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Sample records for coarse grained lipid

  1. 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

  2. Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

    2010-01-01

    of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water....

  3. Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model

    NARCIS (Netherlands)

    Marrink, SJ; Risselada, J; Mark, AE

    The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to 8000 lipids. The critical step in the transformation process is the nucleation of a gel cluster

  4. 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.

  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. Why do arginine and lysine organize lipids differently? Insights from coarse-grained and atomistic simulations.

    Science.gov (United States)

    Wu, Zhe; Cui, Qiang; Yethiraj, Arun

    2013-10-10

    An important puzzle in membrane biophysics is the difference in the behaviors of lysine (Lys) and arginine (Arg) based peptides at the membrane. For example, the translocation of poly-Arg is orders of magnitude faster than that of poly-Lys. Recent experimental work suggests that much of the difference can be inferred from the phase behavior of peptide/lipid mixtures. At similar concentrations, mixtures of phosphatidylethanolamine (PE) and phosphatidylserine (PS) lipids display different phases in the presence of these polypeptides, with a bicontinuous phase observed with poly-Arg peptides and an inverted hexagonal phase observed with poly-Lys peptides. Here we show that simulations with the coarse-grained (CG) BMW-MARTINI model reproduce the experimental results. An analysis using atomistic and CG models reveals that electrostatic and glycerol-peptide interactions play a crucial role in determining the phase behavior of peptide-lipid mixtures, with the difference between Arg and Lys arising from the stronger interactions of the former with lipid glycerols. In other words, the multivalent nature of the guanidinium group allows Arg to simultaneously interact with both phosphate and glycerol groups, while Lys engages solely with phosphate; this feature of amino acid/lipid interactions has not been emphasized in previous studies. The Arg peptides colocalize with PS in regions of high negative Gaussian curvature and stabilize the bicontinuous phase. Decreasing the strength of either the electrostatic interactions or the peptide-glycerol interactions causes the inverted hexagonal phase to become more stable. The results highlight the utility of CG models for the investigation of phase behavior but also emphasize the subtlety of the phenomena, with small changes in specific interactions leading to qualitatively different phases.

  7. 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.

  8. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

    Energy Technology Data Exchange (ETDEWEB)

    Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)

    2010-09-15

    We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

  9. More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization

    Science.gov (United States)

    Bereau, Tristan; Wang, Zun-Jing; Deserno, Markus

    2014-03-01

    Interfacial systems are at the core of fascinating phenomena in many disciplines, such as biochemistry, soft-matter physics, and food science. However, the parametrization of accurate, reliable, and consistent coarse-grained (CG) models for systems at interfaces remains a challenging endeavor. In the present work, we explore to what extent two independently developed solvent-free CG models of peptides and lipids—of different mapping schemes, parametrization methods, target functions, and validation criteria—can be combined by only tuning the cross-interactions. Our results show that the cross-parametrization can reproduce a number of structural properties of membrane peptides (for example, tilt and hydrophobic mismatch), in agreement with existing peptide-lipid CG force fields. We find encouraging results for two challenging biophysical problems: (i) membrane pore formation mediated by the cooperative action of several antimicrobial peptides, and (ii) the insertion and folding of the helix-forming peptide WALP23 in the membrane.

  10. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations

    NARCIS (Netherlands)

    Risselada, H. Jelger; Marrink, Siewert J.

    2009-01-01

    The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high

  11. 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 co...

  12. 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...... macroscopic variables all produce identical long time relaxation behaviors. Hence, CTRW shed no light on the link between microscopic and macroscopic dynamics. We then highlight how a more recent approach, Record Dynamics (RD) provides a viable alternative, based on a very different set of physical ideas......: 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...

  13. Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures.

    Science.gov (United States)

    Pantelopulos, George A; Nagai, Tetsuro; Bandara, Asanga; Panahi, Afra; Straub, John E

    2017-09-07

    Model cellular membranes are known to form micro- and macroscale lipid domains dependent on molecular composition. The formation of macroscopic lipid domains by lipid mixtures has been the subject of many simulation investigations. We present a critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures. In the popular di-C16:0 PC:di-C18:2 PC:cholesterol at 35:35:30 ratio mixture, we find systems with a minimum of 1480 lipids to be necessary for the formation of macroscopic phase separated domains and systems of 10 000 lipids to achieve structurally converged conformations similar to the thermodynamic limit. To understand these results and predict the behavior of any mixture forming two phases, we develop and investigate an analytical Flory-Huggins model which is recursively validated using simulation and experimental data. We find that micro- and macroscale domains can coexist in ternary mixtures. Additionally, we analyze the distributions of specific lipid-lipid interactions in each phase, characterizing domain structures proposed based on past experimental studies. These findings offer guidance in selecting appropriate system sizes for the study of phase separations and provide new insights into the nature of domain structure for a popular ternary lipid mixture.

