AA8079 aluminium alloy, containing 2.5 vol.% of ~2 μm particles, with that in a high purity, single-phase, Al-0.13% Mg...... alloy, deformed identically by ECAE to an effective strain of ten. The materials were analysed by high-resolution EBSD orientation mapping, which revealed that grain refinement occurred at a dramatically higher rate in the particle-containing alloy. A submicron grain structure could be achieved...... by an effective strain of only five in the particle-containing alloy, compared to ten in the single-phase material. The mechanisms that contribute to this acceleration of the grain refinement process are discussed....

  14. Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps.

    Science.gov (United States)

    Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E; Svenning, Jens-Christian

    2015-06-01

    The role of competition for light among plants has long been recognised at local scales, but its importance for plant species distributions at larger spatial scales has generally been ignored. Tree cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of tree cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 species of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and tree cover) at both spatial grains for each species. We used partial regressions to evaluate the independent effects of plot- and landscape-grain tree cover on plot-level plant communities. Finally, the effects on species-specific elevational range limits were assessed by simulating a removal experiment comparing the species distributions under high and low tree cover. Accounting for tree cover improved the model performance, with the probability of the presence of shade-tolerant species increasing with increasing tree cover, whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-level plant communities. With high tree cover, shade-intolerant species exhibited narrower elevational ranges than with low tree cover whereas shade-tolerant species showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb

  15. Tree cover at fine and coarse spatial grains interacts with shade tolerance to shape plant species distributions across the Alps

    Science.gov (United States)

    Nieto-Lugilde, Diego; Lenoir, Jonathan; Abdulhak, Sylvain; Aeschimann, David; Dullinger, Stefan; Gégout, Jean-Claude; Guisan, Antoine; Pauli, Harald; Renaud, Julien; Theurillat, Jean-Paul; Thuiller, Wilfried; Van Es, Jérémie; Vittoz, Pascal; Willner, Wolfgang; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Svenning, Jens-Christian

    2015-01-01

    The role of competition for light among plants has long been recognised at local scales, but its importance for plant species distributions at larger spatial scales has generally been ignored. Tree cover modifies the local abiotic conditions below the canopy, notably by reducing light availability, and thus, also the performance of species that are not adapted to low-light conditions. However, this local effect may propagate to coarser spatial grains, by affecting colonisation probabilities and local extinction risks of herbs and shrubs. To assess the effect of tree cover at both the plot- and landscape-grain sizes (approximately 10-m and 1-km), we fit Generalised Linear Models (GLMs) for the plot-level distributions of 960 species of herbs and shrubs using 6,935 vegetation plots across the European Alps. We ran four models with different combinations of variables (climate, soil and tree cover) at both spatial grains for each species. We used partial regressions to evaluate the independent effects of plot- and landscape-grain tree cover on plot-level plant communities. Finally, the effects on species-specific elevational range limits were assessed by simulating a removal experiment comparing the species distributions under high and low tree cover. Accounting for tree cover improved the model performance, with the probability of the presence of shade-tolerant species increasing with increasing tree cover, whereas shade-intolerant species showed the opposite pattern. The tree cover effect occurred consistently at both the plot and landscape spatial grains, albeit most strongly at the former. Importantly, tree cover at the two grain sizes had partially independent effects on plot-level plant communities. With high tree cover, shade-intolerant species exhibited narrower elevational ranges than with low tree cover whereas shade-tolerant species showed wider elevational ranges at both limits. These findings suggest that forecasts of climate-related range shifts for herb

  16. Construction of a coarse-grain quasi-classical trajectory method. I. Theory and application to N2-N2 system.

    Science.gov (United States)

    Macdonald, R L; Jaffe, R L; Schwenke, D W; Panesi, M

    2018-02-07

    This work aims to construct a reduced order model for energy transfer and dissociation in non-equilibrium nitrogen mixtures. The objective is twofold: to present the Coarse-Grain Quasi-Classical Trajectory (CG-QCT) method, a novel framework for constructing a reduced order model for diatom-diatom systems; and to analyze the physics of non-equilibrium relaxation of the nitrogen molecules undergoing dissociation in an ideal chemical reactor. The CG-QCT method couples the construction of the reduced order model under the coarse-grain model framework with the quasi-classical trajectory calculations to directly construct the reduced model without the need for computing the individual rovibrational specific kinetic data. In the coarse-grain model, the energy states are lumped together into groups containing states with similar properties, and the distribution of states within each of these groups is prescribed by a Boltzmann distribution at the local translational temperature. The required grouped kinetic properties are obtained directly by the QCT calculations. Two grouping strategies are considered: energy-based grouping, in which states of similar internal energy are lumped together, and vibrational grouping, in which states with the same vibrational quantum number are grouped together. A zero-dimensional chemical reactor simulation, in which the molecules are instantaneously heated, forcing the system into strong non-equilibrium, is used to study the differences between the two grouping strategies. The comparison of the numerical results against available experimental data demonstrates that the energy-based grouping is more suitable to capture dissociation, while the energy transfer process is better described with a vibrational grouping scheme. The dissociation process is found to be strongly dependent on the behavior of the high energy states, which contribute up to 50% of the dissociating molecules. Furthermore, up to 40% of the energy required to dissociate the

  17. A comparative study of the luminescence characteristics of polymineral fine grains and coarse-grained K-, and Na-rich feldspars

    DEFF Research Database (Denmark)

    Tsukamoto, Sumiko; Jain, Mayank; Murray, Andrew S.

    2012-01-01

    °C indicate that the signal stabilities are similar among the different feldspar types, when a higher preheat temperature (>320 °C) is used. Thermal activation energies for IRSL and pIRIR signals are largest in K-feldspar and smallest in polymineral fine grains, in both blue and UV detection windows...

  18. Isolation of high-quality RNA from grains of different maize varieties.

    Science.gov (United States)

    Messias, Rafael da Silva; Galli, Vanessa; Buss, Julieti Huch; Borowski, Joyce Moura; Nora, Leonardo; e Silva, Sérgio Delmar dos Anjos; Margis, Rogério; Rombaldi, Cesar Valmor

    2014-10-03

    The study of gene expression in maize varieties represents a powerful tool aiming to increase vitamin A precursors. However, the isolation of RNA from different maize varieties is challenging because these varieties show different levels of polysaccharides, and most methods available for RNA isolation are inappropriate for grain samples. The polysaccharides co-purify and co-precipitate with RNA during isolation, resulting in low-quality RNA, compromising the use of RNA in subsequent applications. Thus, a cetyltrimethylammonium bromide (CTAB)-based method was adapted in this study and compared with six methods for RNA isolation, including commercial reagents and RNA and DNA isolation kits, in order to identify the most appropriate for maize grains from different varieties. Most of the methods evaluated were considered inadequate due to limitations in terms of purity and/or quantity of the isolated RNA, which affected the efficiency of subsequent RT-qPCR analysis, resulting in nonamplification of β-carotene hydroxylase gene (HYD3) or high deviation among replicates. However, the CTAB modified method allowed the study to obtain intact RNA, with high quality and quantity, from 25 maize varieties. Furthermore, this RNA was successfully used to evaluate the expression of HYD3 gene by real-time qualitative polymerase chain reaction (RT-qPCR), and thus represents a simple, efficient, and low-cost strategy.

  19. Coarse-grained molecular dynamics simulations of cobra cytotoxin A3 interactions with a lipid bilayer: penetration of loops into membranes.

    Science.gov (United States)

    Su, Zhi-Yuan; Wang, Yeng-Tseng

    2011-02-10

    Cobra cytotoxins, which are small three-looped proteins composed of approximately 60 amino acid residues, primarily act by destroying the bilayer membranes of cells and artificial vesicles. However, the molecular mechanism governing this process is not yet completely understood. We used coarse-grained molecular dynamics (CGMD) simulations to study the mechanism underlying the penetration of cardiotoxin A3 (CTX A3), the major toxic component of Naja atra (Chinese cobra) venom, into a hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer. We performed CGMD simulations for three different conformations of the cobra cytotoxin-the tail, lying, and harrow conformations. The results of our simulations indicate that two of these, the tail and lying conformations, did not penetrate the bilayer system. Further, for the harrow conformation, loops 2 and 3 played important roles in penetration of CTX A3 into the bilayer system.

  20. Equation for the superfluid gap obtained by coarse graining the Bogoliubov-de Gennes equations throughout the BCS-BEC crossover

    Science.gov (United States)

    Simonucci, S.; Strinati, G. C.

    2014-02-01

    We derive a nonlinear differential equation for the gap parameter of a superfluid Fermi system by performing a suitable coarse graining of the Bogoliubov-de Gennes (BdG) equations throughout the BCS-BEC crossover, with the aim of replacing the time-consuming solution of the original BdG equations by the simpler solution of this novel equation. We perform a favorable numerical test on the validity of this new equation over most of the temperature-coupling phase diagram, by an explicit comparison with the full solution of the original BdG equations for an isolated vortex. We also show that the new equation reduces both to the Ginzburg-Landau equation for Cooper pairs in weak coupling close to the critical temperature and to the Gross-Pitaevskii equation for composite bosons in strong coupling at low temperature.

  1. Dynamics of the Glycophorin A Dimer in Membranes of Native-Like Composition Uncovered by Coarse-Grained Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Nadine Flinner

    Full Text Available Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo or unsaturated lipids (liquid-disordered character, Ld were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.

  2. Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment

    Science.gov (United States)

    Mognetti, B. M.; Virnau, P.; Yelash, L.; Paul, W.; Binder, K.; Müller, M.; MacDowell, L. G.

    2009-01-01

    The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, and short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on thermodynamic perturbation theory is discussed. Molecules are described by coarse grained models, where either the whole molecule (carbon dioxide, benzene, and methane) or a group of a few successive CH2 groups (in the case of alkanes) are lumped into an effective point particle. Interactions among these point particles are fitted by Lennard-Jones (LJ) potentials such that the vapor-liquid critical point of the fluid is reproduced in agreement with experiment; in the case of quadrupolar molecules a quadrupole-quadrupole interaction is included. These models are shown to provide a satisfactory description of the liquid-vapor phase diagram of these pure fluids. Investigations of mixtures, using the Lorentz-Berthelot (LB) combining rule, also produce satisfactory results if compared with experiment, while in some previous attempts (in which polar solvents were modeled without explicitly taking into account quadrupolar interaction), strong violations of the LB rules were required. For this reason, the present investigation is a step towards predictive modeling of polar mixtures at low computational cost. In many cases Monte Carlo simulations of such models (employing the grand-canonical ensemble together with reweighting techniques, successive umbrella sampling, and finite size scaling) yield accurate results in very good agreement with experimental data. Simulation results are quantitatively compared to an analytical approximation for the equation of state of the same model, which is computationally much more efficient, and some systematic discrepancies are discussed. These very simple coarse-grained models of small molecules developed here should be useful, e.g., for simulations of polymer solutions with such molecules as

  3. Distribution, chemical speciation, and mobility of lead and antimony originating from small arms ammunition in a coarse-grained unsaturated surface sand.

    Science.gov (United States)

    Lewis, Jeffrey; Sjöström, Jan; Skyllberg, Ulf; Hägglund, Lars

    2010-01-01

    This study quantified the heavy metal contamination caused by firing 500 high-velocity 7.62-mm jacketed Swedish military rounds. Contamination of solid and aqueous phases was studied, with Pb and Sb being the two contaminants of primary interest. The distribution of the Pb and Sb were measured in terms of depth of penetration in sand and grain size distribution of the bullet particles. The Pb- and Sb-contaminated sand was then used as a source material in two bench-scale unsaturated lysimeters to measure the transport of Pb and Sb through two coarse-grained sands, which were taken from the berms on two Swedish military small arms ranges. The lysimeters were subjected to an infiltration cycle that reproduced spring snowmelt, which is the most significant infiltration event of the year in northern climates. The levels of mobile Pb and Sb were monitored in the effluent from the lysimeters. Extended X-ray absorption fine-structure spectroscopy analysis was performed on the contaminated sands to determine Pb speciation before and after leaching. Ninety-three percent of the mass of bullets was found in the top 30 cm of sand. Lead oxide was the predominant species of Pb before and after leaching. Transport of Pb was small, with aqueous concentrations remaining stable at mobile, with solute breakthrough occurring between 5 and 14 d and concentrations rising to over 125 microg L(-1) within 1 month.

  4. Development of a method to measure unsaturated permeation properties of coarse grained material for rock filled dam (rock material); Rock fill dam soryuzai (rock zai) no fuhowa shinto tokusei sokuteiho no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Shikata, U. [Kansai Electric Power Co. Inc., Osaka (Japan)

    2000-05-10

    For discussion on safety during sudden water level drop in a rock filled dam for an adjusting reservoir of a pumped-storage power plant, non-steady permeation flow is analyzed, level of water remaining in the bank in the upperstream rock zone is estimated, and the safety factor is calculated under that water level condition. Saturated and unsaturated permeation properties of coarse grained materials such as rock material required in analyzing the non-steady permeation flow have no analysis records, hence they have been set by using the experience of the past. The present study is purposed for establishing a method to estimate from indoor experiments the saturated and unsaturated permeation properties of the rock material having equivalent grain size as the actual material, using rock type, density and grain size as the varying factors. The study is also intended to confirm that a dam shape designed by using the derived result is economically superior to the shapes designed according to the conventional methods, and cost reduction effect can be obtained. Tests have never been performed on coarse grained materials, and there is no precedent in experimenting identification of permeation properties of materials having equivalent grain size as the actual material whose maximum particle diameter may reach several ten centimeters. As a result of experiments, a method was established nearly completely, which can identify in indoor experiments the unsaturated permeation properties of coarse grained materials. (NEDO)

  5. Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake.

    Science.gov (United States)

    Lu, Jibao; Miller, Chance; Molinero, Valeria

    2017-07-21

    The design of polymer electrolyte membranes with controlled water uptake is of high importance for high-performance fuel cells, because the water content of the membranes modulates their conductivity, chemical stability and mechanical strength. The water activity aw controls the equilibrium water uptake of a system. Predicting aw of materials is currently a daunting challenge for molecular simulations, because calculations of water activity require grand canonical simulations that are extremely expensive even with classical non-polarizable force fields. Moreover, force fields do not generally reproduce aw of solutions. Here, we first present a general strategy to parameterize force fields that reproduce the experimental aw of solutions, and then implement that strategy to re-parameterize the interactions in FFcomp, a coarse-grained model for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes in which the TMA cation is attached to the PPO backbone and the Cl anion is in the mobile water nanophase. Coarse-grained models based on short-ranged potentials successfully model fuel cell membranes and other concentrated aqueous electrolyte solutions because electrostatic interactions are highly screened in these systems. The new force field, FFpvap, differs from the original FFcomp only in the parameters of the ion-ion interactions, yet it reproduces aw in TMACl solutions with accuracy within 0.5 and 3% of the experimental value in all the concentration range relevant to the operation of fuel cell membranes. We find that the heat needed to vaporize water in solutions with as little as five water molecules per ion pair is essentially the same as in pure water, despite the strong water-ion interactions and their impact on the water activity. We review the literature to demonstrate that this is independent of the model and a general feature of water solutions. FFpvap reproduces the radial distribution functions and captures well the relative

  6. Coarse-grained sediment delivery and distribution in the Holocene Santa Monica Basin, California: Implications for evaluating source-to-sink flux at millennial time scales

    Science.gov (United States)

    Romans, B.W.; Normark, W.R.; McGann, M.M.; Covault, J.A.; Graham, S.A.

    2009-01-01

    Utilizing accumulations of coarse-grained terrigenous sediment from deep-marine basins to evaluate the relative contributions of and history of controls on sediment flux through a source-to-sink system has been difficult as a result of limited knowledge of event timing. In this study, six new radiocarbon (14C) dates are integrated with five previously published dates that have been recalibrated from a 12.5-m-thick turbidite section from Ocean Drilling Program (ODP) Site 1015 in Santa Monica Basin, offshore California. This borehole is tied to high-resolution seismic-reflection profiles that cover an 1100 km2 area of the middle and lower Hueneme submarine fan and most of the basin plain. The resulting stratigraphic framework provides the highest temporal resolution for a thick-bedded Holocene turbidite succession to date, permitting an evaluation of source-to-sink controls at millennial (1000 yr) scales. The depositional history from 7 ka to present indicates that the recurrence interval for large turbidity-current events is relatively constant (300-360 yr), but the volume of sediment deposited on the fan and in the basin plain has increased by a factor of 2 over this period. Moreover, the amount of sand per event on the basin plain during the same interval has increased by a factor of 7. Maps of sediment distribution derived from correlation of seismic-reflection profiles indicate that this trend cannot be attributed exclusively to autogenic processes (e.g., progradation of depocenters). The observed variability in sediment accumulation rates is thus largely controlled by allogenic factors, including: (1) increased discharge of Santa Clara River as a result of increased magnitude and frequency of El Ni??o-Southern Oscillation (ENSO) events from ca. 2 ka to present, (2) an apparent change in routing of coarse-grained sediment within the staging area at ca. 3 ka (i.e., from direct river input to indirect, littoral cell input into Hueneme submarine canyon), and (3

  7. Experimental studies of supercritical bedforms applied to coarse-grained turbidite deposits of the Tabernas Basin (SE Spain, late Miocene)

    Science.gov (United States)

    Cartigny, Matthieu; Postma, George; Kleverlaan, Kick

    2014-05-01

    Modern submarine canyon floors are often covered with bedform patterns linked to supercritical turbidity currents, while recognition of sedimentary structures associated with such bedforms in outcrops are rare. On the basis of experimental work on bed morphodynamics and flow structure of high-density turbidity currents, a 3-dimensional bedform stability diagram and related sedimentary facies diagram have been constructed. To allow scaling of this diagram to natural flows, four non-dimensional parameters are used: 1) densimetric Froude number, 2) modified mobility parameter, 3) dimensionless grain size and 4) basal sediment concentration. Each bedform and basal sediment concentration is then linked to a characteristic facies type. Numerical and theoretical models from the literature and observations from modern turbidite depositional systems are used to estimate characteristic sizes of the bedforms for different flow types. The model is applied to the turbidite fan systems of the Tabernas Basin (SE Spain, late Miocene) and discussed along existing classical models of high density turbidity current deposits. It is concluded that the vertical sequence of supercritical bedforms have been described in these models, yet to date have never been recognized as bedforms in outcrop, presumably because of their large size that easily exceeds the dimensions of commonly available outcrop. On the basis both experimental work and outcrop studies in the Tabernas Basin (SE Spain) a conceptual three-dimensional bedform diagram for recognition of cyclic steps in outcrop is constructed. Experimental data indicates that depositional processes on the stoss-side of a cyclic step are controlled by hydraulic jump, which temporarily stalls the flow and by subsequent waxing of the flow up to supercritical again. The hydraulic jump produces large scours with soft sediment deformation (flames) preserved in Bouma Ta, while near horizontal, massive to stratified top-cut-out turbidite beds are

  8. Depositional character and preservation potential of coarse-grained sediments deposited by flood events in hyper-arid braided channels in the Rift Valley, Arava, Israel

    Science.gov (United States)

    Laronne, Jonathan B.; Shlomi, Yanai

    2007-02-01

    Four coarse-grained braided channels undergoing rapid deposition in the hyper-arid Arava Rift Valley have been studied to determine the dynamics of strata deposition by monitored flood events and to ascertain the sedimentologic character of these event deposits. The systems span granule-sand to sandy-gravel bed material having longitudinal bars with simultaneously increasing grains size, slope and bed relief. Scour and fill were monitored along cross-sections using scour chains and repeat surveys, while event strata (=fill) were described with reference to sediment calibre, type of support, grading, thickness and location. Unlike many previous investigations of gravel sedimentology, the source of information for this study involves not only stratigraphic description but also observation of the concomitant dynamics of the channel bed as expressed by the extent of event deposition. The texture of the deposited sediment generally coarsens in sympathy with the surface bed texture of the studied channels. The thickness of event-deposited sediments increases as the magnitude of flow events increases. The stratigraphic record is characterized by: (1) sub-parallel stratification, (2) no grading, (3) clast-supported gravel infilled with sand-granule matrices and (4) rapid sedimentation rates. This character is hypothesized to mirror the elevated bedload fluxes in this hyper-arid fluvial setting. Lacking densely-vegetated banks, the proximal braidplain of this arid environment often contains no extensive fine-textured floodplain successions. The depth of fill as well as the extent of strata obliteration increase with flood magnitude, explaining the increased preservation potential of event strata with increase in flood magnitude. It also explains why most event strata, including large ones, are only partially preserved.

  9. Inclusions and Microstructure of Ce-Added Weld Metal Coarse Grain Heat-Affected Zone in Twin-Wire Submerged-Arc Welding

    Science.gov (United States)

    Yu, S. F.; Yan, N.; Chen, Y.

    2016-06-01

    In high heat-input multi-pass twin-wire submerged-arc welding, weld metal of previous pass will be affected by the heat input of subsequent one and form coarse-grained heat-affected zone (CGHAZ). This study focused on the effects of welding thermal cycle on the inclusions and microstructure of Ce-alloyed weld metal CGHAZ. According to the study of inclusions and microstructure of weld metal CGHAZ, it was found that the composition and type of the inclusions did not change under the effect of welding thermal cycle. Although the inclusions were coarsened slightly, the promoting ability to acicular ferrite (AF) was not deprived after thermal cycling. There are three types of AF in weld metal CGHAZ, which include oxy-sulfides of Ce inclusions-promoted AF, home-position-precipitated AF, and sympathetic AF. Results showed more than 80% of microstructure was AF, which greatly benefited the mechanical properties of weld metal CGHAZ, even though granular bainite and M-A constituents were generated.

  10. Redefining the Protein-Protein Interface: Coarse Graining and Combinatorics for an Improved Understanding of Amino Acid Contributions to the Protein-Protein Binding Affinity.

    Science.gov (United States)

    Smith, Josh K; Jiang, Shaoyi; Pfaendtner, Jim

    2017-10-24

    The ability to intervene in biological pathways has for decades been limited by the lack of a quantitative description of protein-protein interactions (PPIs). Herein we generate and compare millions of simple PPI models for insight into the mechanisms of specific recognition and binding. We use a coarse-grained approach whereby amino acids are counted in the interface, and these counts are used as binding affinity predictors. We perform lasso regression, a modern regression technique aimed at interpretability, with every possible amino acid combination (over 10(6) unique feature sets) to select only those amino acid predictors that provide more information than noise. This approach circumvents arbitrary binning and assumptions about the binding environment that obscure other binding affinity models. Aggregated analysis of these models trained at various interfacial cutoff distances informs the roles of specific amino acids in different binding contexts. We find that a simple amino acid count model outperforms detailed intermolecular contact and binned residue type models. We identify the prevalence of serine, glycine, and tryptophan in the interface as particularly important for predicting binding affinity across a range of distance cutoffs. Although current sample size limitations prevent a robust consensus model for binding affinity prediction, our approach underscores the relevance of a residue-based description of the protein-protein interface to increase our understanding of specific interactions.

  11. Role of the Electrostatic Interactions in the Stabilization of Ionic Liquid Crystals: Insights from Coarse-Grained MD Simulations of an Imidazolium Model.

    Science.gov (United States)

    Saielli, Giacomo; Wang, Yanting

    2016-09-01

    In order to investigate the role of the electrostatic interactions in stabilizing various phases of ionic liquids, especially smectic ionic liquid crystals, we have employed a coarse-grained model of 1-hexadecyl-3-methylimidazolium nitrate, [C16mim][NO3], to perform molecular dynamics simulations with the partial charges artificially rescaled by a factor from 0.7 to 1.2. The simulated systems have been characterized by means of orientational and translational order parameters and by distribution functions. We have found that increasing the total charge of the ions strongly stabilizes the ionic smectic phase by shifting the clearing point (melting into the isotropic liquid phase) to higher temperatures, while a smaller effect is observed on the stability of the crystal phase. Our results highlight the importance of the electrostatic interactions in promoting the formation of ionic liquid crystals through microphase segregation. Moreover, as the total charge of the model is increased, we observe a transformation from a homogeneous to a nanosegregated isotropic structure typical of ionic liquids. Therefore, a connection can be established between the degree of nanosegregation of ILs and the stability of ILC phases. All the above can be understood by the competition among electrostatic interactions between charged groups (cationic head groups and anions), van der Waals interactions between nonpolar cationic tail groups, and thermal fluctuations.

  12. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Directory of Open Access Journals (Sweden)

    Alessandro Marchiori

    Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  13. Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view

    CERN Document Server

    Joyeux, Marc

    2014-01-01

    The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS protei...

  14. Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide.

    Science.gov (United States)

    Bochicchio, Davide; Pavan, Giovanni M

    2017-08-17

    We report an implicit-solvent coarse-grained (CG) model for a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer. The technical advances guaranteed by this CG model allow simulation of the self-assembly of 1000 BTA monomers and easy variation of the BTA concentration into the system down to experimental dilute conditions. In this way, we can monitor the mechanism of supramolecular polymerization as a function of the concentration at submolecular resolution exceeding the microsecond time scale. While increasing the concentration produces rapid formation of large disordered clusters that are then converted into BTA fibers, moving to very dilute concentrations favors early ordering of the oligomers in solution even at small sizes. Interestingly, we observe that below a certain concentration the oligomers that dynamically grow in solution during the self-assembly present the same level (and amplification) of order of prestacked equilibrated oligomers of the same size, meaning that concentration-dependent kinetic effects have disappeared from the polymerization mechanism.

  15. Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution

    Directory of Open Access Journals (Sweden)

    Xin Qiao

    2015-12-01

    Full Text Available We show the construction of a novel coarse grain model for simulations of HIV capsid assembly based on four structural models of HIV capsid proteins: isolated hexamer 3H47.pdb, tubular assembly 3J34.pdb, isolated pentamer 3P05.pdb and C-terminus dimer 2KOD.pdb. The data demonstrates the derivation of inter-domain motions from all atom Molecular Dynamics simulations and comparison with the motions derived from the analysis of solution NMR results defined in 2M8L.pdb. Snapshots from a representative Monte Carlo simulation with 128 dimeric subunit proteins based on 3J34.pdb are shown in addition to the quantitative analysis of its assembly pathway. Movies of the assembly process are compiled with snapshots of representative simulations of four structural models. The methods and data in this article were utilized in Qiao et al. (in press [1] to probe the mechanism of polymorphism and curvature control of HIV capsid assembly.

  16. Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

    Science.gov (United States)

    Karczyńska, Agnieszka S; Czaplewski, Cezary; Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Liwo, Adam

    2017-12-05

    Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template-restrained canonical molecular dynamics (MD), multiplexed replica-exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse-grained UNRES force field on nine selected proteins, with pseudo-harmonic log-Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non-ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor-quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Coarse Grained Exponential Variational Autoencoders

    KAUST Repository

    Sun, Ke

    2017-02-25

    Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually much more sophisticated. To break this limitation and apply arbitrary parametric distribution during inference, this paper derives a \\\\emph{semi-continuous} latent representation, which approximates a continuous density up to a prescribed precision, and is much easier to analyze than its continuous counterpart because it is fundamentally discrete. We showcase the proposition by applying polynomial exponential family distributions as the posterior, which are universal probability density function generators. Our experimental results show consistent improvements over commonly used VAE models.

  18. Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines.

    Science.gov (United States)

    Kravats, Andrea N; Tonddast-Navaei, Sam; Stan, George

    2016-01-01

    Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation.

  19. Self-assembly dynamics for the transition of a globular aggregate to a fibril network of lysozyme proteins via a coarse-grained Monte Carlo simulation

    Directory of Open Access Journals (Sweden)

    R. B. Pandey

    2015-09-01

    Full Text Available The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues with different numbers of protein chains, Nc = 1,5,10, and 15 (concentration 0.004 – 0.063 is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1 is ultra-slow (quasi-static at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a systematic transition from a globular structure (at low T to a random coil (high T conformation when the proteins are isolated. The crossover from globular to random coil becomes sharper upon increasing the protein concentration (i.e. with Nc = 5,10, with larger Rg at higher temperatures and concentration; Rg becomes smaller on adding more protein chains (e.g. Nc = 15 a non-monotonic response to protein concentration. Analysis of the structure factor (S(q provides an estimate of the effective dimension (D ≥ 3, globular conformation at low temperature, and D ∼ 1.7, random coil, at high temperatures of the isolated protein. With many interacting proteins, the morphology of the self-assembly varies with scale, i.e. at the low temperature (T = 0.015, D ∼ 2.9 on the scale comparable to the radius of gyration of the protein, and D ∼ 2.3 at the large scale over the entire sample. The global network of fibrils appears at high temperature (T = 0.021 with D ∼ 1.7 (i.e. a random coil morphology at large scale involving tenuous distribution of micro-globules (at small scales.

  20. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations.

    Science.gov (United States)

    Frappier, Vincent; Najmanovich, Rafael J

    2014-04-01

    Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.

  1. An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions.

    Directory of Open Access Journals (Sweden)

    Yanping Fan

    Full Text Available In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs. The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+, divalent (Mg(2+ or trivalent (Co(NH(3(6 (3+ cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+, to partial aggregation with Mg(2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.

  2. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

    Science.gov (United States)

    Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H

    2014-11-10

    cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

    Science.gov (United States)

    Condon, Joshua E; Jayaraman, Arthi

    2017-10-04

    Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (Tm) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (Ta) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA Tm in these systems, as the number of ONA-star polymer arms increase, the assembly temperature Ta increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

  4. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations.

    Directory of Open Access Journals (Sweden)

    Vincent Frappier

    2014-04-01

    Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.

  5. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Farmer, B. L.

    2009-01-01

    Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.

  6. GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential.

    Science.gov (United States)

    Chen, Wenduo; Zhu, Youliang; Cui, Fengchao; Liu, Lunyang; Sun, Zhaoyan; Chen, Jizhong; Li, Yunqi

    2016-01-01

    Gay-Berne (GB) potential is regarded as an accurate model in the simulation of anisotropic particles, especially for liquid crystal (LC) mesogens. However, its computational complexity leads to an extremely time-consuming process for large systems. Here, we developed a GPU-accelerated molecular dynamics (MD) simulation with coarse-grained GB potential implemented in GALAMOST package to investigate the LC phase transitions for mesogens in small molecules, main-chain or side-chain polymers. For identical mesogens in three different molecules, on cooling from fully isotropic melts, the small molecules form a single-domain smectic-B phase, while the main-chain LC polymers prefer a single-domain nematic phase as a result of connective restraints in neighboring mesogens. The phase transition of side-chain LC polymers undergoes a two-step process: nucleation of nematic islands and formation of multi-domain nematic texture. The particular behavior originates in the fact that the rotational orientation of the mesogenes is hindered by the polymer backbones. Both the global distribution and the local orientation of mesogens are critical for the phase transition of anisotropic particles. Furthermore, compared with the MD simulation in LAMMPS, our GPU-accelerated code is about 4 times faster than the GPU version of LAMMPS and at least 200 times faster than the CPU version of LAMMPS. This study clearly shows that GPU-accelerated MD simulation with GB potential in GALAMOST can efficiently handle systems with anisotropic particles and interactions, and accurately explore phase differences originated from molecular structures.

  7. GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential.

    Directory of Open Access Journals (Sweden)

    Wenduo Chen

    Full Text Available Gay-Berne (GB potential is regarded as an accurate model in the simulation of anisotropic particles, especially for liquid crystal (LC mesogens. However, its computational complexity leads to an extremely time-consuming process for large systems. Here, we developed a GPU-accelerated molecular dynamics (MD simulation with coarse-grained GB potential implemented in GALAMOST package to investigate the LC phase transitions for mesogens in small molecules, main-chain or side-chain polymers. For identical mesogens in three different molecules, on cooling from fully isotropic melts, the small molecules form a single-domain smectic-B phase, while the main-chain LC polymers prefer a single-domain nematic phase as a result of connective restraints in neighboring mesogens. The phase transition of side-chain LC polymers undergoes a two-step process: nucleation of nematic islands and formation of multi-domain nematic texture. The particular behavior originates in the fact that the rotational orientation of the mesogenes is hindered by the polymer backbones. Both the global distribution and the local orientation of mesogens are critical for the phase transition of anisotropic particles. Furthermore, compared with the MD simulation in LAMMPS, our GPU-accelerated code is about 4 times faster than the GPU version of LAMMPS and at least 200 times faster than the CPU version of LAMMPS. This study clearly shows that GPU-accelerated MD simulation with GB potential in GALAMOST can efficiently handle systems with anisotropic particles and interactions, and accurately explore phase differences originated from molecular structures.

  8. Seasonal and directional variations of aeolian sediment transport on the coarse-grained zibar surface of the Kumtagh Desert, NW China

    Science.gov (United States)

    Qian, Guangqiang; Yang, Zhuanling; Dong, Zhibao; Luo, Wanyin; Zhang, Zhengcai; Lu, Junfeng

    2016-04-01

    The aeolian process over fine to medium sand beds has been thoroughly discussed based on short-term, in-situ observations and wind tunnel tests. However, little is known about the long period variation of aeolian sediment transport as well as the geomorphological significance of saltating process, in particular, on the coarse-grained surface. By means of a segmented, eight-directional sand trap (SEDST) designed by the authors, the aeolian sediment transport on zibar surface was measured in the Kumtagh Desert of NW China. The SEDST has eight sub-traps faced to eight directions, each sub-trap contains a vertical array of samplers with four openings at 0 - 0.1 m, 0.1 - 0.2 m, 0.2 - 0.4 m and 0.4 - 1.0 m, respectively. Each opening is connected with an underground sand chamber. During the 1-yr field observation since May 2014, sediments were collected for six times with an interval of 1 to 3 months depending on the wind strength. The total weight of the captured sediments is 314.76 kg and most of them (54%) were transported within 0.1 m above the ground. The sediment transport rate ranges from 0.43 to 64.47 g/m.min for the six runs, the maximum transport rate occurred during the period of Aug to Oct 2014 with sediments from the north direction. The annual mean transport rate changes between 11.81 and 28.49 g/m.min and the sediments are mainly blown from the N, NE and NW directions. The resultant sediment transport direction (net transport) is SSE (172.92°), which implies the major sediment source direction. The sediment flux profiles can be fitted with the exponential decay function for six runs and all directions. Three groups can be identified from the gradients of the fitting curves, i.e. the N, NE and NW cluster, the S and SE cluster, as well as the E, SE and W cluster. Each cluster represents a particular combination of sediment source features and geomorphological settings that may significantly affect the formation process of zibars. The sediment transport

  9. SAFT-γ force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes.

    Science.gov (United States)

    Avendaño, Carlos; Lafitte, Thomas; Adjiman, Claire S; Galindo, Amparo; Müller, Erich A; Jackson, George

    2013-03-07

    In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement

  10. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nishizawa, Manami; Nishizawa, Kazuhisa, E-mail: kazunet@med.teikyo-u.ac.jp [Teikyo University School of Medical Technology, Itabashi, Tokyo (Japan)

    2014-08-21

    Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT{sup OPLS}). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT{sup OPLS} PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT{sup CHARMM}) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT{sup OPLS} PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA){sub 3} peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These

  11. High-Resolution Coarse-Grained Model of Hydrated Anion-Exchange Membranes that Accounts for Hydrophobic and Ionic Interactions through Short-Ranged Potentials.

    Science.gov (United States)

    Lu, Jibao; Jacobson, Liam C; Perez Sirkin, Yamila A; Molinero, Valeria

    2017-01-10

    Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution. Here, we develop a high-resolution CG force field for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes compatible with the mW water model using a hierarchical parametrization approach based on Uncertainty Quantification and reference atomistic simulations modeled with the Generalized Amber Force Field (GAFF) and TIP4P/2005 water. The parametrization weighs multiple properties, including coordination numbers, radial distribution functions (RDFs), self-diffusion coefficients of water and ions, relative vapor pressure of water in the solution, hydration enthalpy of the tetramethylammonium chloride (TMACl) salt, and cohesive energy of its aqueous solutions. We analyze the interdependence between properties and address how to compromise between the accuracies of the properties to achieve an overall best representability. Our optimized CG model FFcomp quantitatively reproduces the diffusivities and RDFs of the reference atomistic model and qualitatively reproduces the experimental relative vapor pressure of water in solutions of tetramethylammonium chloride. These properties are of utmost relevance for the design and operation of fuel cell membranes. To our knowledge, this is the first CG model that includes explicitly each water and ion and accounts for hydrophobic, ionic, and intramolecular interactions explicitly

  12. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

    Science.gov (United States)

    Xia, Fei; Jin, Guoqing

    2014-06-01

    PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

  13. Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA.

    Science.gov (United States)

    Xia, Fei; Dou, Yong; Zhou, Xingming; Yang, Xuejun; Xu, Jiaqing; Zhang, Yang

    2009-01-30

    In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design. RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%. To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (ViennaPackage - 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU.

  14. Root tensile strength of grey alder and mountain maple grown on a coarse grained eco-engineered slope in the Swiss Alps related to wood anatomical features

    Science.gov (United States)

    Kink, Dimitri; Bast, Alexander; Meyer, Christine; Meier, Wolfgang; Egli, Markus; Gärtner, Holger

    2014-05-01

    . In order to confirm this assumption and possibly find more important root properties which have an influence on soil stabilization, the root systems of seven trees (three grey alder, four mountain maple) were excavated and analyzed. The study site is a catchment, where shallow landslides are common. It is located in the Prättigau valley in the Eastern Swiss Alps and was eco-engineered in 1997. The substrate is coarse-grained morainic material, mean annual air temperature reaches 4.64°C, average precipitation is 1170 mm, and the altitude is about 1000 m a.s.l.. The root system of each tree was uncovered carefully by hand to keep the roots undamaged, before removal it was photographed in situ to document the root distribution. The root systems were then cut into single root pieces of about 20 cm length and the position of each sample was documented. The root samples were then hierarchically classified in several root classes. The tensile strength of more than 500 samples was determined. In addition, the values for age, diameter, and root moisture were ascertained. Since it was assumed, that the cellular structure of the roots has an influence on the tensile strength, two microscopic thin-sections were prepared from all successfully tested root samples. The microscopic analysis focused on anatomical parameters such as the size and number of vessels, their distribution as well as their conductivity. The results for the final correlation between the anatomical characteristics and the root's tensile strength are presented for both tree species.

  15. Erosion and deposition by supercritical density flows during channel avulsion and backfilling: Field examples from coarse-grained deepwater channel-levée complexes (Sandino Forearc Basin, southern Central America)

    Science.gov (United States)

    Lang, Jörg; Brandes, Christian; Winsemann, Jutta

    2017-03-01

    Erosion and deposition by supercritical density flows can strongly impact the facies distribution and architecture of submarine fans. Field examples from coarse-grained channel-levée complexes from the Sandino Forearc Basin (southern Central America) show that cyclic-step and antidune deposits represent common sedimentary facies of these depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. During channel avulsion, large-scale scour-fill complexes (18 to 29 m deep, 18 to 25 m wide, 60 to > 120 m long) were incised by supercritical density flows. The multi-storey infill of the large-scale scour-fill complexes comprises amalgamated massive, normally coarse-tail graded or widely spaced subhorizontally stratified conglomerates and pebbly sandstones, interpreted as deposits of the hydraulic-jump zone of cyclic steps. The large-scale scour-fill complexes can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump zone deposits. Channel fills include repeated successions deposited by cyclic steps with superimposed antidunes. The deposits of the hydraulic-jump zone of cyclic steps comprise regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m long) infilled by intraclast-rich conglomerates or pebbly sandstones, displaying normal coarse-tail grading or backsets. These deposits are laterally and vertically associated with subhorizontally stratified, low-angle cross-stratified or sinusoidally stratified sandstones and pebbly sandstones, which were deposited by antidunes on the stoss side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation rate, grain-size distribution and amalgamation. The deposits of small-scale cyclic

  16. Percent Coarse in wells in 15 meter increments and Texture Model Percent Coarse at Lattice Points for the Central Valley from Faunt (2009)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital dataset contains the percentage of coarse-grained deposits in wells in 15 meter increments and the percentage of coarse-grained deposits in texture...