  14. Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures

    Science.gov (United States)

    Pantelopulos, George A.; Nagai, Tetsuro; Bandara, Asanga; Panahi, Afra; Straub, John E.

    2017-09-01

    Model cellular membranes are known to form micro- and macroscale lipid domains dependent on molecular composition. The formation of macroscopic lipid domains by lipid mixtures has been the subject of many simulation investigations. We present a critical study of system size impact on lipid domain phase separation into liquid-ordered and liquid-disordered macroscale domains in ternary lipid mixtures. In the popular di-C16:0 PC:di-C18:2 PC:cholesterol at 35:35:30 ratio mixture, we find systems with a minimum of 1480 lipids to be necessary for the formation of macroscopic phase separated domains and systems of 10 000 lipids to achieve structurally converged conformations similar to the thermodynamic limit. To understand these results and predict the behavior of any mixture forming two phases, we develop and investigate an analytical Flory-Huggins model which is recursively validated using simulation and experimental data. We find that micro- and macroscale domains can coexist in ternary mixtures. Additionally, we analyze the distributions of specific lipid-lipid interactions in each phase, characterizing domain structures proposed based on past experimental studies. These findings offer guidance in selecting appropriate system sizes for the study of phase separations and provide new insights into the nature of domain structure for a popular ternary lipid mixture.

  15. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 129; Issue 7. Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of α and β toxin nanopores in lipid membranes. RAJAT DESIKAN SWARNA M PATRA KUMAR SARTHAK PRABAL K MAITI K G AYAPPA. REGULAR ARTICLE ...

  16. Coarse Graining Shannon and von Neumann Entropies

    Directory of Open Access Journals (Sweden)

    Ana Alonso-Serrano

    2017-05-01

    Full Text Available The nature of coarse graining is intuitively “obvious”, but it is rather difficult to find explicit and calculable models of the coarse graining process (and the resulting entropy flow discussed in the literature. What we would like to have at hand is some explicit and calculable process that takes an arbitrary system, with specified initial entropy S, and that monotonically and controllably drives the entropy to its maximum value. This does not have to be a physical process, in fact for some purposes it is better to deal with a gedanken-process, since then it is more obvious how the “hidden information” is hiding in the fine-grain correlations that one is simply agreeing not to look at. We shall present several simple mathematically well-defined and easy to work with conceptual models for coarse graining. We shall consider both the classical Shannon and quantum von Neumann entropies, including models based on quantum decoherence, and analyse the entropy flow in some detail. When coarse graining the quantum von Neumann entropy, we find it extremely useful to introduce an adaptation of Hawking’s super-scattering matrix. These explicit models that we shall construct allow us to quantify and keep clear track of the entropy that appears when coarse graining the system and the information that can be hidden in unobserved correlations (while not the focus of the current article, in the long run, these considerations are of interest when addressing the black hole information puzzle.

  17. Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

    DEFF Research Database (Denmark)

    Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.

    2012-01-01

    through its charged and tryptophan residues. Upon binding, CETP rapidly (in about 10 ns) induced the formation of a small hydrophobic patch to the phospholipid surface of the droplet, opening a route from the core of the lipid droplet to the binding pocket of CETP. This was followed by a conformational...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....

  18. Quantum theory of multiscale coarse-graining

    Science.gov (United States)

    Han, Yining; Jin, Jaehyeok; Wagner, Jacob W.; Voth, Gregory A.

    2018-03-01

    Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

  19. Quantum theory of multiscale coarse-graining.

    Science.gov (United States)

    Han, Yining; Jin, Jaehyeok; Wagner, Jacob W; Voth, Gregory A

    2018-03-14

    Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

  20. An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations

    DEFF Research Database (Denmark)

    Siani, Pablo; de Souza, R M; Dias, L G

    2016-01-01

    in cellular systems and also affect physical properties of both biological and model lipid bilayers. In this paper we (i) provide a perspective on the existing literature on simulations of lipid bilayer systems containing oxidized lipid species as well as the main related experimental results, (ii) describe...

  1. Spacetime coarse grainings in nonrelativistic quantum mechanics

    International Nuclear Information System (INIS)

    Hartle, J.B.