  17. Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field

    Science.gov (United States)

    Franco-Gonzalez, Juan Felipe; Ramos, Javier; Cruz, Victor L.; Martinez-Salazar, Javier

    2014-11-01

    Coarse grained (CG) modeling has been applied to study the influence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. We will show that the Martini model performs satisfactorily well, giving results well-matched with those obtained by atomistic models as well as with the experimental information existing on homolog receptors. For example, the extra and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting effect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These findings might help to understand the effect of the antibody on the receptor bioactivity.

  18. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

    Science.gov (United States)

    Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

    2015-05-12

    Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

  19. MicroRNA172 plays a critical role in wheat spike morphogenesis and grain threshability

    Science.gov (United States)

    Wheat domestication from wild species involved mutations in the Q gene. The q allele (wild wheats) is associated with elongated spikes and hulled grains, whereas the mutant Q allele (domesticated wheats) confers subcompact spikes and free-threshing grains. Previous studies showed that Q encodes an ...

  20. Effect of Zr Addition on the Microstructure and Toughness of Coarse-Grained Heat-Affected Zone with High-Heat Input Welding Thermal Cycle in Low-Carbon Steel

    Science.gov (United States)

    Shi, Ming-hao; Yuan, Xiao-guang; Huang, Hong-jun; Zhang, Si

    2017-07-01

    Microstructures and toughness of coarse-grained heat-affected zone (CGHAZ) with high-heat input welding thermal cycle in Zr-containing and Zr-free low-carbon steel were investigated by means of welding thermal cycle simulation. The specimens were subjected to a welding thermal cycle with heat inputs of 100, 400, and 800 kJ cm-1 at peak temperature of 1673 K (1400 °C) using a thermal simulator. The results indicate that excellent impact toughness at the CGHAZ was obtained in Zr-containing steel. The Zr oxide is responsible for AF transformation, providing the nucleation site for the formation AF, promoting the nucleation of AF on the multi-component inclusions. High fraction of acicular ferrite (AF) appears in Zr-containing steel, acting as an obstacle to cleavage propagation due to its high-angle grain boundary. The morphology of M-A constituents plays a key role in impact toughness of CGHAZ. Large M-A constituents with lath form can assist the micro-crack initiation and seriously decrease the crack initiation energy. The relationship of AF transformation and M-A constituents was discussed in detail.

  1. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals

    Science.gov (United States)

    Singh, Amit Kumar; Singh, Rakesh; Subramani, Rajkumar; Kumar, Rajesh; Wankhede, Dhammaprakash P.

    2016-01-01

    Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer’s preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains. PMID:27252585

  2. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    Science.gov (United States)

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  3. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).

    Science.gov (United States)

    Pont, Caroline; Murat, Florent; Confolent, Carole; Balzergue, Sandrine; Salse, Jérôme

    2011-12-02

    Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes. We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a set of 37,695 non-redundant sequence clusters, which is an unprecedented resolution corresponding to an estimated half of the wheat genome unigene repertoire. Using the Brachypodium distachyon genome as a reference for the Triticeae, we classified gene clusters into orthologous, paralogous, and homoeologous relationships. Based on this wheat gene evolutionary classification, older duplicated copies (dating back 50 to 70 million years) exhibit more than 80% gene loss and expression divergence while recent duplicates (dating back 1.5 to 3 million years) show only 54% gene loss and 36 to 49% expression divergence. We suggest that structural shuffling due to duplicated gene loss is a rapid process, whereas functional shuffling due to neo- and/or subfunctionalization of duplicates is a longer process, and that both shuffling mechanisms drive functional redundancy erosion. We conclude that, as a result of these mechanisms, half the gene duplicates in plants are structurally and functionally altered within 10 million years of evolution, and the diploidization process is completed after 45 to 50 million years following polyploidization.

  4. HIRENASD coarse unstructured

    Data.gov (United States)

    National Aeronautics and Space Administration — Unstructured HIRENASD mesh: - coarse size (5.7 million nodes, 14.4 million elements) - for node centered solvers - 01.06.2011 - caution: dimensions in mm

  5. RNA Interference of the Ecdysone Receptor Genes EcR and USP in Grain Aphid (Sitobion avenae F.) Affects Its Survival and Fecundity upon Feeding on Wheat Plants.

    Science.gov (United States)

    Yan, Ting; Chen, Hongmei; Sun, Yongwei; Yu, Xiudao; Xia, Lanqin

    2016-12-14

    RNA interference (RNAi) has been widely used in functional genomics of insects and received intensive attention in the development of RNAi-based plants for insect control. Ecdysone receptor (EcR) and ultraspiracle protein (USP) play important roles in molting, metamorphosis, and reproduction of insects. EcR and USP orthologs and their function in grain aphid (Sitobion avenae F.) have not been documented yet. Here, RT-PCR, qRT-PCR, dsRNA feeding assay and aphid bioassay were employed to isolate EcR and USP orthologs in grain aphid, investigate their expression patterns, and evaluate the effect of RNAi on aphid survival and fecundity, and its persistence. The results indicated that SaEcR and SaUSP exhibited similar expression profiles at different developmental stages. Oral administration of dsRNAs of SaEcR and dsSaUSP significantly decreased the survival of aphids due to the down-regulation of these two genes, respectively. The silencing effect was persistent and transgenerational, as demonstrated by the reduced survival and fecundity due to knock-down of SaEcR and SaUSP in both the surviving aphids and their offspring, even after switching to aphid-susceptible wheat plants. Taken together, our results demonstrate that SaEcR and SaUSP are essential genes in aphid growth and development, and could be used as RNAi targets for wheat aphid control.

  6. Fatgraph models of RNA structure

    Directory of Open Access Journals (Sweden)

    Huang Fenix

    2017-01-01

    Full Text Available In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs.We motivate and discuss the main intuition behind the fatgraph model and showcase its applicability to canonical as well as noncanonical base pairs. Recent discoveries regarding novel recursions of pseudoknotted (pk configurations as well as their translation into context-free grammars for pk-structures are discussed. This is shown to allow for extending the concept of partition functions of sequences w.r.t. a fixed structure having non-crossing arcs to pk-structures. We discuss minimum free energy folding of pk-structures and combine these above results outlining how to obtain an inverse folding algorithm for PK structures.

  7. Compositions of coarse and fine particles in martian soils at gale: A window into the production of soils

    Science.gov (United States)

    Cousin, A.; Meslin, P. Y.; Wiens, R. C.; Rapin, W.; Mangold, N.; Fabre, C.; Gasnault, O.; Forni, O.; Tokar, R.; Ollila, A.; Schröder, S.; Lasue, J.; Maurice, S.; Sautter, V.; Newsom, H.; Vaniman, D.; Le Mouélic, S.; Dyar, D.; Berger, G.; Blaney, D.; Nachon, M.; Dromart, G.; Lanza, N.; Clark, B.; Clegg, S.; Goetz, W.; Berger, J.; Barraclough, B.; Delapp, D.

    2015-03-01

    The ChemCam instrument onboard the Curiosity rover provides for the first time an opportunity to study martian soils at a sub-millimeter resolution. In this work, we analyzed 24 soil targets probed by ChemCam during the first 250 sols on Mars. Using the depth profile capability of the ChemCam LIBS (Laser-Induced Breakdown Spectroscopy) technique, we found that 45% of the soils contained coarse grains (>500 μm). Three distinct clusters have been detected: Cluster 1 shows a low SiO2 content; Cluster 2 corresponds to coarse grains with a felsic composition, whereas Cluster 3 presents a typical basaltic composition. Coarse grains from Cluster 2 have been mostly observed exposed in the vicinity of the landing site, whereas coarse grains from Clusters 1 and 3 have been detected mostly buried, and were found all along the rover traverse. The possible origin of these coarse grains was investigated. Felsic (Cluster 2) coarse grains have the same origin as the felsic rocks encountered near the landing site, whereas the origin of the coarse grains from Clusters 1 and 3 seems to be more global. Fine-grained soils (particle size Gale. Although they contain a certain amount of hydrated amorphous component depleted in SiO2, possibly present as a surface coating, their overall chemical homogeneity and their close-to-basaltic composition suggest limited, or isochemical alteration, and a limited interaction with liquid water. Fine particles and coarse grains from Cluster 1 have a similar composition, and the former could derive from weathering of the latter. Overall martian soils have a bulk composition between that of fine particles and coarse grains. This work shows that the ChemCam instrument provides a means to study the variability of soil composition at a scale not achievable by bulk chemical analyses.

  8. Expression of Arabidopsis glycine-rich RNA-binding protein AtGRP2 or AtGRP7 improves grain yield of rice (Oryza sativa) under drought stress conditions.

    Science.gov (United States)

    Yang, Deok Hee; Kwak, Kyung Jin; Kim, Min Kyung; Park, Su Jung; Yang, Kwang-Yeol; Kang, Hunseung

    2014-01-01

    Although posttranscriptional regulation of RNA metabolism is increasingly recognized as a key regulatory process in plant response to environmental stresses, reports demonstrating the importance of RNA metabolism control in crop improvement under adverse environmental stresses are severely limited. To investigate the potential use of RNA-binding proteins (RBPs) in developing stress-tolerant transgenic crops, we generated transgenic rice plants (Oryza sativa) that express Arabidopsis thaliana glycine-rich RBP (AtGRP) 2 or 7, which have been determined to harbor RNA chaperone activity and confer stress tolerance in Arabidopsis, and analyzed the response of the transgenic rice plants to abiotic stresses. AtGRP2- or AtGRP7-expressing transgenic rice plants displayed similar phenotypes comparable with the wild-type plants under high salt or cold stress conditions. By contrast, AtGRP2- or AtGRP7-expressing transgenic rice plants showed much higher recovery rates and grain yields compared with the wild-type plants under drought stress conditions. The higher grain yield of the transgenic rice plants was due to the increases in filled grain numbers per panicle. Collectively, the present results show the importance of posttranscriptional regulation of RNA metabolism in plant response to environmental stress and suggest that GRPs can be utilized to improve the yield potential of crops under stress conditions. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  9. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

    Science.gov (United States)

    Jain, Swati; Schlick, Tamar

    2017-11-24

    Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Vesicles and vesicle fusion: coarse-grained simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    Biological cells are highly dynamic, and continually move material around their own volume and between their interior and exterior. Much of this transport encapsulates the material inside phospholipid vesicles that shuttle to and fro, fusing with, and budding from, other membranes. A feature of v...

  11. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560 012, India; Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bengaluru 560 012, India; Department of Chemistry, R V Engineering College, Mysore Road, Bangalore, Karnataka 560 059, India; Center for ...

  12. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Rajat Desikan

    lectin CEL-III heptamerizes via a large struc- tural transition from α-barrel during the transmem- brane pore formation process J. Biol. Chem. 289. 12805. 46. TanakaK,CaaveiroJMM,MoranteK,González-Manas. J M and Tsumoto K 2015 Structural basis for self- assembly of a cytolytic pore lined by protein and lipid. Nat.

  13. MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers

    NARCIS (Netherlands)

    Lopez, Cesar A.; Bellesia, Giovanni; Redondo, Antonio; Langan, Paul; Chundawat, Shishir P. S.; Dale, Bruce E.; Marrink, Siewert J.; Gnanakaran, S.

    2015-01-01

    Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and

  14. Towards Software Defined Radios Using Coarse-Grained Reconfigurable Hardware

    NARCIS (Netherlands)

    Rauwerda, G.K.; Jha, N.K.; Heysters, P.M.; Smit, Gerardus Johannes Maria

    Mobile wireless terminals tend to become multimode wireless communication devices. Furthermore, these devices become adaptive. Heterogeneous reconfigurable hardware provides the flexibility, performance, and efficiency to enable the implementation of these devices. The implementation of a wideband

  15. Geometry and Coarse-Grained Representations of Landscapes

    DEFF Research Database (Denmark)

    Qin, Jing; Stadler, Peter; Klemm, Konstantin

    2014-01-01

    Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and ComputationVolume 6, 2014, pp 153-176......Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and ComputationVolume 6, 2014, pp 153-176...

  16. Coarsegrained molecular dynamics simulation of cross – linking ...

    African Journals Online (AJOL)

    user

    properties thus derived are essentially 'parameter-free', 'first principle' estimates. ... We apply the same procedure as outline in Tschop et al. .... NPT control. ... boundary conditions applied simulate an infinite slab of crosslinked DGEBA ... crosslinking continuous pathways spanning the thickness of the layer are established.

  17. Coarse graining of master equations with fast and slow states

    DEFF Research Database (Denmark)

    Pigolotti, Simone; Vulpiani, Angelo

    2008-01-01

    We propose a general method for simplifying master equations by eliminating from the description rapidly evolving states. The physical recipe we impose is the suppression of these states and a renormalization of the rates of all the surviving states. In some cases, this decimation procedure can...... be analytically carried out and is consistent with other analytical approaches, such as in the problem of the random walk in a double well potential. We discuss the application of our method to nontrivial examples: diffusion in a lattice with defects and a model of an enzymatic reaction outside the steady state...

  18. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions

    Science.gov (United States)

    Shi, Ya-Zhou; Jin, Lei; Wang, Feng-Hua; Zhu, Xiao-Long; Tan, Zhi-Jie

    2015-01-01

    A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions. PMID:26682822

  19. Theoretical Analysis of Non-equilibrium Grain Boundaries Diffusion Properties Recovery during Ultra-fine Grain Metals and Alloys Annealing

    Directory of Open Access Journals (Sweden)

    Vladimir N. Chuvil’deev

    2013-01-01

    Full Text Available The article presents the results of theoretical analysis of non-equilibrium grain boundaries diffusion properties recovery during ultra-fine grain (UFG materials annealing, produced by severe plastic deformation (SPD method. The paper proves that activation energy and grain boundary diffusion coefficient of UFG materials depend on density of defects, cumulated by grain boundary during SPD.Annealing causes diffusion redistribution of defects in grain boundaries, which results in diffusion properties change. Diffusion properties recovery rate depends on grain size and it is much higher in UFG materials than in coarse-grained materials.

  20. Grain orientation dependence of deformation twinning in pure Cu subjected to dynamic plastic deformation

    DEFF Research Database (Denmark)

    Hong, C.S.; Tao, N.R.; Lu, K.

    2009-01-01

    A clear grain orientation dependence of deformation twinning has been identified in coarse-grained copper subjected to dynamic plastic deformation. Deformation twins tend to occur in grains with orientations near the [0 0 1] corner but not in grains near the [1 0 1] corner, which can be explained...

  1. Continuous coarse ash depressurization system

    Science.gov (United States)

    Liu, Guohai; Peng, Wan Wang; Vimalchand, Pannalal

    2012-11-13

    A system for depressurizing and cooling a high pressure, high temperature dense phase solids stream having coarse solid particles with entrained gas therein. In one aspect, the system has an apparatus for at least partially depressurizing and cooling the high pressure, high temperature dense phase solids stream having gas entrained therein and a pressure letdown device for further depressurization and separating cooled coarse solid particles from a portion of the entrained gas, resulting in a lower temperature, lower pressure outlet of solid particles for downstream processing or discharge to a storage silo for future use and/or disposal. There are no moving parts in the flow path of the solids stream in the system.

  2. Sticking properties of ice grains

    Science.gov (United States)

    Jongmanns, M.; Kumm, M.; Wurm, G.; Wolf, D. E.; Teiser, J.

    2017-06-01

    We study the size dependence of pull-off forces of water ice in laboratory experiments and numerical simulations. To determine the pull-off force in our laboratory experiments, we use a liquid nitrogen cooled centrifuge. Depending on its rotation frequency, spherical ice grains detach due to the centrifugal force which is related to the adhesive properties. Numerical simulations are conducted by means of molecular dynamics simulations of hexagonal ice using a standard coarse-grained water potential. The pull-off force of a single contact between two spherical ice grains is measured due to strain controlled simulations. Both, the experimental study and the simulations reveal a dependence between the pull-off force and the (reduced) particle radii, which differ significantly from the linear dependence of common contact theories.

  3. Sticking properties of ice grains

    Directory of Open Access Journals (Sweden)

    Jongmanns M.

    2017-01-01

    Full Text Available We study the size dependence of pull-off forces of water ice in laboratory experiments and numerical simulations. To determine the pull-off force in our laboratory experiments, we use a liquid nitrogen cooled centrifuge. Depending on its rotation frequency, spherical ice grains detach due to the centrifugal force which is related to the adhesive properties. Numerical simulations are conducted by means of molecular dynamics simulations of hexagonal ice using a standard coarse-grained water potential. The pull-off force of a single contact between two spherical ice grains is measured due to strain controlled simulations. Both, the experimental study and the simulations reveal a dependence between the pull-off force and the (reduced particle radii, which differ significantly from the linear dependence of common contact theories.

  4. Grain boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Balluffi, R.W.; Bristowe, P.D.

    1991-01-01

    The present document is a progress report describing the work accomplished to date during the second year of our four-year grant (February 15, 1990--February 14, 1994) to study grain boundaries. The research was focused on the following three major efforts: Study of the atomic structure of grain boundaries by means of x-ray diffraction, transmission electron microscopy and computer modeling; study of short-circuit diffusion along grain boundaries; and development of a Thin-film Deposition/Bonding Apparatus for the manufacture of high purity bicrystals.

  5. Grain boundaries

    Science.gov (United States)

    Balluffi, R. W.; Bristowe, P. D.

    The present document is a progress report describing the work accomplished to date during the second year of our four-year grant (February 15, 1990 to February 14, 1994) to study grain boundaries. The research was focused on the following three major efforts: study of the atomic structure of grain boundaries by means of x-ray diffraction, transmission electron microscopy and computer modeling; study of short-circuit diffusion along grain boundaries; and development of a Thin-film Deposition/Bonding Apparatus for the manufacture of high purity bicrystals.

  6. Preparation of bimodal grain size 7075 aviation aluminum alloys and their corrosion properties

    Directory of Open Access Journals (Sweden)

    Wenming TIAN

    2017-10-01

    Full Text Available The bimodal grain size metals show improved strength and ductility compared to traditional metals; however, their corrosion properties are unknown. In order to evaluate the corrosion properties of these metals, the bimodal grain size 7075 aviation aluminum alloys containing different ratios of coarse (100 μm in diameter and fine (10 μm in diameter grains were prepared by spark plasma sintering (SPS. The effects of grain size as well as the mixture degree of coarse and fine grains on general corrosion were estimated by immersion tests, electrochemical measurements and complementary techniques such as scanning electron microscope (SEM and transmission electron microscope-energy disperse spectroscopy (TEM-EDS. The results show that, compared to fine grains, the coarse grains have a faster dissolution rate in acidic NaCl solution due to the bigger size, higher alloying elements content and larger area fraction of second phases in them. In coarse grains, the hydrogen ions have a faster reduction rate on cathodic second phases, therefore promoting the corrosion propagation. The mixture of coarse and fine grains also increases the electrochemical heterogeneity of alloys in micro-scale, and thus the increased mixture degree of these grains in metal matrix accelerates the corrosion rate of alloys in acidic NaCl solution.

  7. RNAmute: RNA secondary structure mutation analysis tool

    Directory of Open Access Journals (Sweden)

    Barash Danny

    2006-04-01

    Full Text Available Abstract Background RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation. Results Selecting a category in each one of the processed tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical drawing of the single point mutation and the wild type, and includes basic information such as associated energies, representations and distances. RNAMute can be used successfully with very little previous experience and without choosing any parameter value alongside the initial RNA sequence. The package runs under LINUX operating system. Conclusion RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs. In several cases of substantial interest, notably in virology, a point mutation may lead to a loss of important functionality such as the RNA virus replication and translation initiation because of a conformational rearrangement in the secondary structure.

  8. Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes.

    Science.gov (United States)

    Li, Rongzhong; Ge, Heming W; Cho, Samuel S

    2013-10-24

    The folding of bacterial tRNAs with disparate sequences has been observed to proceed in distinct folding mechanisms despite their structural similarity. To explore the folding landscapes of tRNA, we performed ion concentration-dependent coarse-grained TIS model MD simulations of several E. coli tRNAs to compare their thermodynamic melting profiles to the classical absorbance spectra of Crothers and co-workers. To independently validate our findings, we also performed atomistic empirical force field MD simulations of tRNAs, and we compared the base-to-base distances from coarse-grained and atomistic MD simulations to empirical base-stacking free energies. We then projected the free energies to the secondary structural elements of tRNA, and we observe distinct, parallel folding mechanisms whose differences can be inferred on the basis of their sequence-dependent base-stacking stabilities. In some cases, a premature, nonproductive folding intermediate corresponding to the Ψ hairpin loop must backtrack to the unfolded state before proceeding to the folded state. This observation suggests a possible explanation for the fast and slow phases observed in tRNA folding kinetics.

  9. Coarse analysis of collective behaviors: Bifurcation analysis of the optimal velocity model for traffic jam formation

    Science.gov (United States)

    Miura, Yasunari; Sugiyama, Yuki

    2017-12-01

    We present a general method for analyzing macroscopic collective phenomena observed in many-body systems. For this purpose, we employ diffusion maps, which are one of the dimensionality-reduction techniques, and systematically define a few relevant coarse-grained variables for describing macroscopic phenomena. The time evolution of macroscopic behavior is described as a trajectory in the low-dimensional space constructed by these coarse variables. We apply this method to the analysis of the traffic model, called the optimal velocity model, and reveal a bifurcation structure, which features a transition to the emergence of a moving cluster as a traffic jam.

  10. Grain boundary and triple junction diffusion in nanocrystalline copper

    Energy Technology Data Exchange (ETDEWEB)

    Wegner, M., E-mail: m.wegner@uni-muenster.de; Leuthold, J.; Peterlechner, M.; Divinski, S. V., E-mail: divin@uni-muenster.de [Institut für Materialphysik, Universität Münster, Wilhelm-Klemm-Straße 10, D-48149, Münster (Germany); Song, X., E-mail: xysong@bjut.edu.cn [College of Materials Science and Engineering, Beijing University of Technology, 100124 Beijing (China); Wilde, G. [Institut für Materialphysik, Universität Münster, Wilhelm-Klemm-Straße 10, D-48149, Münster (Germany); Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, 200444 Shanghai (China)

    2014-09-07

    Grain boundary and triple junction diffusion in nanocrystalline Cu samples with grain sizes, 〈d〉, of ∼35 and ∼44 nm produced by spark plasma sintering were investigated by the radiotracer method using the {sup 63}Ni isotope. The measured diffusivities, D{sub eff}, are comparable with those determined previously for Ni grain boundary diffusion in well-annealed, high purity, coarse grained, polycrystalline copper, substantiating the absence of a grain size effect on the kinetic properties of grain boundaries in a nanocrystalline material at grain sizes d ≥ 35 nm. Simultaneously, the analysis predicts that if triple junction diffusion of Ni in Cu is enhanced with respect to the corresponding grain boundary diffusion rate, it is still less than 500⋅D{sub gb} within the temperature interval from 420 K to 470 K.

  11. Bimodal grain-size distribution of Chinese loess, and its palaeoclimatic implications

    NARCIS (Netherlands)

    Sun, D.G.; Bloemendal, J.; Rea, D.K.; An, Z.S.; Vandenberghe, J.; Lu, H.; Su, R.; Liu, T.S.

    2004-01-01

    Grain-size analysis indicates that Chinese loess generally shows a bimodal distribution with a coarse and a fine component. The coarse component, comprising the main part of the loess, has pronounced kurtosis and is well sorted, which is interpreted to be the product of dust storms generated by

  12. Simulations of RNA interactions with monovalent ions.

    Science.gov (United States)

    Chen, Alan A; Marucho, Marcelo; Baker, Nathan A; Pappu, Rohit V

    2009-01-01

    RNA folding and binding reactions are mediated by interactions with ions that make up the surrounding aqueous electrolytic milieu. Although Mg(2+) ions are often implicated as being crucial for RNA folding, it is known that folding is feasible in high concentrations of monovalent alkali-halide salts. Experiments have yielded important information regarding the salt dependence of RNA stability. Recent work has shown that molecular simulations based on explicit representations of solvent molecules and monovalent ions can also provide useful insights regarding the ionic atmospheres around model RNA systems. These insights can help rationalize intriguing observations regarding the dependence of RNA stability on cation type providing one pays attention to important considerations that go into the proper design of molecular simulations. These issues are discussed in detail and the methods are applied to an A-form RNA and B-form DNA sequence. The results of these simulations are compared to previous work on a kissing-loop system with analogous sequence. In particular, ionic atmospheres obtained from molecular simulations are compared to those obtained using the nonlinear Poisson Boltzmann model for continuum electrostatics for these three different nucleic acid systems. The comparisons indicate reasonable agreement in terms of coarse-grained observables such as the numbers of counterions accumulated around the solutes. However, details of the ionic atmospheres, captured in terms of spatial free energy density profiles, are quite different between the two approaches. These comparisons suggest the need for improvements in continuum models to capture sequence-specific effects, ion-ion correlation, and the effects of partial dehydration of ions. Copyright © 2009 Elsevier Inc. All rights reserved.

  13. Privacy Protection in Participatory Sensing Applications Requiring Fine-Grained Locations

    DEFF Research Database (Denmark)

    Dong, Kai; Gu, Tao; Tao, Xianping

    2010-01-01

    The emerging participatory sensing applications have brought a privacy risk where users expose their location information. Most of the existing solutions preserve location privacy by generalizing a precise user location to a coarse-grained location, and hence they cannot be applied in those...... applications requiring fine-grained location information. To address this issue, in this paper we propose a novel method to preserve location privacy by anonymizing coarse-grained locations and retaining fine-grained locations using Attribute Based Encryption (ABE). In addition, we do not assume the service...

  14. Identification of nonregular indication according to change of grain size/surface geometry in nuclear power plant (NPP reactor vessel (RV-upper head alloy 690 penetration

    Directory of Open Access Journals (Sweden)

    Kyungcho Kim

    2017-10-01

    From the computer simulation and experimental investigation results, it was possible to obtain the nonregular TOFD indications from the coarse grains in the alloy 690 penetration tube of RVHP; these nonregular indications may be classified as PWSCC. By comparing the computer simulation and experimental results, we were able to confirm a clear difference between the coarse grain signal and the PWSCC signal.

  15. NEW RSW & Wall Coarse Tet Only Grid

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the RSW Coarse Tet Only grid with the root viscous tunnel wall. This grid is for a node-based unstructured solver. Quad Surface Faces= 0 Tria Surface Faces=...

  16. NEW RSW & Wall Coarse Mixed Element Grid

    Data.gov (United States)

    National Aeronautics and Space Administration — This is the Coarse Mixed Element Grid for the RSW with a viscous wall at the root. This grid is for a node-based unstructured solver. Quad Surface Faces= 9728 Tria...

  17. Martensitic Transformation in Ultrafine-Grained Stainless Steel AISI 304L Under Monotonic and Cyclic Loading

    Directory of Open Access Journals (Sweden)

    Heinz Werner Höppel

    2012-02-01

    Full Text Available The monotonic and cyclic deformation behavior of ultrafine-grained metastable austenitic steel AISI 304L, produced by severe plastic deformation, was investigated. Under monotonic loading, the martensitic phase transformation in the ultrafine-grained state is strongly favored. Under cyclic loading, the martensitic transformation behavior is similar to the coarse-grained condition, but the cyclic stress response is three times larger for the ultrafine-grained condition.

  18. Coarse bedload routing and dispersion through tributary confluences

    Science.gov (United States)

    Imhoff, K. S.; Wilcox, A. C.

    2015-12-01

    Sediment routing fundamentally influences channel morphology and propagation of disturbances. However, the transport and storage of bedload particles in headwater channel confluences, which may be significant nodes of the channel network in terms of sediment routing, morphology, and habitat, is poorly understood. To characterize routing processes through confluences of headwater channels, we investigate how sediment routing patterns through headwater confluences compare to those described in low-gradient gravel bed river systems, and how confluences affect the dispersive behavior of coarse bedload particles compared to non-confluence reaches. We address these questions with a field tracer experiment using passive-integrated transponder and radio-frequency identification technology in the East Fork Bitterroot River basin, Montana, USA. Within the confluence zone, transport occurs along scour hole margins in narrow, efficient transport corridors that mirror those observed in finer-grained experiments and field studies. Coarse particles entering confluences experience reduced depositional probabilities, in contrast to the size-selective transport observed in a control reach. Stochastic transport modeling, tail analysis, and use of a dimensionless impulse (I*) suggest that transport distance and variance growth are enhanced through confluences for a given flow strength. We suggest that confluences absent of disturbances enhance sediment transport and dispersive growth through headwater networks.

  19. Vfold: a web server for RNA structure and folding thermodynamics prediction.

    Science.gov (United States)

    Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

    2014-01-01

    The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

  20. Experimental investigation of grain trapping capabilities in cyanobacterial vs. algal mats: Implications for grain size in stromatolites through time

    Science.gov (United States)

    Petryshyn, V.; Frantz, C. M.; Corsetti, F. A.; Shapiro, R. S.; Cox, C.; Mills, D. B.; Boidi, F.; Duran, V.; Archberger, A.

    2012-12-01

    In general, Archean and Proterozoic stromatolites are fine-grained (predominantly composed of micrite) whereas most modern marine examples are comparatively coarse-grained. Given that the modern marine forms are commonly studied as analogues to ancient forms, it is important to understand the processes responsible for these textural differences. Cyanobacteria are typically considered the dominant stromatolite builders through time, but it is well known that many modern marine stromatolites also contain, or are even dominated by, eukaryotic phototrophs. Thus, we conducted experiments to test the grain trapping and binding capabilities of cyanobacterial-dominated mats versus eukaryotic algal mats in order to better understand the grain size trends in stromatolites through time. Cyanobacterial mats were collected from Catalina Harbor by the 2012 International Geobiology Course, and eukaryotic mats consisting of filamentous algae were collected from the outflow of seawater tanks at the USC Wrigley Marine Institute on Catalina Island. Mats were cut into rectangles of known area, placed in Petri dishes of known weight, and inclined at six angles (15° increments from 0-75°) in circulating seawater tanks. Known masses of fine (0.125-0.250 mm), medium (0.50-1.0 mm), and coarse (1.0-2.0 mm) sediments were carefully delivered to the inclined mats. Mats were then exposed to one 24 hour light/dark cycle while the grains settled. The mats were removed from the tanks, dried, and imaged under SEM to assess the degree of binding of the sediment. The sediment left over in the Petri dishes was weighed, and the amount trapped by the mats was calculated by difference. The cyanobacterial mats were able to trap fine grains consistently at all angles. At angles higher than 45°, medium and coarse grains were not trapped as efficiently, essentially obeying the predicted angle of repose response. The algal mats trapped medium and coarse grains at all angles. Interestingly, the algal mats

  1. A measure on the space of RNA folding pathways: towards a new scheme of statistical inference

    Science.gov (United States)

    Fernández, Ariel

    1994-10-01

    In this work we define constructively a measure η on the space of sequential folding (SF) pathways for RNA with the aim of making probabilistic inferences on kinetically-controlled folding. This measure will be shown to be adequate for those RNA species known to search for their structure concurrently with their progressive assembling by sequential nucleotide incorporation. We shall validate our approach by showing that the measure is actually concentrated on the SF pathway that has been experimentally confirmed by pulse-chase kinetic probes. The space of SF pathways will be represented as a product of suitably coarse-grained conformation spaces, one for each length of the growing chain. In this context, the measure is induced by a Markovian stochastic process whose specific realizations are precisely the SF pathways. The coarse-graining is necessary to represent only the essential dynamics of SF: We identify rapidly-interconverting structures by regarding the folding dynamics concurrent with chain growth modulo kinetic barriers of order Nα ( {1}/{4}⩽α⩽ {1}/{2}). Thus, a pathway corresponds to a sequence of clusters of rapidly-equilibrated structures. Within this representation, we show in specific examples that the measure is concentrated solely on the biologically-significant folding pathway whose destination or final structure is functionally-competent, different appreciably from the global free energy minimum.

  2. Producing laminated NiAl with bimodal distribution of grain size by solid–liquid reaction treatment

    DEFF Research Database (Denmark)

    Fan, G.H.; Wang, Q.W.; Du, Y.

    2014-01-01

    The prospect of combining laminated structure design and grain size tailoring to toughen brittle materials is examined. Laminated NiAl consisting of coarse-grained layers and fine-grained layers was fabricated by solid–liquid reaction treatment of stacking Ni and Al foils. The fracture toughness...

  3. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.

    Science.gov (United States)

    Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M

    2014-10-01

    Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Grain interaction effects in polycrystalline Cu

    DEFF Research Database (Denmark)

    Thorning, C.; Somers, Marcel A.J.; Wert, John A.

    2005-01-01

    Crystal orientation maps for a grain in a deformed Cu polycrystal have been analysed with the goal of understanding the effect of grain interactions on orientation subdivision. The polycrystal was incrementally strained in tension to 5, 8, 15 and 25% extension; a crystal orientation map was measu......Crystal orientation maps for a grain in a deformed Cu polycrystal have been analysed with the goal of understanding the effect of grain interactions on orientation subdivision. The polycrystal was incrementally strained in tension to 5, 8, 15 and 25% extension; a crystal orientation map...... range of Tailor solutions for axisymmetric strain; grain interactions are not required to account for the coarse domain structure. Special orientation domains extend 20-100 µm into the grain at various locations around its periphery. The special orientation domain morphologies include layers along...... boundary segments, lobes that may be further subdivided, and plates. Detailed analysis of the crystal rotations in the special domains provides strong evidence that they result from grain interactions....

  5. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

    Science.gov (United States)

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

  6. Dependency of annealing behaviour on grain size in Al–TiC ...

    Indian Academy of Sciences (India)

    cycle ARB-processed Al–TiC composite having ultrafine grains. Furthermore, annealing treatment significantly enhanced elongation for both ultrafine as well as coarse-grained Al–TiC composites in spite of the fact that yield and ultimate strength ...

  7. Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.

    Science.gov (United States)

    Huang, Xuhui; Yao, Yuan; Bowman, Gregory R; Sun, Jian; Guibas, Leonidas J; Carlsson, Gunnar; Pande, Vijay S

    2010-01-01

    Simulating biologically relevant timescales at atomic resolution is a challenging task since typical atomistic simulations are at least two orders of magnitude shorter. Markov State Models (MSMs) provide one means of overcoming this gap without sacrificing atomic resolution by extracting long time dynamics from short simulations. MSMs coarse grain space by dividing conformational space into long-lived, or metastable, states. This is equivalent to coarse graining time by integrating out fast motions within metastable states. By varying the degree of coarse graining one can vary the resolution of an MSM; therefore, MSMs are inherently multi-resolution. Here we introduce a new algorithm Super-level-set Hierarchical Clustering (SHC), to our knowledge, the first algorithm focused on constructing MSMs at multiple resolutions. The key insight of this algorithm is to generate a set of super levels covering different density regions of phase space, then cluster each super level separately, and finally recombine this information into a single MSM. SHC is able to produce MSMs at different resolutions using different super density level sets. To demonstrate the power of this algorithm we apply it to a small RNA hairpin, generating MSMs at four different resolutions. We validate these MSMs by showing that they are able to reproduce the original simulation data. Furthermore, long time folding dynamics are extracted from these models. The results show that there are no metastable on-pathway intermediate states. Instead, the folded state serves as a hub directly connected to multiple unfolded/misfolded states which are separated from each other by large free energy barriers.

  8. Grain trapping by filamentous cyanobacterial and algal mats: implications for stromatolite microfabrics through time.

    Science.gov (United States)

    Frantz, C M; Petryshyn, V A; Corsetti, F A

    2015-09-01

    Archean and Proterozoic stromatolites are sparry or fine-grained and finely laminated; coarse-grained stromatolites, such as many found in modern marine systems, do not appear until quite late in the fossil record. The cause of this textural change and its relevance to understanding the evolutionary history of stromatolites is unclear. Cyanobacteria are typically considered the dominant stromatolite builders through time, but studies demonstrating the trapping and binding abilities of cyanobacterial mats are limited. With this in mind, we conducted experiments to test the grain trapping and binding capabilities of filamentous cyanobacterial mats and trapping in larger filamentous algal mats in order to better understand grain size trends in stromatolites. Mats were cut into squares, inclined in saltwater tanks at angles from 0 to 75° (approximating the angle of lamina in typical stromatolites), and grains of various sizes (fine sand, coarse sand, and fine pebbles) were delivered to their surface. Trapping of grains by the cyanobacterial mats depended strongly on (i) how far filaments protruded from the sediment surface, (ii) grain size, and (iii) the mat's incline angle. The cyanobacterial mats were much more effective at trapping fine grains beyond the abiotic slide angle than larger grains. In addition, the cyanobacterial mats actively bound grains of all sizes over time. In contrast, the much larger algal mats trapped medium and coarse grains at all angles. Our experiments suggest that (i) the presence of detrital grains beyond the abiotic slide angle can be considered a biosignature in ancient stromatolites where biogenicity is in question, and, (ii) where coarse grains are present within stromatolite laminae at angles beyond the abiotic angle of slide (e.g., most modern marine stromatolites), typical cyanobacterial-type mats are probably not solely responsible for the construction, giving insight into the evolution of stromatolite microfabrics through time.

  9. Anomalous permittivity in fine-grain barium titanate

    Science.gov (United States)

    Ostrander, Steven Paul

    Fine-grain barium titanate capacitors exhibit anomalously large permittivity. It is often observed that these materials will double or quadruple the room temperature permittivity of a coarse-grain counterpart. However, aside from a general consensus on this permittivity enhancement, the properties of the fine-grain material are poorly understood. This thesis examines the effect of grain size on dielectric properties of a self-consistent set of high density undoped barium titanate capacitors. This set included samples with grain sizes ranging from submicron to ˜20 microns, and with densities generally above 95% of the theoretical. A single batch of well characterized powder was milled, dry-pressed then isostatically-pressed. Compacts were fast-fired, but sintering temperature alone was used to control the grain size. With this approach, the extrinsic influences are minimized within the set of samples, but more importantly, they are normalized between samples. That is, with a single batch of powder and with identical green processing, uniform impurity concentration is expected. The fine-grain capacitors exhibited a room temperature permittivity of ˜5500 and dielectric losses of ˜2%. The Curie-temperature decreased by {˜}5sp°C from that of the coarse-grain material, and the two ferroelectric-ferroelectric phase transition temperatures increased by {˜}10sp°C. The grain size induced permittivity enhancement was only active in the tetragonal and orthorhombic phases. Strong dielectric anomalies were observed in samples with grain size as small as {˜}0.4\\ mum. It is suggested that the strong first-order character observed in the present data is related to control of microstructure and stoichiometry. Grain size effects on conductivity losses, ferroelectric losses, ferroelectric dispersion, Maxwell-Wagner dispersion, and dielectric aging of permittivity and loss were observed. For the fine-grain material, these observations suggest the suppression of domain wall

  10. Influence of composition, grain size, and oxide particles on the strength of consolidated ball-milled iron

    Science.gov (United States)

    Benito, J. A.; Gregoire, V.; Casas, C.; Cabrera, J. M.