    1991-01-01

    Sum-over-histories generalizations of nonrelativistic quantum mechanics are explored in which probabilities are predicted, not just for alternatives defined on spacelike surfaces, but for alternatives defined by the behavior of spacetime histories with respect to spacetime regions. Closed, nonrelativistic systems are discussed whose histories are paths in a given configuration space. The action and the initial quantum state are assumed fixed and given. A formulation of quantum mechanics is used which assigns probabilities to members of sets of alternative coarse-grained histories of the system, that is, to the individual classes of a partition of its paths into exhaustive and exclusive classes. Probabilities are assigned to those sets which decohere, that is, whose probabilities are consistent with the sum rules of probability theory. Coarse graining by the behavior of paths with respect to regions of spacetime is described. For example, given a single region, the set of all paths may be partitioned into those which never pass through the region and those which pass through the region at least once. A sum-over-histories decoherence functional is defined for sets of alternative histories coarse-grained by spacetime regions. Techniques for the definition and effective computation of the relevant sums over histories by operator-product formulas are described and illustrated by examples. Methods based on Euclidean stochastic processes are also discussed and illustrated. Models of decoherence and measurement for spacetime coarse grainings are described. Issues of causality are investigated. Such spacetime generalizations of nonrelativistic quantum mechanics may be useful models for a generalized quantum mechanics of spacetime geometry

  2. The gravitational description of coarse grained microstates

    Energy Technology Data Exchange (ETDEWEB)

    Alday, Luis F. [Institute for Theoretical Physics and Spinoza Institute, Utrecht University, 3508 TD Utrecht (Netherlands); Boer, Jan de [Instituut voor Theoretische Fysica, Valckenierstraat 65, 1018XE Amsterdam (Netherlands); Messamah, Ilies [Instituut voor Theoretische Fysica, Valckenierstraat 65, 1018XE Amsterdam (Netherlands)

    2006-12-15

    In this paper we construct a detailed map from pure and mixed half-BPS states of the D1-D5 system to half-BPS solutions of type IIB supergravity. Using this map, we can see how gravity arises through coarse graining microstates, and we can explicitly confirm the microscopic description of conical defect metrics, the M = 0 BTZ black hole and of small black rings. We find that the entropy associated to the natural geometric stretched horizon typically exceeds that of the mixed state from which the geometry was obtained.

  3. Coarse-Grained Modeling of Polyelectrolyte Solutions

    Science.gov (United States)

    Denton, Alan R.; May, Sylvio

    2014-03-01

    Ionic mixtures, such as electrolyte and polyelectrolyte solutions, have attracted much attention recently for their rich and challenging combination of electrostatic and non-electrostatic interparticle forces and their practical importance, from battery technologies to biological systems. Hydration of ions in aqueous solutions is known to entail ion-specific effects, including variable solubility of organic molecules, as manifested in the classic Hofmeister series for salting-in and salting-out of proteins. The physical mechanism by which the solvent (water) mediates effective interactions between ions, however, is still poorly understood. Starting from a microscopic model of a polyelectrolyte solution, we apply a perturbation theory to derive a coarse-grained model of ions interacting through both long-range electrostatic and short-range solvent-induced pair potentials. Taking these effective interactions as input to molecular dynamics simulations, we calculate structural and thermodynamic properties of aqueous ionic solutions. This work was supported by the National Science Foundation under Grant No. DMR-1106331.

  4. 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.

  5. 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

  6. 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...

  7. 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...

  8. 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.

  9. 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

  10. The MARTINI coarse-grained force field : Extension to proteins

    NARCIS (Netherlands)

    Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier; Larson, Ronald G.; Tieleman, D. Peter; Marrink, Siewert-Jan

    Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on

  11. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations

    NARCIS (Netherlands)

    Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules.

  12. A general-purpose coarse-grained molecular dynamics program

    Science.gov (United States)

    Aoyagi, Takeshi; Sawa, Fumio; Shoji, Tatsuya; Fukunaga, Hiroo; Takimoto, Jun-ichi; Doi, Masao

    2002-05-01

    In this article, we describe a general-purpose coarse-grained molecular dynamics program COGNAC ( COarse Grained molecular dynamics program by NAgoya Cooperation). COGNAC has been developed for general molecular dynamics simulation, especially for coarse-grained polymer chain models. COGNAC can deal with general molecular models, in which each molecule consists of coarse-grained atomic units connected by chemical bonds. The chemical bonds are specified by bonding potentials for the stretching, bending and twisting of the bonds, each of which are the functions of the position coordinates of the two, three and four atomic units. COGNAC can deal with both isotropic and anisotropic interactions between the non-bonded atomic units. As an example, the Gay-Berne potential is implemented. New potential functions can be added to the list of existing potential functions by users. COGNAC can do simulations for various situations such as under constant temperature, under constant pressure, under shear and elongational deformation, etc. Some new methods are implemented in COGNAC for modeling multiphase structures of polymer blends and block copolymers. A density biased Monte Carlo method and a density biased potential method can generate equilibrium chain configurations from the results of the self-consistent field calculations. Staggered reflective boundary conditions can generate interfacial structures with smaller system size compared with those of periodic boundary conditions.