    2014-08-01

    In this paper iron powders with two oxygen content (0.2 and 0.6% wt.) have been mechanically milled and consolidated by hot static pressing at different temperatures to obtain different grain sizes. At lower temperatures the grain size was in the nanostructured and ultrafine range and with increasing temperature abnormal grain growth was observed for both compositions. This led to the development of bimodal grain size distributions. In the samples with lower oxygen content the grain size and the percentage of coarse grain areas were larger than in the case of high oxygen content. The strength and ductility have been determined by tensile tests. For low oxygen content, the presence of large coarse grains allowed plastic strain in some cases, and for the samples consolidated at higher temperatures, yield strength of 865 MPa with a 8% total strain were obtained. For the samples with high oxygen content plastic deformation was no possible in any case. The observed stress for both compositions was analysed by two approaches, one based exclusively in grain boundary strengthening and the other one based in two effects acting at the same time: grain boundary and particle strengthening. Whereas grain boundary strengthening seems to fit with the strength of the samples in the nanostructured range, when coarse ferrite grains appear the addition of particle strengthening help to get better results. This indicates that the presence of oxides dissolved inside the large grains reinforce the structure of ball-milled iron.

  11. Effect of Grain Refinement on Deformation Mechanism and Mechanical Properties of Austenitic Stainless Steel

    Directory of Open Access Journals (Sweden)

    WAN Xiang-liang

    2016-08-01

    Full Text Available The concept of phase reversion involving cold deformation of metastable austenite to generate strain-induced martensite, followed by temperature-time annealing sequence, was used to obtain grain size of nanograined/ultrafine-grained and coarse-grained austenitic stainless steels. The mechanical properties of austenitic stainless steels with different grain sizes were obtained by tensile testing, the deformation microstructure and fracture surface were analyzed by TEM and SEM observations, respectively. The results indicate that deformation twins contribute to excellent ductility in high yield strength nanograined/ultrafine-grained steel, while in the low yield strength coarse-grained steel, the high ductility is due to strain-induced martensite transformation. Interestingly, the tensile fracture of the two austensite stainless steels with different deformation mechanism is ductile fracture. The deformation mechanism from deformation twins to strain-induced martensite in the coarse-grained structure in nanograined/ultrafine-grained structures is owing to the increased stability of austenite with grain refining.

  12. Early agglomeration monitor of coarse cohesive particles

    Energy Technology Data Exchange (ETDEWEB)

    Wang Xi; You Changfu; Yang Ruichang, E-mail: xiwang06@mails.tsinghua.edu.c, E-mail: youcf@tsinghua.edu.c, E-mail: yangrc@mail.tsinghua.edu.c [Key laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Thermal Engineering, Tsinghua University, Beijing 100084 (China)

    2009-02-01

    This paper established a three-dimensional visualization experimental system. Paraffin particles were chosen as a test of raw material to simulate the movement and bonded process of coarse cohesive particles. Experimental study on fluidization process of coarse cohesive particles has been done by high-speed camera. The study shows that: from the normal fluidization to shut-down, it can be divided into two phases. The former is a slower phase of the bond and the formation of core grew up phase; the second stage is the huge bonded core turn to bridge fast and shutdown happens with great velocity. Then, comparison of different methods has been done to deal with the experimental date of pressure, the results show that: Compared to the average pressure and pressure deviation method, S attractor method that is based on chaotic theory could monitor the agglomeration much earlier, reflect the degrees of bond with the specific numerical value and also demonstrate the velocity of agglomeration. Thus, it could be applied to the early monitor of agglomeration of coarse cohesive particles.

  13. Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce.

    Science.gov (United States)

    Zhang, Boyu; Yehdego, Daniel T; Johnson, Kyle L; Leung, Ming-Ying; Taufer, Michela

    2013-01-01

    Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction of the secondary structures is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole. The chunking, prediction, and reconstruction processes can use different methods and parameters, some of which produce more accurate predictions than others. In this paper, we study the prediction accuracy and efficiency of three different chunking methods using seven popular secondary structure prediction programs that apply to two datasets of RNA with known secondary structures, which include both pseudoknotted and non-pseudoknotted sequences, as well as a family of viral genome RNAs whose structures have not been predicted before. Our modularized MapReduce framework based on Hadoop allows us to study the problem in a parallel and robust environment. On average, the maximum accuracy retention values are larger than one for our chunking methods and the seven prediction programs over 50 non-pseudoknotted sequences, meaning that the secondary structure predicted using chunking is more similar to the real structure than the secondary structure predicted by using the whole sequence. We observe similar results for the 23 pseudoknotted sequences, except for the NUPACK program using the centered chunking method. The performance analysis for 14 long RNA sequences from the Nodaviridae virus family outlines how the coarse-grained mapping of chunking and predictions in the MapReduce framework exhibits shorter turnaround times for short RNA sequences. However, as the lengths of

  14. Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

    Science.gov (United States)

    Mustoe, Anthony M; Liu, Xin; Lin, Paul J; Al-Hashimi, Hashim M; Fierke, Carol A; Brooks, Charles L

    2015-03-18

    Mammalian mitochondrial tRNA(Ser(UCN)) (mt-tRNA(Ser)) and pyrrolysine tRNA (tRNA(Pyl)) fold to near-canonical three-dimensional structures despite having noncanonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these noncanonical tRNAs compensate for their loss of tertiary interactions remains unclear. Furthermore, in human mt-tRNA(Ser), lengthening the variable loop by the 7472insC mutation reduces mt-tRNA(Ser) concentration in vivo through poorly understood mechanisms and is strongly associated with diseases such as deafness and epilepsy. Using simulations of the TOPRNA coarse-grained model, we show that increased topological constraints encoded by the unique secondary structure of wild-type mt-tRNA(Ser) decrease the entropic cost of folding by ∼2.5 kcal/mol compared to canonical tRNA, offsetting its loss of tertiary interactions. Further simulations show that the pathogenic 7472insC mutation disrupts topological constraints and hence destabilizes the mutant mt-tRNA(Ser) by ∼0.6 kcal/mol relative to wild-type. UV melting experiments confirm that insertion mutations lower mt-tRNA(Ser) melting temperature by 6-9 °C and increase the folding free energy by 0.8-1.7 kcal/mol in a largely sequence- and salt-independent manner, in quantitative agreement with our simulation predictions. Our results show that topological constraints provide a quantitative framework for describing key aspects of RNA folding behavior and also provide the first evidence of a pathogenic mutation that is due to disruption of topological constraints.

  15. Ribonucleic acids of wheat grain and its endosperm during development and ripening

    Directory of Open Access Journals (Sweden)

    Stanisław Weidner

    2015-01-01

    Full Text Available The work present quantitative changes and synthesis od: RNA fractions in wheat grain and endosperm during development and ripening. It was found that share of rRNA in total RNA decreases during development both, in the endosperm and in grain. Rapid drop of rRNA content in total RNA takes place in the endosperm since 31st day after blooming, and in grain - since 45th day after blooming. Absolute amount of rRNA, as calculated per 100 grains or endosperms, increases in the first half of grain formation period, and then decreases till the end of development. As a result of degradation of ribosomal RNA in endosperm, low-molecule fraction – 4 S, significantly increased at final stage of development. Decrease of rRNA fraction at final stage of development is not accompanied by an increase of absolute amount of 4 S RNA fraction. Incorporation of 3H-,uriidine into grain and endosperm RNA is highest at the begining of development. Further on it gradually decreases till the end of development. Synthesis of RNA in grain takes place throughout the whole development. Contrary to this, no incorporation of precursor into rRNA was noted during waxy and full ripeness of wheat grain.

  16. Identifying grain-size dependent errors on global forest area estimates and carbon studies

    Science.gov (United States)

    Daolan Zheng; Linda S. Heath; Mark J. Ducey

    2008-01-01

    Satellite-derived coarse-resolution data are typically used for conducting global analyses. But the forest areas estimated from coarse-resolution maps (e.g., 1 km) inevitably differ from a corresponding fine-resolution map (such as a 30-m map) that would be closer to ground truth. A better understanding of changes in grain size on area estimation will improve our...

  17. incaRNAfbinv: a web server for the fragment-based design of RNA sequences.

    Science.gov (United States)

    Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2016-07-08

    In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Coarse mode aerosols in the High Arctic

    Science.gov (United States)

    Baibakov, K.; O'Neill, N. T.; Chaubey, J. P.; Saha, A.; Duck, T. J.; Eloranta, E. W.

    2014-12-01

    Fine mode (submicron) aerosols in the Arctic have received a fair amount of scientific attention in terms of smoke intrusions during the polar summer and Arctic haze pollution during the polar winter. Relatively little is known about coarse mode (supermicron) aerosols, notably dust, volcanic ash and sea salt. Asian dust is a regular springtime event whose optical and radiative forcing effects have been fairly well documented at the lower latitudes over North America but rarely reported for the Arctic. Volcanic ash, whose socio-economic importance has grown dramatically since the fear of its effects on aircraft engines resulted in the virtual shutdown of European civil aviation in the spring of 2010 has rarely been reported in the Arctic in spite of the likely probability that ash from Iceland and the Aleutian Islands makes its way into the Arctic and possibly the high Arctic. Little is known about Arctic sea salt aerosols and we are not aware of any literature on the optical measurement of these aerosols. In this work we present preliminary results of the combined sunphotometry-lidar analysis at two High Arctic stations in North America: PEARL (80°N, 86°W) for 2007-2011 and Barrow (71°N,156°W) for 2011-2014. The multi-years datasets were analyzed to single out potential coarse mode incursions and study their optical characteristics. In particular, CIMEL sunphotometers provided coarse mode optical depths as well as information on particle size and refractive index. Lidar measurements from High Spectral Resolution lidars (AHSRL at PEARL and NSHSRL at Barrow) yielded vertically resolved aerosol profiles and gave an indication of particle shape and size from the depolarization ratio and color ratio profiles. Additionally, we employed supplementary analyses of HYSPLIT backtrajectories, OMI aerosol index, and NAAPS (Navy Aerosol Analysis and Prediction System) outputs to study the spatial context of given events.

  19. Early deterioration of coarse woody debris.

    Energy Technology Data Exchange (ETDEWEB)

    Tainter, Frank, H.; McMinn, James, W.

    1999-02-16

    Tainter, F.H., and J.W. McMinn. 1999. Early deterioration of coarse woody debris. In: Proc. Tenth Bien. South. Silv. Res. Conf. Shreveport, LA, February 16-18, 1999. Pp. 232-237 Abstract - Coarse woody debris (CWD) is an important structural component of southern forest ecosystems. CWD loading may be affected by different decomposition rates on sites of varying quality. Bolts of red oak and loblolly pine were placed on plots at each of three (hydric, mesic. and xerlc) sites at the Savannah River Site and sampled over a I6-week period. Major changes were in moisture content and nonstructural carbohydrate content (total carbohydrates, reducing sugars, and starch) of sapwood. Early changes in nonstructural carbohydrate levels following placement of the bolts were likely due to reallocation of these materials by sapwood parenchyma cells. These carbohydrates later formed pools increasingly metabolized by bacteria and invading fungi. Most prevalent fungi in sapwood were Ceratocysfis spp. in pine and Hypoxy/on spp. in oak. Although pine sapwood became blue stained and oak sapwood exhibited yellow soft decay with black zone lines, estimators of decay (specific gravity, sodium hydroxide solubility, and holocellulose content) were unchanged during the 16-week study period. A small effect of site was detected for starch content of sapwood of both species. Fungal biomass in sapwood of both species, as measured by ergosterol content, was detectable at week zero, increased somewhat by week three and increased significantly by week 16.

  20. Microbiota of kefir grains

    Directory of Open Access Journals (Sweden)

    Tomislav Pogačić

    2013-03-01

    Full Text Available Kefir grains represent the unique microbial community consisting of bacteria, yeasts, and sometimes filamentous moulds creating complex symbiotic community. The complexity of their physical and microbial structures is the reason that the kefir grains are still not unequivocally elucidated. Microbiota of kefir grains has been studied by many microbiological and molecular approaches. The development of metagenomics, based on the identification without cultivation, is opening new possibilities for identification of previously nonisolated and non-identified microbial species from the kefir grains. Considering recent studies, there are over 50 microbial species associated with kefir grains. The aim of this review is to summarise the microbiota composition of kefir grains. Moreover, because of technological and microbiological significance of the kefir grains, the paper provides an insight into the microbiological and molecular methods applied to study microbial biodiversity of kefir grains.

  1. RNA folding kinetics using Monte Carlo and Gillespie algorithms.

    Science.gov (United States)

    Clote, Peter; Bayegan, Amir H

    2017-08-05

    RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

  2. Physical mechanism of grain refinement in solidification of undercooled melts

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, M.; Karma, A.; Eckler, K.; Herlach, D.M. (Institut fuer Raumsimulation, Deutsche Forschungsanstalt fuer Luft- und Raumfahrt, D-51140 Koeln (Germany) Physics Department, Northeastern University, Boston, Massachusetts 02115 (United States))

    1994-09-05

    It is proposed that the widely observed transitions in solidification of undercooled melts from a coarse grained dendritic to a grain refined equiaxed microstructure result from the fragmentation of dendrites by remelting during the period following recalescence where the inter-dendritic melt solidifies. This mechanism is supported by the experimental demonstration in Cu-Ni alloys that the transition undercoolings vary with cooling rate in a way which is relatively well described quantitatively by a simple fragmentation model. The latter also predicts the occurrence of two transitions, both of which are observed.

  3. On the importance of grain size in luminescence dating using quartz

    DEFF Research Database (Denmark)

    Timar-Gabor, A.; Buylaert, Jan-Pieter; Guralnik, B.

    2017-01-01

    There are two major problems commonly encountered when applying Optically Stimulated Luminescence (OSL) dating in the high dose range: (i) age discrepancy between different grain sizes, and (ii) age underestimation. A marked and systematic discrepancy between fine-grain (4-11 μm) and coarse...... exponential functions, whose saturation characteristics (D0 values) are clearly anticorrelated with grain diameter (ϕ) through an inverse square root relationship, D0 = A/√ϕ, where A is a scaling factor. While the mechanism behind this grain-size dependency of saturation characteristics still needs...

  4. Power-Aware Rationale for Using Coarse-Grained Transponders in IP-Over-WDM Networks

    DEFF Research Database (Denmark)

    Saldaña Cercos, Silvia; Resendo, Leandro C.; Ribeiro, Moises R. N.

    2015-01-01

    a comprehensive analysis on the trade-off between power consumption and available optical capacity, and power consumption and capital expenditure (CAPEX) for three different scenarios, defining the impact of provisioning the network with higher granularity transmission technology. Regarding the available optical...

  5. Nanoparticle-Mediated Mechanical Destruction of Cell Membranes: A Coarse-Grained Molecular Dynamics Study.

    Science.gov (United States)

    Zhang, Liuyang; Zhao, Yiping; Wang, Xianqiao

    2017-08-16

    The effects of binding mode, shape, binding strength, and rotational speed of actively rotating nanoparticles on the integrity of cell membranes have been systematically studied using dissipative particle dynamics simulations. With theoretical analyses of lipid density, surface tension, stress distribution, and water permeation, we demonstrate that the rotation of nanoparticles can provide a strong driving force for membrane rupture. The results show that nanoparticles embedded inside a cell membrane via endocytosis are more capable of producing large membrane deformations under active rotation than nanoparticles attached on the cell membrane surface. Nanoparticles with anisotropic shapes produce larger deformation and have a higher rupture efficiency than those with symmetric shapes. Our findings provide useful design guidelines for a general strategy based on utilizing mechanical forces to rupture cell membranes and therefore destroy the integrity of cells.

  6. Electro-acoustic behavior of the mitotic spindle: a semi-classical coarse-grained model.

    Directory of Open Access Journals (Sweden)

    Daniel Havelka

    Full Text Available The regulation of chromosome separation during mitosis is not fully understood yet. Microtubules forming mitotic spindles are targets of treatment strategies which are aimed at (i the triggering of the apoptosis or (ii the interruption of uncontrolled cell division. Despite these facts, only few physical models relating to the dynamics of mitotic spindles exist up to now. In this paper, we present the first electromechanical model which enables calculation of the electromagnetic field coupled to acoustic vibrations of the mitotic spindle. This electromagnetic field originates from the electrical polarity of microtubules which form the mitotic spindle. The model is based on the approximation of resonantly vibrating microtubules by a network of oscillating electric dipoles. Our computational results predict the existence of a rapidly changing electric field which is generated by either driven or endogenous vibrations of the mitotic spindle. For certain values of parameters, the intensity of the electric field and its gradient reach values which may exert a not-inconsiderable force on chromosomes which are aligned in the spindle midzone. Our model may describe possible mechanisms of the effects of ultra-short electrical and mechanical pulses on dividing cells--a strategy used in novel methods for cancer treatment.

  7. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations

    NARCIS (Netherlands)

    Treptow, W.; Marrink, S.J.; Tarek, M.

    2008-01-01

    Voltage-gated potassium (Kv) channels are ubiquitous transmembrane proteins involved in electric signaling of excitable tissues. A fundamental property of these channels is the ability to open or close in response to changes in the membrane potential. To date, their structure-based activation

  8. Controls on the size and occurrence of pools in coarse-grained forest rivers

    Science.gov (United States)

    John M. Buffington; Thomas E. Lisle; Richard D. Woodsmith; Sue Hilton

    2002-01-01

    Controls on pool formation are examined in gravel- and cobble-bed rivers in forest mountain drainage basins of northern California, southern Oregon, and southeastern Alaska. We demonstrate that the majority of pools at our study sites are formed by flow obstructions and that pool geometry and frequency largely depend on obstruction characteristics (size, type, and...

  9. Shark: SQL and Analytics with Cost-Based Query Optimization on Coarse-Grained Distributed Memory

    Science.gov (United States)

    2014-01-13

    hashes , properties like pre-image resis- tance are not as relevant as speed and collision resistance. Because cryptographic hashes like MD5 , SHA-1, or SHA...comparison of using MurmurHash, SHA-1, SHA-256 and MD5 hashes as input to HyperLogLog reveals no significant difference in accuracy between them [28]. Given...I/O cost of interme- diate shuffles, since MapReduce often requires hefty volumes of intermediate data to be written to disk. Given Shark’s hash

  10. RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields

    Directory of Open Access Journals (Sweden)

    Pierre de Buyl

    2017-01-01

    Full Text Available The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations, and chemically active solvent particles and catalytic colloids. The main usage of RMPCDMD is the simulation of chemically powered nanomotors, but other setups are considered: colloids in the presence of a thermal gradients or forced flows. RMPCDMD is developed in Fortran 2008 with OpenMP for multithreaded operation and uses the HDF5-based H5MD file format for storing data. RMPCDMD comes with documentation and a tutorial for the simulation of chemically powered nanomotors.

  11. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

    Science.gov (United States)

    Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo

    Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.

  12. Microplastic deformation of submicrocrystalline and coarse-grained titanium at room and elevated temperatures

    Science.gov (United States)

    Dudarev, E. F.; Pochivalova, G. P.; Kolobov, Yu. R.; Bakach, G. P.; Skosyrskii, A. B.; Zhorovkov, M. F.

    2012-12-01

    Results obtained from a comparison study on the deformation behavior of submicrocrystalline and coarsegrained titanium in the temperature interval 295-773 K are presented. The microplastic strain mechanisms underlying a change in the deformation behavior of submicrocrystalline titanium in the melting temperature interval 0.35-0.40 Т m and a reduction in the strain hardening effect due to formation of submicrocrystalline structure of the material are examined. A multiscale model for development of microplastic deformation in submicrocrystalline metals and alloys is offered.

  13. Expressing Coarse-Grain Dependencies Among Tasks in Shared Memory Programs

    DEFF Research Database (Denmark)

    Larsen, Per; Karlsson, Sven; Madsen, Jan

    2011-01-01

    Designers of embedded systems face tight constraints on resources, response time and cost. The ability to analyze embedded systems is essential to timely delivery of new designs. Many analysis techniques model parallel programs as task graphs. Task graphs capture the worst-case execution times of...

  14. Covering all the bases : Coarse-grained model design and application for nucleic acids

    NARCIS (Netherlands)

    Uusitalo, Jaakko Juhani

    2016-01-01

    Nucleic acids play a crucial role in the storage, transportation and expression of our genetic information. They have also become an interesting tool for many applications in nanotechnology. Studying biomolecular systems containing nucleic acids using experimental and imaging techniques has its

  15. MEGA Node: an implementation of a coarse-grain totally reconfigurable parallel machine

    Science.gov (United States)

    Blum, M. B.; Burrer, Caroline

    1990-09-01

    The MEGA Node is a loosely coupled highly parallel computer based on transputers. One of its main characteristics is its ability to change the topology of the network using an electronic switch. It covers a range from 128 to 1024 " worker processors" delivering from 550 to 4400 Mflops peak performance. To achieve these performances a hierarchical structure has been adopted. This highly parallel machine is issued from the Esprit I P1085 " Supernode" project. The software has to support a wide spectrum of users going from those who wish to obtain maximum performance from the machine to those who wish to use it as a general purpose multi-user parallel machine. This paper describes the different ways to use the MEGA Node and the software environments provided to satisfy all kind of users. The Helios environment is a good example to explain how an operating system can control this machine particularly the networking management and the fundamental problem of mapping. The MEGA Node has already been used for a wide range of applications like signal/image processing (high and low level) image synthesis scientific and engineering numbercrunching neural network simulation and logic simulation. Only a few of them are discussed in this paper: medical image analysis and vision and ray tracing. 1 Esprit I P1085 project The work done under the Esprit I P1085 project [1] partially funded by CEC was related the development and applications of a low cost high performance multiprocessor machine. The project involved Royal Signals and Radar Establishment (RSRE prime contractor) Inmos Thorn-Emi CRL University of Southampton University of Liverpool Aptor University of Grenoble(Imag) and Telmat Informatique. The objectives of the project were to develop a highly parallel architecture based on transputers and associated system software and applications. To achieve this Inmos developed the T800 transputer starting from the T414 and the consortium defined the whole machine architecture. Started in December 1985 this 3 years project led to significant industrial products: the T800 transputer the machine architecture and part of the associated software. SPIE Vol. 1360 Visual Communications and Image Processing ''90 / 109

  16. Localness of energy cascade in a hydrodynamic turbulence, I. Smooth coarse-graining

    Energy Technology Data Exchange (ETDEWEB)

    Aluie, Hussein [Los Alamos National Laboratory; Eyink, Gregory L [JOHNS HOPKINS UNIV.

    2009-01-01

    We introduce a novel approach to scale-decomposition of the fluid kinetic energy (or other quadratic integrals) into band-pass contributions from a series of length-scales. Our decomposition is based on a multiscale generalization of the 'Germano identity' for smooth, graded filter kernels. We employ this method to derive a budget equation that describes the transfers of turbulent kinetic energy both in space and in scale. It is shown that the inter-scale energy transfer is dominated by local triadic interactions, assuming only the scaling properties expected in a turbulent inertial-range. We derive rigorous upper bounds on the contributions of non-local triads, extending the work of Eyink (2005) for low-pass filtering. We also propose a physical explanation of the differing exponents for our rigorous upper bounds and for the scaling predictions of Kraichnan (1966,1971). The faster decay predicted by Kraichnan is argued to be the consequence of additional cancellations in the signed contributions to transfer from non-local triads, after averaging over space. This picture is supported by data from a 512 pseudospectral simulation of Navier-Stokes turbulence with phase-shift dealiasing.

  17. mineral elements content of some coarse grains used as staple food

    African Journals Online (AJOL)

    DR. AMINU

    2014-06-01

    Jun 1, 2014 ... maize, sorghum, wheat, cowpea and rice are the most popular agricultural products consumed for ... adverse effect upon human and animals at excessively high concentration if included in the diet (Okoye et al., ... brain iron accumulation and other disorders. (Sadrzadeh and Saffari, 2004). The objective of ...

  18. Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning

    Science.gov (United States)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

    2017-04-01

    Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

  19. A coarse-grained model based on core-softened potentials for ...

    Indian Academy of Sciences (India)

    Departamento de Física, Universidade Federal de Ouro Preto, Ouro Preto, MG 35400-000, Brazil; Coordenadoria Especial de Física, Química e Matemática, Universidade Federal de Santa Catarina, Rua Pedro João Pereira, 150, Araranguá, SC 88900-000, Brazil; Instituto de Física, Universidade Federal do Rio Grande do ...

  20. A coarse-grained molecular model of graphene: application to graphene-based multilayered nanocomposites

    OpenAIRE

    Ruiz, Luis

    2014-01-01

    Single-layer graphene exhibits remarkable electronic and thermal properties and it is the strongest material known, thus it offers great promise for a broad range of nanotechnological applications. Despite the exceptional properties exhibited by pristine graphene monolayers, harnessing the mechanical performance of single-sheets at larger length scales or for higher material hierarchies (e.g., graphene paper) remains a bottleneck. One promising strategy is to enhance the interlayer shear stre...

  1. An OFDM receiver implemented on the coarse-grain reconfigurable Montium processor

    NARCIS (Netherlands)

    Rauwerda, G.K.; Heysters, P.M.; Smit, Gerardus Johannes Maria

    Future mobile terminals become multimode communication systems. In order to handle different standards, we propose to perform baseband processing in heterogeneous reconfigurable hardware. OFDM is one of the techniques that exists in multimode communication systems. As an example, we present the

  2. Probabilistic Equilibrium Sampling of Protein Structures from SAXS Data and a Coarse Grained Debye Formula

    DEFF Research Database (Denmark)

    Andreetta, Christian

    of protein structures all fitting the experimental data. For the first time, we describe in full atomic detail a set of different conformations attainable by flexible polypeptides in solution. This method is not limited by assumptions in shape or size of the samples. It allows therefore to investigate......The present work describes the design and the implementation of a protocol for arbitrary precision computation of Small Angle X-ray Scattering (SAXS) profiles, and its inclusion in a probabilistic framework for protein structure determination. This protocol identifies a set of maximum...

  3. Phase behavior of supported lipid bilayers: A systematic study by coarse-grained molecular dynamics simulations

    DEFF Research Database (Denmark)

    Poursoroush, Asma; Sperotto, Maria Maddalena; Laradji, Mohamed

    2017-01-01

    Solid-supported lipid bilayers are utilized by experimental scientists as models for biological membranes because of their stability. However, compared to free standing bilayers, their close proximity to the substrate may affect their phase behavior. As this is still poorly understood, and few...... computational studies have been performed on such systems thus far, here we present the results from a systematic study based on molecular dynamics simulations of an implicit-solvent model for solid-supported lipid bilayers with varying lipid-substrate interactions. The attractive interaction between...

  4. CHARACTERISTICS OF SELECTED PHYSICOCHEMICAL INDICES OF UPLAND CARBONATE STREAM WATER WITH COARSE-GRAINED SUBSTRATE

    Directory of Open Access Journals (Sweden)

    Agnieszka Policht-Latawiec

    2014-10-01

    Full Text Available Hydrochemical research was conducted in 2011 at three measurement-control points on the Sztoła river, a left-bank tributary to the Biała Przemsza river. Water temperature and pH, dissolved oxygen concentration, oxygen saturation and electrolytic conductivity were measured directly in the field. 11 selected physicochemical indices of the Sztoła surface water were assessed in the laboratory. The analysis of the research results revealed that the water of the Sztoła along the analyzed river reach was first class quality. The analysis of water usable qualities proved that at point 1 it can be used for water supply after high-performance physical and chemical treatment, whereas at other points after a typical physical and chemical treatment, due to high manganese concentrations. Water does not meet the requirements of natural habitat for the Salmonoid fish only at point 1 because of exceeded standard values for nitrites. The Cyprinid fish have the proper habitat conditions along the examined river reach. Among 15 analysed physiochemical indices of water, 7 were statistically higher in the lower course, but they did not affect worsening of the Sztoła river water quality. Greater water pollution in the central and lower river reach is caused by the anthropogenic pressure connected mainly with the operations of extraction industry in the catchment.

  5. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel N.; Marrink, Siewert J.; Praprotnik, Matej

    2015-01-01

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that

  6. Adaptive coarse graining method for energy transfer and dissociation kinetics of polyatomic species.

    Science.gov (United States)

    Sahai, A; Lopez, B; Johnston, C O; Panesi, M

    2017-08-07

    A novel reduced-order method is presented for modeling reacting flows characterized by strong non-equilibrium of the internal energy level distribution of chemical species in the gas. The approach seeks for a reduced-order representation of the distribution function by grouping individual energy states into macroscopic bins, and then reconstructing state population using the maximum entropy principle. This work introduces an adaptive grouping methodology to identify and lump together groups of states that are likely to equilibrate faster with respect to each other. To this aim, two algorithms have been considered: the modified island algorithm and the spectral clustering method. Both methods require a measure of dissimilarity between internal energy states. This is achieved by defining "metrics" based on the strength of the elementary rate coefficients included in the state-specific kinetic mechanism. Penalty terms are used to avoid grouping together states characterized by distinctively different energies. The two methods are used to investigate excitation and dissociation of N2 (Σg+1) molecules due to interaction with N(Su4) atoms in an ideal chemical reactor. The results are compared with a direct numerical simulation of the state-specific kinetics obtained by solving the master equations for the complete set of energy levels. It is found that adaptive grouping techniques outperform the more conventional uniform energy grouping algorithm by providing a more accurate description of the distribution function, mole fraction and energy profiles during non-equilibrium relaxation.

  7. Analytical structure, dynamics, and coarse graining of a kinetic model of an active fluid

    Science.gov (United States)

    Gao, Tong; Betterton, Meredith D.; Jhang, An-Sheng; Shelley, Michael J.

    2017-09-01

    We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile "extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several experimental systems, such as recently studied tripartite rods that create extensile flows by consuming a chemical fuel. We first describe the system through a Doi-Onsager kinetic theory based on microscopic modeling. This theory captures the active stresses produced by the particles that can drive hydrodynamic instabilities, as well as the steric interactions of rodlike particles that lead to nematic alignment. This active nematic system yields complex flows and disclination defect dynamics very similar to phenomenological Landau-deGennes Q -tensor theories for active nematic fluids, as well as by more complex Doi-Onsager theories for polar microtubule-motor-protein systems. We apply the quasiequilibrium Bingham closure, used to study suspensions of passive microscopic rods, to develop a nonstandard Q -tensor theory. We demonstrate through simulation that this B Q -tensor theory gives an excellent analytical and statistical accounting of the suspension's complex dynamics, at a far reduced computational cost. Finally, we apply the B Q -tensor model to study the dynamics of extensor suspensions in circular and biconcave domains. In circular domains, we reproduce previous results for systems with weak nematic alignment, but for strong alignment we find unusual dynamics with activity-controlled defect production and absorption at the boundaries of the domain. In biconcave domains, a Fredericks-like transition occurs as the width of the neck connecting the two disks is varied.

  8. Coarse graining the Bethe-Goldstone equation: Nucleon-nucleon high-momentum components

    Science.gov (United States)

    Simo, I. Ruiz; Pérez, R. Navarro; Amaro, J. E.; Arriola, E. Ruiz

    2017-11-01

    The δ -shell representation of the nuclear force allows a simplified treatment of nuclear correlations. We show how this applies to the Bethe-Goldstone equation as an integral equation in coordinate space with a few mesh points, which is solved by inversion of a five-dimensional square matrix in the single channel cases and a 10 ×10 matrix for the tensor-coupled channels. This allows us to readily obtain the high-momentum distribution, for all partial waves, of a back-to-back correlated nucleon pair in nuclear matter. We find that the probability of finding a high-momentum correlated neutron-proton pair is about 18 times that of a proton-proton one, as a result of the strong tensor force, thus confirming in an independent way previous results and measurements.

  9. Theory of Wavelet-Based Coarse-Graining Hierarchies for Molecular Dynamics

    Science.gov (United States)

    2017-04-01

    Vn+1 ⊕Wn+1, where Vn+1 = Pε(T 2n+1)Vn (9) and Wn+1 = kerPε(T 2n+1|Vn) (10) are iteratively associated with orthonormal bases via QR -decompositions, T...Spaces The wavelets are derived iteratively from a filter T using the QR decomposition. At each iteration, T is cast in the “Q” basis of the previous...iteration,( n∏ i=0 Qi )T T 2 n+1 ( n∏ i=0 Qi ) = Qn+1Rn+1. (84) Therefore, repeated application (with infinite precision) is equivalent to the QR al

  10. Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction

    Science.gov (United States)

    2008-07-29

    parameters for the cation of (A) were derived from the work of Canongia Lopes and Padua1 for linear phosphonium cations and applied to the cyclic...Experimental Subsection Α. Project Justification and Synthetic Target Selection: Hydrazinium Salts as Potential Energetic Material Candidate...component anion or cation. 2-Hydroxyethyl-Hydrazinium Salts : Justification for the choice of the specific cation for investigation: Salts based

  11. A two-level real-time vision machine combining coarse and fine grained parallelism

    DEFF Research Database (Denmark)

    Jensen, Lars Baunegaard With; Kjær-Nielsen, Anders; Pauwels, Karl

    2010-01-01

    In this paper, we describe a real-time vision machine having a stereo camera as input generating visual information on two different levels of abstraction. The system provides visual low-level and mid-level information in terms of dense stereo and optical flow, egomotion, indicating areas...... a factor 90 and a reduction of latency of a factor 26 compared to processing on a single CPU--core. Since the vision machine provides generic visual information it can be used in many contexts. Currently it is used in a driver assistance context as well as in two robotic applications....

  12. Interaction between polymer-coated carbon nanotubes with coarse-grained computations

    Science.gov (United States)

    Vo, Minh D.; Papavassiliou, Dimitrios V.

    2017-10-01

    Dissipative particle dynamics computations were used to study the interaction between two carbon nanotubes (CNTs) stabilized with a polymer in an aqueous solution. The calculated interaction forces quantitatively described the steric effects of the adsorbed polymer on CNT agglomeration. It was found that the repulsive peak depended on the orientation of the CNTs relative to each other. A general equation describing the forces between polymer-stabilized CNTs was established, and its parameters were evaluated based on the results of the simulations. The procedure can be extended to other adsorbed molecules, like surfactants or biomolecules.

  13. Structuring effects in binary nucleation : Molecular dynamics simulatons and coarse-grained nucleation theory

    NARCIS (Netherlands)

    Braun, S.; Kraska, T.; Kalikmanov, V.I.

    2013-01-01

    Binary clusters formed by vapor-liquid nucleation are frequently nonhomogeneous objects in which components are not well mixed. The structure of a cluster plays an important role in nucleation and cluster growth. We demonstrate structuring effects by studying high-pressure nucleation and cluster

  14. Coarse-grained particle model for pedestrian flow using diffusion maps

    DEFF Research Database (Denmark)

    Marschler, Christian; Starke, Jens; Liu, Ping

    2014-01-01

    Interacting particle systems constitute the dynamic model of choice in a variety of application areas. A prominent example is pedestrian dynamics, where good design of escape routes for large buildings and public areas can improve evacuation in emergency situations, avoiding exit blocking...

  15. Physical Modelling of Large Diameter Piles in Coarse-Grained Soil

    DEFF Research Database (Denmark)

    Brødbæk, K. T.; Augustesen, Anders Hust; Møller, M.

    2011-01-01

    modelling (large- or small-scale). This paper investigates the effects of diameter on the initial part of the p-y curves by small-scale testing. A new and innovative test setup is presented. In order to minimize scale effects the tests are successfully carried out in a pressure tank enabling the possibility...... of increasing the effective stresses. The test setup is thoroughly described in the paper. Two non-slender aluminium pipe piles subjected to lateral loads have been tested in the laboratory. The piles are heavily instrumented with strain gauges in order to obtain p-y curves, displacement and bending moment...

  16. A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

    NARCIS (Netherlands)

    Ilie, Ioana Mariuca; den Otter, Wouter K.; Briels, Willem J.

    2016-01-01

    Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We

  17. De novo inference of protein function from coarse-grained dynamics.

    Science.gov (United States)

    Bhadra, Pratiti; Pal, Debnath

    2014-10-01

    Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

  18. Concretes with red mud coarse aggregates

    Directory of Open Access Journals (Sweden)

    Dênio Ramam Carvalho de Oliveira

    2012-06-01

    Full Text Available Red mud (RM is a mineral waste, residue of the Bayer process used to obtain alumina from bauxite. While the exploration of rolled pebble damages the environment and is much more controlled by the government, the huge RM disposal areas do not stop increasing and polluting soil, rivers and groundwater sources in Amazon. In this work, the material mixtures used to produce coarse aggregates presented up to 80% of RM, 30% of metakaolin and 30% of active silica as recycled waste. Several tests were carried out to determine the aggregates physical properties and to evaluate the mechanical performance of the concretes with the new aggregates, including hydraulic abrasion strength, and the results were compared to the reference ones, i.e. rolled pebble concretes. Additionally, the sintering process neutralizes any toxic substance as occur in some RM products like tiles and bricks, and these results have encouraged an industrial or semi-industrial production of RM aggregates for concretes.

  19. Abrasion and algal fouling of coarse material on the Murman littoral

    Directory of Open Access Journals (Sweden)

    Malavenda S. V.

    2017-03-01

    Full Text Available On the Murmansk coast of the Barents Sea the boulder littoral zone is widely spread mostly covered by Fucus communities. This is one of the most productive benthic communities of the Barents Sea. The studies of intertidal communities have the long history, but the dynamics of intertidal ecosystems due to surf and storms is not clear. The goal of the work is to identify the leading factors that determine the rate of abrasion of coarse material and fouling algae-macrophytes of the intertidal zone of Murman. The study has been conducted in the Zelenetskaya Bay of the Barents Sea on the basis of the biological station of the MMBI KSC RAS. The rate of abrasion has been carried out during 2004–2013, phyto-overgrowing – 2009–2013. In three pilot landfills 12 samples of coarse material have been exposed during the year (from July to next July. The weight change of the sample as well as species composition and biomass of algae of fouling communities have been investigated. The influence of the surf intensity, temperature of water and air has been analyzed (univariate analysis of variance ANOVA has been applied. It has been shown that on the littoral of the Murmansk coast the abrasion of coarse material is determined primarily by the number of storms, so the storm rate has been proposed. It has been revealed that the density of fouling boulders with macroalgae depends primarily on the intensity of the surf and the average gradient of air temperature. The basis for the emerging communities of annual species are green (Acrosiphonia arcta, Blidingia minima, Spongomorpha aeruginosa and brown algae (Pylaiella littoralis, Dictyosiphon chordaria. These algae groups are found everywhere in Fucus communities of the boulder intertidal zone of the Murman coast and probably they are the intermediate stage of fouling the coarse-grained material

  20. Study on the effect of temperature rise on grain refining during fabrication of nanocrystalline copper under explosive loading

    Science.gov (United States)

    Wang, Jinxiang; Yang, Rui; Jiang, Li; Wang, Xiaoxu; Zhou, Nan

    2013-11-01

    Nanocrystalline (NC) copper was fabricated by severe plastic deformation of coarse-grained copper at a high strain rate under explosive loading. The feasibility of grain refinement under different explosive loading and the influence of overall temperature rise on grain refinement under impact compression were studied in this paper. The calculation model for the macroscopic temperature rise was established according to the adiabatic shock compression theory. The calculation model for coarse-grained copper was established by the Voronoi method and the microscopic temperature rise resulted from severe plastic deformation of grains was calculated by ANSYS/ls-dyna finite element software. The results show that it is feasible to fabricate NC copper by explosively dynamic deformation of coarse-grained copper and the average grain size of the NC copper can be controlled between 200˜400 nm. The whole temperature rise would increase with the increasing explosive thickness. Ammonium nitrate fuel oil explosive was adopted and five different thicknesses of the explosive, which are 20 mm, 25 mm, 30 mm, 35 mm, 45 mm, respectively, with the same diameter using 20 mm to the fly plate were adopted. The maximum macro and micro temperature rise is up to 532.4 K, 143.4 K, respectively, which has no great effect on grain refinement due to the whole temperature rise that is lower than grain growth temperature according to the high pressure melting theory.

  1. Euhedral metallic-Fe-Ni grains in extraterrestrial samples

    Science.gov (United States)

    Rubin, Alan E.