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

    African Journals Online (AJOL)

    Analysis of mineral elements were carried out on some coarse grains used as staple food in Kano metropolis. The levels of Magnesium, Calcium, Manganese, Iron, Copper and Zinc were determined using atomic absorption spectrophotometer (AAS), and that of Sodium and Potassium were obtained using flame photometer ...

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

    African Journals Online (AJOL)

    In this work we attempt to predict the work of separation of crosslinked diglycidyl ether of bisphenol (A) (DGEBA) adhesive confined between two rigid adherends. To this end we start from merely the molecular structure of DGEBA and coarse grain the molecule into a chain comprised of three superatoms. These three ...

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

    African Journals Online (AJOL)

    Coarsegrained molecular dynamics simulation of cross – linking of DGEBA epoxy resin and estimation of the adhesive strength. ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like more ...

  16. Shear localization and microstructure in coarse grained beta titanium alloy

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Bingfeng, E-mail: biw009@ucsd.edu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Key Lab of Nonferrous Materials, Ministry of Education, Central South University, Changsha, Hunan (China); Wang, Xiaoyan [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Li, Zezhou [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Ma, Rui [School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhao, Shiteng [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Xie, Fangyu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhang, Xiaoyong [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China)

    2016-01-15

    Adiabatic shear localization plays an important role in the deformation and failure of the coarse grained beta titanium alloy Ti-5 Al-5 Mo-5 V-1 Cr-1 Fe with grain size about 1 mm at high strain rate deformation. Hat shaped specimens with different nominal shear strains are used to induce the formation of shear bands under the controlled shock-loading experiments. The true stress in the specimens can reach about 1040 MPa where the strain is about 1.83. The whole shear localization process lasts about 35 μs. The microstructures within the shear band are investigated by optical microscopy, scanning electron microscopy / electron backscatter diffraction, and transmission electron microscopy. The results show that the width of the shear bands decreases with increasing nominal shear strain, and the grains in the transition region near the shear band are elongated along the shear band, and the core of the shear band consists of the ultrafine deformed grains with width of 0.1 μm and heavy dislocations. With the aims of accommodating the imposed shear strain and maintaining neighboring grain compatibility, the grain subdivision continues to take place within the band. A fiber texture is formed in the core of the shear band. The calculated temperature rise in the shear band can reach about 722 K. Dynamic recovery is responsible for the formation of the microstructure in coarse grained beta titanium alloy.

  17. 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.

  18. Coarse grainings and irreversibility in quantum field theory

    International Nuclear Information System (INIS)

    Anastopoulos, C.

    1997-01-01

    In this paper we are interested in studying coarse graining in field theories using the language of quantum open systems. Motivated by the ideas of Hu and Calzetta on correlation histories we employ the Zwanzig projection technique to obtain evolution equations for relevant observables in self-interacting scalar field theories. Our coarse-graining operation consists in concentrating solely on the evolution of the correlation functions of degree less than n, a treatment which corresponds to the familiar truncation of the BBKGY hierarchy at the nth level. We derive the equations governing the evolution of mean-field and two-point functions thus identifying the terms corresponding to dissipation and noise. We discuss possible applications of our formalism, the emergence of classical behavior, and the connection to the decoherent histories framework. copyright 1997 The American Physical Society

  19. Towards coarse graining of discrete Lorentzian quantum gravity

    Science.gov (United States)

    Eichhorn, Astrid

    2018-02-01

    A first step towards implementing a notion of coarse graining in an intrinsically Lorentzian, discrete quantum-gravity approach, namely causal set quantum gravity, is taken. It makes use of an abstract notion of scale, based on counting the number of discrete elements. To that end, the space of actions for causal set quantum gravity is written in a matrix-model-like language, and a flow equation for the effective action of the model is derived from the path integral.