    1993-01-01

    Metallic Fe-Ni is rare in terrestrial rocks, being largely restricted to serpentinized peridotites and volcanic rocks that assimilated carbonaceous material. In contrast, metallic Fe-Ni is nearly ubiquitous among extraterrestrial samples (i.e., meteorites, lunar rocks, and interplanetary dust particles). Anhedral grains are common. For example, in eucrites and lunar basalts, most of the metallic Fe-Ni occurs interstitially between silicate grains and thus tends to have irregular morphologies. In many porphyritic chondrules, metallic Fe-Ni and troilite form rounded blebs in the mesostasis because their precursors were immiscible droplets. In metamorphosed ordinary chondrites, metallic Fe-Ni and troilite form coarse anhedral grains. Some of the metallic Fe-Ni and troilite grains has also been mobilized and injected into fractures in adjacent silicate grains where local shock-reheating temperatures reached the Fe-FeS eutectic (988 C). In interplanetary dust particles metallic Fe-Ni most commonly occurs along with sulfide as spheroids and fragments. Euhedral metallic Fe-Ni grains are extremely rare. Several conditions must be met before such grains can form: (1) grain growth must occur at free surfaces, restricting euhedral metallic Fe-Ni grains to systems that are igneous or undergoing vapor-deposition; (2) the metal (+/-) sulfide assemblage must have an appropriate bulk composition so that taenite is the liquidus phase in igneous systems or the stable condensate phase in vapor-deposition systems; and (3) metallic Fe-Ni grains must remain underformed during subsequent compaction, thermal metamorphism, and shock. Because of these restrictions, the occurrence of euhedral metallic Fe-Ni grains in an object can potentially provide important petrogenetic information. Despite its rarity, euhedral metallic Fe-Ni occurs in a wide variety of extraterrestrial materials. Some of these materials formed in the solar nebula; others formed on parent body surfaces by meteoroid

  2. Grain-size Statistical Parameters of Sandy Sediment in Kuala Gigieng, Aceh Besar District

    OpenAIRE

    Purnawan, Syahrul; Haekal A. Haridhi; Setiawan, Ichsan; Marwantim,

    2015-01-01

    Study of sediment distribution at Kuala Gigieng was to assess the information of sediment related to the occurrence of hydro-oceanographic processes. The sediment samples were collected from nine stations using coring method. Granulometric method was used to analyze the grain size distributions. The results showed different sediment distribution patterns in each area at estuary Kuala Gigieng. The outer area of estuary indicated skewed to coarse grains, while at the inner area of estuary indic...

  3. Characterization of Soil-Water Retention with Coarse Fragments in ...

    African Journals Online (AJOL)

    The presence of coarse fragments can have profound impact on soil moisture retention characteristics. The study was conducted to assess the effects of coarse fragments on the moisture retention characteristics of 16 soil series, developed over five different parent materials in the Densu basin. Soil profiles were excavated ...

  4. Impacts of benthic coarse particulate organic matter variations on ...

    African Journals Online (AJOL)

    An investigation to assess the relationship between coarse particulate organic matter (CPOM) and macroinvertebrate communities was undertaken in the Njoro River, Kenya during 2010. Significantly lower macroinvertebrate densities and diversities were observed in study sites with low Coarse Particulate Organic Matter ...

  5. Texture measurements in fine grained polyphase aggregates

    Science.gov (United States)

    Kilian, R.; Heilbronner, R.; Stünitz, H.

    2009-04-01

    When analyzing natural and experimental microstructures, we routinely use the two methods for orientation imaging and texture measurements: (a) the computer-integrated polarization microscopy (CIP, Panozzo Heilbronner & Pauli, 1993) and (b) the electron back scatter diffractometry (EBSD, e.g. Kunze et al., 1994). The CIP method yields orientation maps and pole figures of c-axes (of uni-axial materials), while the EBSD method yields complete textural data for all crystallographic orientations. In order to compare the orientation images the Euler maps (obtained from EBSD) are recalculated and presented with the more intuitive colour look-up tables (CLUTs) of the CIP method. In this contribution we compare and contrast the results achieved by these two methods using two different samples taken from a metagranodiorite (Kilian et al., 2009): (1) a coarse grained mylonitic rock with polycrystalline quartz aggregates and (2) a very fine grained ultramylonitic rock with single quartz grains dispersed in a polymineralic matrix. For the coarse grained sample (1) both methods yield the same (strong) c-axis pole figure: the geometry of the c-axis polefigure as well as the texture intensity (maximum of polefigure) are identical. The texture of sample (2) - where small quartz grains are dispersed in the polymineralic matrix - is very weak to random. The CIP and EBSD c-axis pole figures are different and - as noted previously - these differences arise from a machine specific bias of the EBSD (Schmocker 2002). In addition to texture analysis, both methods are capable of image segmentation (identification and separation of individual grains in the orientation image) as well as shape and grain size analysis. However due to the entirely different approach taken, the results may differ significantly. For example, when deriving the grain size distribution for sample (2) EBSD (combined with with the OIM® analysis software) yields a positively skewed histogram (with the mode occurring

  6. Microbiota of kefir grains

    OpenAIRE

    Tomislav Pogačić; Sanja Šinko; Šimun Zamberlin; Dubravka Samaržija

    2013-01-01

    Kefir grains represent the unique microbial community consisting of bacteria, yeasts, and sometimes filamentous moulds creating complex symbiotic community. The complexity of their physical and microbial structures is the reason that the kefir grains are still not unequivocally elucidated. Microbiota of kefir grains has been studied by many microbiological and molecular approaches. The development of metagenomics, based on the identification without cultivation, is opening new possibilities f...

  7. Grain Boundary Complexions

    Science.gov (United States)

    2014-05-01

    deter- mine bulk materials behavior and properties such as superplasticity, creep, fatigue, corrosion , strength and conductivity [2]. Grain boundary...interface (i.e. lattice mismatch accommodated by interface dislocations ), wetting transitions will not occur. A wetting transition is possible in the case...melting only starts around dislocations at low- angle grain boundaries; the grain boundary structure con- sists of isolated liquid pools separated by

  8. Compaction of cereal grain

    OpenAIRE

    Wychowaniec, J.; Griffiths, I.; Gay, A; Mughal, A.

    2013-01-01

    We report on simple shaking experiments to measure the compaction of a column of Firth oat grain. Such grains are elongated anisotropic particles with a bimodal polydispersity. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical shaking evolve to a dense state with evidence of nematic-like structure at the surface of the confining tube. This is accompanied by an increase in the packing fraction of the grain.

  9. Compaction of cereal grain

    Science.gov (United States)

    Wychowaniec, J.; Griffiths, I.; Gay, A.; Mughal, A.

    2013-11-01

    We report on simple shaking experiments to measure the compaction of a column of Firth oat grain. Such grains are elongated anisotropic particles with a bimodal polydispersity. In these experiments, the particle configurations start from an initially disordered, low-packing-fraction state and under vertical shaking evolve to a dense state with evidence of nematic-like structure at the surface of the confining tube. This is accompanied by an increase in the packing fraction of the grain.

  10. ASSIMILATION OF COARSE-SCALEDATAUSINGTHE ENSEMBLE KALMAN FILTER

    KAUST Repository

    Efendiev, Yalchin

    2011-01-01

    Reservoir data is usually scale dependent and exhibits multiscale features. In this paper we use the ensemble Kalman filter (EnKF) to integrate data at different spatial scales for estimating reservoir fine-scale characteristics. Relationships between the various scales is modeled via upscaling techniques. We propose two versions of the EnKF to assimilate the multiscale data, (i) where all the data are assimilated together and (ii) the data are assimilated sequentially in batches. Ensemble members obtained after assimilating one set of data are used as a prior to assimilate the next set of data. Both of these versions are easily implementable with any other upscaling which links the fine to the coarse scales. The numerical results with different methods are presented in a twin experiment setup using a two-dimensional, two-phase (oil and water) flow model. Results are shown with coarse-scale permeability and coarse-scale saturation data. They indicate that additional data provides better fine-scale estimates and fractional flow predictions. We observed that the two versions of the EnKF differed in their estimates when coarse-scale permeability is provided, whereas their results are similar when coarse-scale saturation is used. This behavior is thought to be due to the nonlinearity of the upscaling operator in the case of the former data. We also tested our procedures with various precisions of the coarse-scale data to account for the inexact relationship between the fine and coarse scale data. As expected, the results show that higher precision in the coarse-scale data yielded improved estimates. With better coarse-scale modeling and inversion techniques as more data at multiple coarse scales is made available, the proposed modification to the EnKF could be relevant in future studies.

  11. RNA topology

    OpenAIRE

    Frank-Kamenetskii, Maxim D.

    2013-01-01

    A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.

  12. The influence of grain size, grain color, and suspended-sediment concentration on light attenuation: why fine-grained terrestrial sediment is bad for coral reef ecosystems

    Science.gov (United States)

    Storlazzi, Curt; Norris, Benjamin; Rosenberger, Kurt

    2015-01-01

    Sediment has been shown to be a major stressor to coral reefs globally. Although many researchers have tested the impact of sedimentation on coral reef ecosystems in both the laboratory and the field and some have measured the impact of suspended sediment on the photosynthetic response of corals, there has yet to be a detailed investigation on how properties of the sediment itself can affect light availability for photosynthesis. We show that finer-grained and darker-colored sediment at higher suspended-sediment concentrations attenuates photosynthetically active radiation (PAR) significantly more than coarser, lighter-colored sediment at lower concentrations and provide PAR attenuation coefficients for various grain sizes, colors, and suspended-sediment concentrations that are needed for biophysical modeling. Because finer-grained sediment particles settle more slowly and are more susceptible to resuspension, they remain in the water column longer, thus causing greater net impact by reducing light essential for photosynthesis over a greater duration. This indicates that coral reef monitoring studies investigating sediment impacts should concentrate on measuring fine-grained lateritic and volcanic soils, as opposed to coarser-grained siliceous and carbonate sediment. Similarly, coastal restoration efforts and engineering solutions addressing long-term coral reef ecosystem health should focus on preferentially retaining those fine-grained soils rather than coarse silt and sand particles.

  13. Multiple age components in individual molybdenite grains

    Science.gov (United States)

    Aleinikoff, John N.; Creaser, Robert A.; Lowers, Heather; Magee, Charles W.; Grauch, Richard I.

    2012-01-01

    Re–Os geochronology of fractions composed of unsized, coarse, and fine molybdenite from a pod of unusual monazite–xenotime gneiss within a granulite facies paragneiss, Hudson Highlands, NY, yielded dates of 950.5 ± 2.5, 953.8 ± 2.6, and 941.2 ± 2.6 Ma, respectively. These dates are not recorded by co-existing zircon, monazite, or xenotime. SEM–BSE imagery of thin sections and separated grains reveals that most molybdenite grains are composed of core and rim plates that are approximately perpendicular. Rim material invaded cores, forming irregular contacts, probably reflecting dissolution/reprecipitation. EPMA and LA-ICP-MS analyses show that cores and rims have different trace element concentrations (for example, cores are relatively enriched in W). On the basis of inclusions of zircon with metamorphic overgrowths, we conclude that molybdenite cores and rims formed after high-grade regional metamorphism. The discovery of cores and rims in individual molybdenite grains is analogous to multi-component U-Pb geochronometers such as zircon, monazite, and titanite; thus, molybdenite should be carefully examined before dating to ensure that the requirement of age homogeneity is fulfilled.

  14. Holocene marine transgression as interpreted from bathymetry and sand grain size parameters off Gopalpur

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, K.M.; Rajamanickam, G.V.; Rao, T.C.S.

    sorting. These are leptokurtic. The coarse-grained sand beyond 15 m water depth has positive or negative skewness and moderate sorting. These are platy kurtic. Bivariate plot of mean vs skewness indicates two types of sample spread, keeping approximately 2...

  15. Bran hydration and physical treatments improve the bread-baking quality of whole grain wheat flour

    Science.gov (United States)

    Fine and coarse bran particles of a hard red and a hard white wheat were used to study the influences of bran hydration and physical treatments such as autoclaving and freezing as well as their combinations on the dough properties and bread-baking quality of whole grain wheat flour (WWF). For both h...

  16. Rapid grain size fining in modern and Pliocene Himalayan rivers

    Science.gov (United States)

    Dubille, Matthieu; Lave, Jerome

    2013-04-01

    Rapid grain size changes between two main units of a sedimentary megacycle in a foreland basin are commonly interpreted to result from changes in tectonic activity or climate in the adjacent mountain range. In central Nepal, the Cenozoic Siwaliks molasse deposits exposed in the frontal Himalayan folds are characterized by such a radical grain size transition. Locally gravel deposits completely replace sands in the upward sequence within about a hundred meters, the median grain size (D50) displaying a sharp increase by a factor of ~100. Such a rapid gravel-sand transition is also observed in present-day river channels about 8-20 km downstream from the outlet of the frontal Himalaya. The passage from gravel-covered channel reaches (proximal alluvial fans) to sand-covered channel reaches (distal alluvial fans) occurs within a few kilometres on the Gangetic Plain in central Nepal, and the D50 ratio between the two types of channels equals ~100. We propose that the dramatic and remarkably similar decrease in grain size observed in the Siwaliks series and along modern rivers in the Gangetic foreland basin, results from a similar hydrological process, i.e. a grain sorting process during the selective deposition of the sediment load. Such behaviour is quite well reproduce by simple grain-size-dependent sediment transport models if we account for the initial grain size distribution of the eroded sediments. By analogy with modern rivers behaviour, the sudden grain size decrease observed in the Cenozoic Siwaliks molasse deposits is interpreted as the crossing of this sorting transition during progressive southward migration of the depositional facies in response to continuous Himalayan orogen construction. This study demonstrates that an abrupt change in grain size does not necessarily relate to a change in tectonic or climatic forcing, but can simply arise from internal adjustment of the piedmont rivers to the deposition of coarse bedload and grain segregation processes.

  17. Non-Galerkin Coarse Grids for Algebraic Multigrid

    Energy Technology Data Exchange (ETDEWEB)

    Falgout, Robert D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Schroder, Jacob B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-06-26

    Algebraic multigrid (AMG) is a popular and effective solver for systems of linear equations that arise from discretized partial differential equations. And while AMG has been effectively implemented on large scale parallel machines, challenges remain, especially when moving to exascale. Particularly, stencil sizes (the number of nonzeros in a row) tend to increase further down in the coarse grid hierarchy, and this growth leads to more communication. Therefore, as problem size increases and the number of levels in the hierarchy grows, the overall efficiency of the parallel AMG method decreases, sometimes dramatically. This growth in stencil size is due to the standard Galerkin coarse grid operator, $P^T A P$, where $P$ is the prolongation (i.e., interpolation) operator. For example, the coarse grid stencil size for a simple three-dimensional (3D) seven-point finite differencing approximation to diffusion can increase into the thousands on present day machines, causing an associated increase in communication costs. We therefore consider algebraically truncating coarse grid stencils to obtain a non-Galerkin coarse grid. First, the sparsity pattern of the non-Galerkin coarse grid is determined by employing a heuristic minimal “safe” pattern together with strength-of-connection ideas. Second, the nonzero entries are determined by collapsing the stencils in the Galerkin operator using traditional AMG techniques. The result is a reduction in coarse grid stencil size, overall operator complexity, and parallel AMG solve phase times.

  18. Residential indoor and outdoor coarse particles and associated endotoxin exposures

    Science.gov (United States)

    Wheeler, Amanda J.; Dobbin, Nina A.; Lyrette, Ninon; Wallace, Lance; Foto, Mark; Mallick, Ranjeeta; Kearney, Jill; Van Ryswyk, Keith; Gilbert, Nicolas L.; Harrison, Ian; Rispler, Kathleen; Héroux, Marie-Eve

    2011-12-01

    There is a growing body of evidence demonstrating that coarse particles (PM 10-2.5) have detrimental impacts upon health, especially for respiratory effects. There are limited data available for indoor residential exposures. Some data exist regarding the composition of this PM size fraction with emphasis on crustal elements and biological components. This study includes data from 146 homes sampled in Regina, Saskatchewan (SK) where 5-day integrated concurrent monitoring of indoor and outdoor coarse particles was conducted during the winter and summer of 2007. The coarse particle filters were subsequently analysed for endotoxin content to determine the contribution of this compound. Winter indoor geometric mean concentrations of coarse particles exceeded outdoor concentrations (3.73 μg m -3 vs 2.49 μg m -3; paired t-test p < 0.0001); however the reverse was found in summer (4.34 μg m -3 vs 8.82 μg m -3; paired t-test p < 0.0001). Linear regression indicated that winter predictors of indoor coarse particles were outdoor coarse particles, ventilation and presence of at least two or more occupants. During the summer, increased use of central air conditioning was associated with reduced coarse particles, while smoking and the presence of two or more occupants resulted in increased coarse particles. Endotoxin concentrations (EU μg -1) were lower indoors than outdoors in both seasons. Spatial variability of ambient coarse particles was assessed to determine the suitability of using a single monitoring station within a city to estimate exposure. The coefficients of variation between homes sampled simultaneously and the central monitoring station were calculated (median COV in summer = 15% and winter = 24%) and showed significant variability by week, especially during the summer months, suggesting a single site may be insufficient for characterizing exposure. Future studies should consider daily measurements per home to understand shorter term exposures and day to day

  19. Austenite Grain Growth in Peritectic Solidified Carbon Steels Analyzed by Phase-Field Simulation

    Science.gov (United States)

    Ohno, Munekazu; Tsuchiya, Shingo; Matsuura, Kiyotaka

    2012-06-01

    The formation of coarse columnar grains (CCGs) in the as-cast austenite structure of peritectic carbon steels is a serious problem in continuous casting processes. Recently, it was elucidated that the formation of CCGs is ascribed to a discontinuous grain growth. Furthermore, the critical condition for the discontinuous growth to occur was elicited on the basis of phase-field simulations and a theory of grain growth. In this study, by means of the phase-field simulations, the detailed investigation is carried out for the grain coarsening of the as-cast austenite structure. It is demonstrated in the two-dimensional simulations that the coarsest grain structure emerges by the discontinuous growth in the vicinity of the critical condition. In addition, a model for predicting the upper limit of grain size during the discontinuous growth is proposed. The model successfully describes the experimental result with reasonable accuracy.

  20. Nonlinear Multigrid solver exploiting AMGe Coarse Spaces with Approximation Properties

    DEFF Research Database (Denmark)

    Christensen, Max la Cour; Villa, Umberto; Engsig-Karup, Allan Peter

    The paper introduces a nonlinear multigrid solver for mixed finite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstructured problems is the guaranteed approximation property of the AMGe coarse...... properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on unstructured meshes has the ability to be as powerful/successful as FAS on geometrically refined meshes. For comparison, Newton’s method and Picard iterations with an inner state-of-the-art linear solver...

  1. Nonlinear multigrid solvers exploiting AMGe coarse spaces with approximation properties

    DEFF Research Database (Denmark)

    Christensen, Max la Cour; Vassilevski, Panayot S.; Villa, Umberto

    2017-01-01

    discretizations on general unstructured grids for a large class of nonlinear partial differential equations, including saddle point problems. The approximation properties of the coarse spaces ensure that our FAS approach for general unstructured meshes leads to optimal mesh-independent convergence rates similar...... in evaluating the nonlinear coarse operators and the degradation in convergence rates that characterized previous attempts to extend FAS to algebraic multilevel hierarchies on general unstructured grids. Specifically, the AMGe technique employed in this paper allows to derive stable and accurate coarse...

  2. Two-level method with coarse space size independent convergence

    Energy Technology Data Exchange (ETDEWEB)

    Vanek, P.; Brezina, M. [Univ. of Colorado, Denver, CO (United States); Tezaur, R.; Krizkova, J. [UWB, Plzen (Czech Republic)

    1996-12-31

    The basic disadvantage of the standard two-level method is the strong dependence of its convergence rate on the size of the coarse-level problem. In order to obtain the optimal convergence result, one is limited to using a coarse space which is only a few times smaller than the size of the fine-level one. Consequently, the asymptotic cost of the resulting method is the same as in the case of using a coarse-level solver for the original problem. Today`s two-level domain decomposition methods typically offer an improvement by yielding a rate of convergence which depends on the ratio of fine and coarse level only polylogarithmically. However, these methods require the use of local subdomain solvers for which straightforward application of iterative methods is problematic, while the usual application of direct solvers is expensive. We suggest a method diminishing significantly these difficulties.