  20. Spreading of a Unilamellar Liposome on Charged Substrates: A Coarse-Grained Molecular Simulation.

    Science.gov (United States)

    Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng

    2016-04-19

    Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biomimetic applications. Although liposome spreading represents a common procedure for preparation of SLBs, the underlying mechanism is not yet fully understood, particularly from a molecular perspective. The present study examines the effects of the substrate charge on unilamellar liposome spreading on the basis of molecular dynamics simulations for a coarse-grained model of the solvent and lipid molecules. Liposome transformation into a lipid bilayer of different microscopic structures suggests three types of kinetic pathways depending on the substrate charge density, that is, top-receding, parachute, and parachute with wormholes. Each pathway leads to a unique distribution of the lipid molecules and thereby distinctive properties of SLBs. An increase of the substrate charge density results in a magnified asymmetry of the SLBs in terms of the ratio of charged lipids, parallel surface movements, and the distribution of lipid molecules. While the lipid mobility in the proximal layer is strongly correlated with the substrate potential, the dynamics of lipid molecules in the distal monolayer is similar to that of a freestanding lipid bilayer. For liposome spreading on a highly charged surface, wormhole formation promotes lipid exchange between the SLB monolayers thus reduces the asymmetry on the number density of lipid molecules, the lipid order parameter, and the monolayer thickness. The simulation results reveal the important regulatory role of electrostatic interactions on liposome spreading and the properties of SLBs.

  1. 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.

  2. Coarse-Grained Modeling of Molecular Machines in AAA+ Family

    Science.gov (United States)

    Yoshimoto, Kenji; Brooks, Charles L., III

    2007-03-01

    We present a new coarse-grained model of the large protein complexes which belong to AAA+ (ATPase associated with diverse cellular activities) family. The AAA+ proteins are highly efficient molecular machines driven by the ATP (adenosine triphosphate) binding and hydrolysis and are involved in various cellular events. While a number of groups are developing various coarse-grained models for different AAA+ proteins, the molecular details of ATP binding and hydrolysis are often neglected. In this study, we provide a robust approach to coarse-graining both the AAA+ protein and the ATP (or ADP) molecules. By imposing the distance restraints between the phosphates of the ATP and the neighboring Cα of the proteins, which are used to conserve a typical motif of ATP binding pocket, we are able to predict large conformational changes of the AAA+ proteins, such as replicative hexameric helicases. In the case of the hexameric LTag (large tumor antigen), the backbone RMSD between the predicted ATP-bound structure and the X-ray structure is 1.2 å, and the RMSD between the predicted ADP-bound structure and the X-ray structure is 1.5 å. Using the same approach, we also investigate conformational changes in the hexameric E1 protein, whose X-ray structure was recently solved with ssDNA, and give some insights into the molecular mechanisms of DNA translocation.

  3. Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

    Science.gov (United States)

    Bulacu, Monica; Goga, Nicolae; Zhao, Wei; Rossi, Giulia; Monticelli, Luca; Periole, Xavier; Tieleman, D Peter; Marrink, Siewert J

    2013-08-13

    Potentials routinely used in atomistic molecular dynamics simulations are not always suitable for modeling systems at coarse-grained resolution. For example, in the calculation of traditional torsion angle potentials, numerical instability is often encountered in the case of very flexible molecules. To improve the stability and accuracy of coarse-grained molecular dynamics simulations, we propose two approaches. The first makes use of improved forms for the angle potentials: the restricted bending (ReB) potential prevents torsion angles from visiting unstable or unphysical configurations and the combined bending-torsion (CBT) potential smoothly flattens the interactions when such configurations are sampled. In the second approach, dummy-assisted dihedral (DAD), the torsion potential is applied differently: instead of acting directly on the beads, it acts on virtual beads, bound to the real ones. For simple geometrical reasons, the unstable region is excluded from the accessible conformational space. The benefits of the new approaches are demonstrated in simulations of polyethylene glycol (PEG), polystyrene (PS), and polypeptide molecules described by the MARTINI coarse-grained force field. The new potentials are implemented in an in-house version of the Gromacs package, publicly available.

  4. 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.

  5. Static Recrystallized Grain Size of Coarse-Grained Austenite in an API-X70 Pipeline Steel

    Science.gov (United States)

    Sha, Qingyun; Li, Guiyan; Li, Dahang

    2013-12-01

    The effects of initial grain size and strain on the static recrystallized grain size of coarse-grained austenite in an API-X70 steel microalloyed with Nb, V, and Ti were investigated using a Gleeble-3800 thermomechanical simulator. The results indicate that the static recrystallized grain size of coarse-grained austenite decreases with decreasing initial grain size and increasing applied strain. The addition of microalloying elements can lead to a smaller initial grain size for hot deformation due to the grain growth inhibition during reheating, resulting in decreasing of static recrystallized grain size. Based on the experimental data, an equation for the static recrystallized grain size was derived using the least square method. The grain sizes calculated using this equation fit well with the measured ones compared with the equations for fine-grained austenite and for coarse-grained austenite of Nb-V microalloyed steel.

  6. 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.

  7. Coarse-grained modeling of RNA 3D structure.

    Science.gov (United States)

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  8. An exactly solvable coarse-grained model for species diversity

    International Nuclear Information System (INIS)

    Suweis, Samir; Maritan, Amos; Rinaldo, Andrea

    2012-01-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)

  9. 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.

  10. Fatigue damage in coarse-grained lean duplex stainless steels

    Energy Technology Data Exchange (ETDEWEB)

    Strubbia, R., E-mail: strubbia@ifir-conicet.gov.ar; Hereñú, S.; Marinelli, M.C.; Alvarez-Armas, I.

    2016-04-06

    The present investigation is focused on assessing the effect of a thermal treatment for grain coarsening on the low cycle fatigue damage evolution in two types of Lean Duplex Stainless Steels (LDSSs). The dislocation structure developed during cycling is observed by transmission electron microscopy (TEM). Additionally, a detailed analysis of short crack initiated and grown during low cycle fatigue (LCF) is performed by means of optical and scanning electron (SEM) microscopy in combination with automated electron back-scattered diffraction (EBSD) technique. Though in both coarse-grained LDSSs the short cracks nucleate in the ferrite phase, in each steels its origin is different. The embrittlement caused by the Cr{sub 2}N precipitation and the plastic activity sustained by each phase can explain this difference. The propagation behavior of the short cracks present two alternative growing mechanisms: the crack grows along a favorable slip plane with high Schmid Factor (SF) or the crack alternates between two slip systems. In both cases, the crack follows the path with the smallest tilt angle (β) at a grain boundary.

  11. 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)

  12. 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...

  13. Coarse-grain parallelism using remote method invocation

    International Nuclear Information System (INIS)

    Hebert, A.

    2003-01-01

    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)

  14. Classical predictability and coarse-grained evolution of the quantum baker's map

    International Nuclear Information System (INIS)

    Scherer, Artur; Soklakov, Andrei N.; Schack, Ruediger

    2006-01-01

    We investigate how classical predictability of the coarse-grained evolution of the quantum baker's map depends on the character of the coarse-graining. Our analysis extends earlier work by Brun and Hartle [Phys. Rev. D 60, 123503 (1999)] to the case of a chaotic map. To quantify predictability, we compare the rate of entropy increase for a family of coarse-grainings in the decoherent histories formalism. We find that the rate of entropy increase is dominated by the number of scales characterizing the coarse-graining

  15. Theory of Wavelet-Based Coarse-Graining Hierarchies for Molecular Dynamics

    Science.gov (United States)

    2017-04-01

    atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal. Soft Matter. 2008;4:859-869. 25. Ismail AE, Rutledge GC, Stephanopoulos G...Ismail AE, Stephanopoulos G, Rutledge GC. Topological coarse graining of polymer chains using wavelet-accelerated Monte Carlo. II. Self-avoiding chains. J

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

    African Journals Online (AJOL)

    DR. AMINU

    2014-06-01

    Jun 1, 2014 ... Analysis of mineral elements were carried out on some coarse grains used as staple food in Kano ... major part of human diets, are the most widely staple food used. At present, coarse grains have attracted more attention to common diet because they contain ..... retention of ascorbic acid, riboflavin and.

  17. 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

  18. 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.

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

    Science.gov (United States)

    Hoiles, William; Gupta, Rini; Cornell, Bruce; Cranfield, Charles; Krishnamurthy, Vikram

    2016-01-01

    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.

  20. 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.

  1. 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.

  2. Coarse-grained molecular simulations of allosteric cooperativity

    Energy Technology Data Exchange (ETDEWEB)

    Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)

    2016-03-14

    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 Ca{sup 2+} 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 are treated implicitly within the grand canonical ensemble. 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 energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.

  3. 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.