  3. Recycled tires as coarse aggregate in concrete pavement mixtures.

    Science.gov (United States)

    2013-07-01

    The reuse potential of tire chips as coarse aggregates in pavement concrete was examined in this research by : investigating the effects of low- and high-volume tire chips on fresh and hardened concrete properties. One concrete : control mixture was ...

  4. RSW Node Centered Coarse Grid w/ Split Walls Modified

    Data.gov (United States)

    National Aeronautics and Space Administration — Dr. Chwalowski, We just generated a modified version of the coarse node centered grid with split walls. Here the red and green sections you highlighted in the email...

  5. Effects of oil palm shell coarse aggregate species on high strength lightweight concrete

    National Research Council Canada - National Science Library

    Yew, Ming Kun; Bin Mahmud, Hilmi; Ang, Bee Chin; Yew, Ming Chian

    2014-01-01

    ...) coarse aggregates on the properties of high strength lightweight concrete (HSLWC). Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study...

  6. Effects of Oil Palm Shell Coarse Aggregate Species on High Strength Lightweight Concrete

    National Research Council Canada - National Science Library

    Yew, Ming Kun; Bin Mahmud, Hilmi; Ang, Bee Chin; Yew, Ming Chian

    2014-01-01

    ...) coarse aggregates on the properties of high strength lightweight concrete (HSLWC). Original and crushed OPS coarse aggregates of different species and age categories were investigated in this study...

  7. Sedimentary differentiation of aeolian grains at the White Sands National Monument, New Mexico, USA

    Science.gov (United States)

    Fenton, Lori K.; Bishop, Janice L.; King, Sara; Lafuente, Barbara; Horgan, Briony; Bustos, David; Sarrazin, Philippe

    2017-06-01

    Gypsum (CaSO4·2H2O) has been identified as a major component of part of Olympia Undae in the northern polar region of Mars, along with the mafic minerals more typical of Martian dune fields. The source and age of the gypsum is disputed, with the proposed explanations having vastly different implications for Mars' geological history. Furthermore, the transport of low density gypsum grains relative to and concurrently with denser grains has yet to be investigated in an aeolian setting. To address this knowledge gap, we performed a field study at White Sands National Monument (WSNM) in New Mexico, USA. Although gypsum dominates the bulk of the dune field, a dolomite-rich [CaMg(CO3)2] transport pathway along the northern border of WSNM provides a suitable analog site to study the transport of gypsum grains relative to the somewhat harder and denser carbonate grains. We collected samples along the stoss slope of a dune and on two coarse-grained ripples at the upwind margin of the dune field where minerals other than gypsum were most common. For comparison, additional samples were taken along the stoss slope of a dune outside the dolomite transport pathway, in the center of the dune field. Visible and near-infrared (VNIR), X-ray powder diffraction (XRD), and Raman analyses of different sample size fractions reveal that dolomite is only prevalent in grains larger than ∼1 mm. Other minerals, most notably calcite, are also present in smaller quantities among the coarse grains. The abundance of these coarse grains, relative to gypsum grains of the same size, drops off sharply at the upwind margin of the dune field. In contrast, gypsum dominated the finer fraction (wind-transported grains occurs gradually in creep, the process is much more rapid when winds are strong enough to saltate the ⩾1 mm grains. The observed grain segregation is consistent with the WSNM dune field formative friction velocity (0.39 m/s) proposed by Jerolmack et al. (2011): winds significantly

  8. Pore-size distribution and compressibility of coarse sandy subsoil with added biochar

    DEFF Research Database (Denmark)

    Petersen, C. T.; Hansen, E.; Larsen, H. H.

    2016-01-01

    the effects of two fine-grained gasification biochars made of straw (LTST) and other materials (LTSN) and of one fast pyrolysis straw biochar (FPST) on pore-size distribution and soil compressibility when added to coarse sandy subsoil. Water retention and therefore pore-size distribution were affected...... systematically. All biochars converted drainable pore space with pore diameters in the range 60–300 µm into water-retaining pores of size 0.2–60 µm, which was taken as an estimate of available water capacity (AWC). Effects were linear over the whole range of biochar (0–4% by mass). The effect of LTST and LTSN...

  9. Investigation into the Flow Properties of Coarse Solid Fuels for Use in Industrial Feed Systems

    Directory of Open Access Journals (Sweden)

    James M. Craven

    2015-01-01

    Full Text Available Material feeding and handling systems have been cited as one of the most common causes of process downtime where thermochemical conversion processes are concerned. New and emerging fuels come in a variety of forms, and if such fuels are to be deployed widely it is imperative that material feeding and handling systems are designed appropriately. This study proposes an approach for designing material feeding and handling systems for use with coarse solid fuels. The data obtained from this study indicates particle size to be one of the key issues affecting the flowability of bulk solids further to the uniformity in particle shape. Coarse bulk solid samples were shown to flow more freely than their milled and pulverised counterparts, generating higher degrees of flowability. The results from this study were also applied to a new feed system used for feeding solid fuels to high pressure processes named the Hydraulic Lock Hopper. In this study the Hydraulic Lock Hopper demonstrated the feeding of wood pellets, torrefied spruce pellets, and ground anthracite coal grains against a pressure of 25 barg in two modes of operation. Energy savings compared to conventional lock hopper systems were recorded in the region of 80%.

  10. Comparative Performance Analysis of Coarse Solvers for Algebraic Multigrid on Multicore and Manycore Architectures

    Energy Technology Data Exchange (ETDEWEB)

    Druinsky, A; Ghysels, P; Li, XS; Marques, O; Williams, S; Barker, A; Kalchev, D; Vassilevski, P

    2016-04-02

    In this paper, we study the performance of a two-level algebraic-multigrid algorithm, with a focus on the impact of the coarse-grid solver on performance. We consider two algorithms for solving the coarse-space systems: the preconditioned conjugate gradient method and a new robust HSS-embedded low-rank sparse-factorization algorithm. Our test data comes from the SPE Comparative Solution Project for oil-reservoir simulations. We contrast the performance of our code on one 12-core socket of a Cray XC30 machine with performance on a 60-core Intel Xeon Phi coprocessor. To obtain top performance, we optimized the code to take full advantage of fine-grained parallelism and made it thread-friendly for high thread count. We also developed a bounds-and-bottlenecks performance model of the solver which we used to guide us through the optimization effort, and also carried out performance tuning in the solver’s large parameter space. Finally, as a result, significant speedups were obtained on both machines.

  11. Modeling of particle removal in the first coarse media of direct horizontal-flow roughing filtration.

    Science.gov (United States)

    Ahn, H W; Park, N S; Kim, S; Park, S Y; Wang, C K

    2007-03-01

    Horizontal-Flow Roughing Filtration (HRF) is an alternative pretreatment method e.g. prior to Slow Sand Filtration (SSF). However, some of its limitations are that the effluent quality drops drastically at higher turbidity (>200NTU) and at higher filtration rate (>1 m h(-1)). To overcome these drawbacks, we suggested Direct Horizontal-Flow Roughing Filtration (DHRF), which is a modified system of Horizontal-Flow Roughing Filtration (HRF) by addition of a low dose of coagulant prior to filtration. To optimize the DHRF configuration, a conceptual and mathematical model for the coarse compartment has been developed in analogy with multi-plate settler. Data from simple column settling test can be used in the model to predict the filter performance. Furthermore, the model developed herein has been validated by successive experiments. The conventional column settling test has been found to be handy and useful to predict the performance of DHRF for different raw water characteristics (e.g. coagulated or uncoagulated water, different amounts of organic matter, etc.) and different initial process conditions (e.g. coagulant dose, mixing time and intensity, etc.). An optimum filter design for the coarse compartment (grain size 20 mm) has been found to be of 3m h(-1) filtration rate with filter length of 4-4.5 m.

  12. Grain boundaries: Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Balluffi, R.W.; Bristowe, P.D.

    1988-02-01

    Quantitative measurements of grain boundary structure factors using x-ray diffraction have been performed on low angle (001) twist boundaries in gold. Also, a computer atomistic simulation program is being implemented to examine the equilibrium properties of a series of boundaries in gold. Simulation of boundaries at room temperature have been performed. Electron microscopy of grain boundary melting in aluminum was also performed. Results indicated an absence of melting. (CBS)

  13. Behaviors of Deformation, Recrystallization and Textures Evolution of Columnar Grains in 3%Si Electrical Steel Slabs

    Directory of Open Access Journals (Sweden)

    SHAO Yuan-yuan

    2017-11-01

    Full Text Available The behaviors of deformation and recrystallization and textures evolution of 3% (mass fraction Si columnar-grained electrical steel slabs were investigated by electron backscatter diffractometer technique and X-ray diffraction. The results indicate that the three columnar-grained samples have different initial textures with the long axes arranged along rolling, transverse and normal directions. Three shear orientations can be obtained in surface layer after hot rolling, of which Goss orientation is formed easily. The α and γ fibre rolling orientations are obtained in RD sample, while strong γ fibre orientations in TD sample and sharp {100} orientations in ND sample are developed respectively. In addition, cube orientation can be found in all the three samples. The characteristics of hot rolled orientations in center region reveal distinct dependence on initial columnar-grained orientations. Strong {111}〈112〉 orientation in RD and TD samples separately comes from Goss orientation of hot rolled sheets, and sharp rotated cube orientation in ND sample originates from the initial {100} orientation of hot rolled sheets after cold rolling. Influenced by initial deviated orientations and coarse grain size, large orientation gradient of rotated cube oriented grain can be observed in ND sample. The coarse {100} orientated grains of center region in the annealed sheets show the heredity of the initial columnar-grained orientations.

  14. Tensile Properties of Medium Mn Steel with a Bimodal UFG α + γ and Coarse δ-Ferrite Microstructure

    Science.gov (United States)

    Lee, Seonjong; Shin, Sunmi; Kwon, Minhyeok; Lee, Kyooyoung; De Cooman, Bruno C.

    2017-04-01

    While the tensile strength and elongation obtained for medium Mn steel would appear to make it a candidate material in applications which require formable ultra-high strength materials, many secondary aspects of the microstructure-properties relationships have not yet been given enough attention. In this contribution, the microstructural and tensile properties of medium Mn steel with a bimodal microstructure consisting of an ultra-fine grained ferrite + austenite constituent and coarse-grained delta-ferrite are therefore reviewed in detail. The tensile properties of ultra-fine-grained intercritically annealed medium Mn steel reveal a complex dependence on the intercritical annealing temperature. This dependence is related to the influence of the intercritical annealing temperature on the activation of the plasticity-enhancing mechanisms in the microstructure. The kinetics of deformation twinning and strain-induced transformation in the ultra-fine grained austenite play a prominent role in determining the strain hardening of medium Mn steel. While excellent strength-ductility combinations are obtained when deformation twinning and strain-induced transformation occur gradually and in sequence, large elongations are also observed when strain-induced transformation plasticity is not activated. In addition, the localization of plastic flow is observed to occur in samples after intercritical annealing at intermediate temperatures, suggesting that both strain hardening and strain rate sensitivity are influenced by the properties of the ultra-fine-grained austenite.

  15. Retaining {1 0 0} texture from initial columnar grains in 6.5 wt% Si electrical steels

    Science.gov (United States)

    Liang, Ruiyang; Yang, Ping; Mao, Weimin

    2017-11-01

    6.5 wt% Si electrical steel is a superior soft magnetic material with excellent magnetic properties which highly depends on texture. In this study, based on the heredity of orientation in columnar grains, columnar grains are used as the initial material to prepare non-oriented 6.5 wt% Si electrical steel with excellent magnetic properties. EBSD and XRD techniques are adopted to explore the structure and texture evolution during hot rolling, warm rolling, cold rolling and annealing. The results show that, due to the heredity of ;structure and texture; from the initial strong {1 0 0} columnar grains, annealed sheet with {1 0 0} texture had better magnetic properties, which can be used as non-oriented high-silicon electrical steel. Both preferred cube grain nucleation in deformed {1 1 3} grains in subsurface and coarse {1 0 0} deformed grains in center layer show the effect of initial columnar grains with {1 0 0} texture.

  16. Development of two-stage grain grinder

    Directory of Open Access Journals (Sweden)

    V. N. Trubnikov

    2016-01-01

    Full Text Available The most important task in the development of the diet of farm animals feeding is a selection of the most balanced in its composition and most nutritious feeds, which are safe and meet all the necessary requirements at the same time. To evaluate the productive value of feeds and their effectiveness the rate of food productive action η was proposed. This ratio reflects the productive part of the total value of the exchange energy of the daily feed ration and is an essential criterion of the feed quality indicators. In the feed rations of animals the most expensive, but energy-rich feed is a mixed fodder, a mixture of grinded seeds of agricultural crops and protein, mineral and vitamin additives. In the diet for its nutritional value, this feed product is for cattle – 50, pigs – 60… 100 and birds – 100%. The basic operation in the production of mixed fodder is seeds grinding, i.e. their destruction under the influence of external forces, exceeding the forces of molecular adhesion of the grains particles. To grind the grain different ways are used: chopping, grinding, impact «in flight», crushing, etc. In the production of mixed fodder on the existing production equipment, there is the problem of getting the grain mixed fodder the necessary degree of grinding and uniform in its particle size distribution at the same time. When receiving too coarse grinding there is a problem of difficult digestibility of mixed fodder by farm animals. Moreover grinding process is accompanied by a high energy consumption. Grain grinder, the principle of which is based on the implementation of two ways of grinding grain: splitting and impact «in flight» is proposed. The proposed constructive solutions allow to obtain a high-performance technical means for crushing seeds of crops, as well as reduce energy costs that arise during the course of the process of obtaining of mixed fodder. The methodology justification of degree of grain grinding by

  17. The statistical mechanics of kinetically-controlled RNA folding pathways

    Science.gov (United States)

    Fernández, Ariel

    By systematically assigning weights to kinetically-controlled folding pathways we introduce a novel scheme of statistical inference. We provide supporting experimental evidence to show that this approach is suitable to explain the expediency and robustness of RNA folding. The statistical scheme is constructed in four stages, the last of which leads to a suitable representation that allows for direct comparison with experiment: a) An appropriate space of folding histories is defined; b) The space is endowed with a measure and in this way an ensemble is defined; c) The ensemble is systematically simplified by coarse-graining each copy or replica of conformation space. This procedure entails lumping together rapidly-interconverting conformations; d) A base-pair probability matrix (BPPM) is introduced by representing all structures contributing to the ensemble at a given instant. Thus, we take a convenient cross-section of the ensemble by taking a fixed instant in time. The BPPM is contrasted vis-a-vis experimental information on biologically-competent conformations. This last procedure is paramount to verify the theory. Moreover, the essential properties of folding are captured by showing that the statistical weight is concentrated on a very limited domain of closely-related folding pathways whose biological competence has been established experimentally.

  18. Sediment transport processes in the Pearl River Estuary as revealed by grain-size end-member modeling and sediment trend analysis

    Science.gov (United States)

    Li, Tao; Li, Tuan-Jie

    2017-07-01

    The analysis of grain-size distribution enables us to decipher sediment transport processes and understand the causal relations between dynamic processes and grain-size distributions. In the present study, grain sizes were measured from surface sediments collected in the Pearl River Estuary and its adjacent coastal areas. End-member modeling analysis attempts to unmix the grain sizes into geologically meaningful populations. Six grain-size end-members were identified. Their dominant modes are 0 Φ, 1.5 Φ, 2.75 Φ, 4.5 Φ, 7 Φ, and 8 Φ, corresponding to coarse sand, medium sand, fine sand, very coarse silt, silt, and clay, respectively. The spatial distributions of the six end-members are influenced by sediment transport and depositional processes. The two coarsest end-members (coarse sand and medium sand) may reflect relict sediments deposited during the last glacial period. The fine sand end-member would be difficult to transport under fair weather conditions, and likely indicates storm deposits. The three remaining fine-grained end-members (very coarse silt, silt, and clay) are recognized as suspended particles transported by saltwater intrusion via the flood tidal current, the Guangdong Coastal Current, and riverine outflow. The grain-size trend analysis shows distinct transport patterns for the three fine-grained end-members. The landward transport of the very coarse silt end-member occurs in the eastern part of the estuary, the seaward transport of the silt end-member occurs in the western part, and the east-west transport of the clay end-member occurs in the coastal areas. The results show that grain-size end-member modeling analysis in combination with sediment trend analysis help to better understand sediment transport patterns and the associated transport mechanisms.

  19. NONLINEAR MULTIGRID SOLVER EXPLOITING AMGe COARSE SPACES WITH APPROXIMATION PROPERTIES

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, Max La Cour [Technical Univ. of Denmark, Lyngby (Denmark); Villa, Umberto E. [Univ. of Texas, Austin, TX (United States); Engsig-Karup, Allan P. [Technical Univ. of Denmark, Lyngby (Denmark); Vassilevski, Panayot S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-01-22

    The paper introduces a nonlinear multigrid solver for mixed nite element discretizations based on the Full Approximation Scheme (FAS) and element-based Algebraic Multigrid (AMGe). The main motivation to use FAS for unstruc- tured problems is the guaranteed approximation property of the AMGe coarse spaces that were developed recently at Lawrence Livermore National Laboratory. These give the ability to derive stable and accurate coarse nonlinear discretization problems. The previous attempts (including ones with the original AMGe method, [5, 11]), were less successful due to lack of such good approximation properties of the coarse spaces. With coarse spaces with approximation properties, our FAS approach on un- structured meshes should be as powerful/successful as FAS on geometrically re ned meshes. For comparison, Newton's method and Picard iterations with an inner state-of-the-art linear solver is compared to FAS on a nonlinear saddle point problem with applications to porous media ow. It is demonstrated that FAS is faster than Newton's method and Picard iterations for the experiments considered here. Due to the guaranteed approximation properties of our AMGe, the coarse spaces are very accurate, providing a solver with the potential for mesh-independent convergence on general unstructured meshes.

  20. Role of electrostatics in the assembly pathway of a single-stranded RNA virus.

    Science.gov (United States)

    Garmann, Rees F; Comas-Garcia, Mauricio; Koay, Melissa S T; Cornelissen, Jeroen J L M; Knobler, Charles M; Gelbart, William M

    2014-09-01

    We have recently discovered (R. D. Cadena-Nava et al., J. Virol. 86:3318-3326, 2012, doi:10.1128/JVI.06566-11) that the in vitro packaging of RNA by the capsid protein (CP) of cowpea chlorotic mottle virus is optimal when there is a significant excess of CP, specifically that complete packaging of all of the RNA in solution requires sufficient CP to provide charge matching of the N-terminal positively charged arginine-rich motifs (ARMS) of the CPs with the negatively charged phosphate backbone of the RNA. We show here that packaging results from the initial formation of a charge-matched protocapsid consisting of RNA decorated by a disordered arrangement of CPs. This protocapsid reorganizes into the final, icosahedrally symmetric nucleocapsid by displacing the excess CPs from the RNA to the exterior surface of the emerging capsid through electrostatic attraction between the ARMs of the excess CP and the negative charge density of the capsid exterior. As a test of this scenario, we prepare CP mutants with extra and missing (relative to the wild type) cationic residues and show that a correspondingly smaller and larger excess, respectively, of CP is needed for complete packaging of RNA. Cowpea chlorotic mottle virus (CCMV) has long been studied as a model system for the assembly of single-stranded RNA viruses. While much is known about the electrostatic interactions within the CCMV virion, relatively little is known about these interactions during assembly, i.e., within intermediate states preceding the final nucleocapsid structure. Theoretical models and coarse-grained molecular dynamics simulations suggest that viruses like CCMV assemble by the bulk adsorption of CPs onto the RNA driven by electrostatic attraction, followed by structural reorganization into the final capsid. Such a mechanism facilitates assembly by condensing the RNA for packaging while simultaneously concentrating the local density of CP for capsid nucleation. We provide experimental evidence of