  4. Emerging dynamics arising from coarse-grained quantum systems

    Science.gov (United States)

    Duarte, Cristhiano; Carvalho, Gabriel Dias; Bernardes, Nadja K.; de Melo, Fernando

    2017-09-01

    The purpose of physics is to describe nature from elementary particles all the way up to cosmological objects like cluster of galaxies and black holes. Although a unified description for all this spectrum of events is desirable, this would be highly impractical. To not get lost in unnecessary details, effective descriptions are mandatory. Here we analyze the dynamics that may emerge from a full quantum description when one does not have access to all the degrees of freedom of a system. More concretely, we describe the properties of the dynamics that arise from quantum mechanics if one has access only to a coarse-grained description of the system. We obtain that the effective maps are not necessarily of Kraus form, due to correlations between accessible and nonaccessible degrees of freedom, and that the distance between two effective states may increase under the action of the effective map. We expect our framework to be useful for addressing questions such as the thermalization of closed quantum systems, as well as the description of measurements in quantum mechanics.

  5. A coarse-grained model for DNA origami

    Science.gov (United States)

    Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

    2018-01-01

    Abstract Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version. PMID:29267876

  6. 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.

  7. 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.

  8. Coarse-grained potentials of single-walled carbon nanotubes

    Science.gov (United States)

    Zhao, Junhua; Jiang, Jin-Wu; Wang, Lifeng; Guo, Wanlin; Rabczuk, Timon

    2014-11-01

    We develop the coarse-grained (CG) potentials of single-walled carbon nanotubes (SWCNTs) in CNT bundles and buckypaper for the study of the static and dynamic behaviors. The explicit expressions of the CG stretching, bending and torsion potentials for the nanotubes are obtained by the stick-spiral and the beam models, respectively. The non-bonded CG potentials between two different CG beads are derived from analytical results based on the cohesive energy between two parallel and crossing SWCNTs from the van der Waals interactions. We show that the CG model is applicable to large deformations of complex CNT systems by combining the bonded potentials with non-bonded potentials. Checking against full atom molecular dynamics calculations and our analytical results shows that the present CG potentials have high accuracy. The established CG potentials are used to study the mechanical properties of the CNT bundles and buckypaper efficiently at minor computational cost, which shows great potential for the design of micro- and nanomechanical devices and systems.

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

    Science.gov (United States)

    Ceres, N.; Lavery, R.

    2015-12-01

    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.

  10. A coarse-grained model for DNA origami.

    Science.gov (United States)

    Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

    2018-02-16

    Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

  11. 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.

  12. Coarse-grained Simulations of Substrate Export through Multidrug Efflux Transporter AcrB

    Science.gov (United States)

    Jewel, Yead; Dutta, Prashanta; Liu, Jin

    2017-11-01

    The treatment of bacterial infectious diseases hampered by the overexpression of multidrug resistance (MDR) systems. The MDR system actively pumps the antibiotic drugs as well as other toxic compounds out of the cells. During the pumping, AcrB (one of the key MDR components) undergoes a series of large-scale proton/substrate dependent conformational changes. In this work, we implement a hybrid coarse-grained PACE force field that couples the united-atom protein model with the coarse-grained MARTINI water/lipid, to investigate the conformational changes of AcrB. We first develop the substrate force field which is compatible with PACE, then we implement the force field to explore large scale structural changes of AcrB in microsecond simulations. The effects of the substrate and the protonation states of two key residues: Asp407 and Asp408, are investigated. Our results show that the drug export through AcrB is proton as well as substrate dependent. Our simulations explain molecular mechanisms of substrate transport through AcrB complex, as well as provide valuable insights for designing proper antibiotic drugs. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM122081.

  13. Coarse-Grained Simulations of 3D Printing

    Science.gov (United States)

    Wang, Zilu; Dobrynin, Andrey

    3D printing is a revolutionary manufacturing technique which makes it possible to fabricate a 3D object of any shape and size that is hard to make by traditional methods. We use coarse-grained molecular dynamics simulations to model the Continuous Liquid Interface Production (CLIP) 3D printing techniques. This technique utilizes a continuous curing of the liquid precursor by the UV light within a thin layer during pulling the crosslinked polymeric object out of a liquid pool. Our simulations show that the quality of the shape of the 3D printed objects is determined by a fine interplay between elastic and capillary forces. With decreasing the size of the printed features, the object shape deformations are controlled by optimization of the surface area of the exposed interface. This results in large deviations of the printed shape from the programed one. The high quality of the printed features is obtained when its size is larger than the elastocapillary length - ratio of the surface tension and modulus of crosslinked polymeric material. The condition when size of the feature becomes comparable with the elastocapillary length could be considered as a resolution limit for this 3D printing technique. Using our simulation results we have identified the source of the object shape deformations and developped a set of rules for calibration of the parameters to meet the accuracy requirements. To improve printing quality we have redesigned the CLIP 3D technique. Our simulations show that the proposed modifications of the printing process could improve printing quality. DMR-1624569.

  14. 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.

  15. Microscopic derivation of particle-based coarse-grained dynamics

    Science.gov (United States)

    Izvekov, Sergei

    2013-04-01

    In this paper we revisit the derivation of equations of motion for coarse-grained (CG) particles from the microscopic Hamiltonian dynamics of the underlying atomistic system in equilibrium. The derivation is based on the projection operator method and time-convolution equation. We demonstrate that due to the energy exchange between CG and intraparticle phase space coordinates in the microscopic system, the choice of projection operator is not unique, leading to different CG equations of motion that have the form of the nonlinear generalized Langevin equation (GLE). We derive the idempotence properties for the projection operators along the system trajectories and show that these properties result in streaming terms of the respective GLEs that are conservative forces and allow the expression of the non-conservative forces explicitly through thermodynamic averages, which can be measured from the microscopic simulations. The difference between GLEs that are presented herein lies in how the non-conservative forces are partitioned into dissipative and projected contributions. We compute the projected force and analyze conditions under which the projected (stochastic) force is orthogonal to (uncorrelated with) the momenta of CG particles, therefore justifying a transition to a framework of stochastic differential equations. We show that a position- and momentum-independent memory function appears only if the projected force is fully decoupled from the past CG positions and momenta, respectively. In the case of non-vanishing correlations between the projected force and the CG coordinates in past times, we derive explicitly the position- and momentum-dependent memory function in a form of projection onto a space spanned by N-order Hermite polynomials. The expressions presented herein can be used to construct a hierarchy of thermodynamically consistent CG models with momentum-dependent memory functions. They can also be used to design computational schemes for obtaining the

  16. Coarse-grained modeling of hybrid block copolymer system

    Science.gov (United States)

    Su, Yongrui

    This thesis is comprised of three major projects of my research. In the first project, I proposed a nanoparticle model and combined it with the Theoretically Informed Coarse Grained (TICG) model for pure polymer systems and the grand canonical slip springs model developed in our group to build a new model for entangled nanocomposites. With Molecule Dynamics(MD) simulation, I studied the mechanic properties of the nanocomposites, for example the influence of nanoparticles size and volume fraction on entanglements, the diffusion of polymers and nanoparticles, and the influence of nanoparticles size and volume fraction on viscosity et al.. We found that the addition of small-size nanoparticles reduces the viscosity of the nanocomposites, which is in contrary to what Einstein predicted a century ago. However, when particle increases its size to micrometers the Einstein predictions is recovered. From our simulation, we believe that small-size nanoparticles can more effectively decrease the entanglements of nanocomposites than larger particles. The free volume effect introduced by small-size nanoparticles also helps decrease the viscosity of the whole system. In the second project, I combined the Ohta-Kawasaki (OK) model [3] and the Covariance Matrix Adaptation Evolutionary Strategy(CMA-ES) to optimize the block copolymer blends self-assembly in the hole-shrink process. The aim is to predict the optimal composition and the optimal surface energy to direct the block copolymer blends self-assembly process in the confined hole. After optimization in the OK model, we calibrated the optimal results by the more reliable TICG model and got the same morphology. By comparing different optimization process, we found that the homopolymers which are comprised of the same monomers as either block of the block copolymer can form a perfect perforated hole and might have better performance than the pure block copolymer. While homopolymers which are comprised of a third-party monomers

  17. Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations.

    Science.gov (United States)

    Yoo, Jejoong; Cui, Qiang

    2009-10-21

    Although many membrane additives are known to modulate the activities of membrane proteins via perturbing the properties of lipid membrane, the underlying mechanism is often not precisely understood. In this study, we investigate the impact of asymmetrically incorporating single-tailed lysophosphatidylcholine (LPC) into a membrane bilayer using coarse-grained molecular dynamics simulations. Using a simple computational protocol designed to approximately mimic a micropipette setting, we show that asymmetric incorporation of LPC can lead to significant curvature in a bilayer. Detailed analysis of geometrical and mechanical properties (pressure profile) of the resulting mound structure indicates that the degree of pressure profile perturbation is determined not by the local curvature per se but by the packing of lipid headgroups (i.e., area-per-lipid). The findings help provide a concrete basis for understanding the activation mechanism of mechanosensitive channels by asymmetric incorporation of LPC into membrane patches in patch-clamp experiments. The calculated local pressure profiles are valuable to the construction of realistic membrane models for the analysis of mechanosensation in a continuum mechanics framework.

  18. Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

    Science.gov (United States)

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-01-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

  19. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model

    Science.gov (United States)

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

  20. 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...

  1. 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.

  2. 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.

  3. The role of microstructural aspects on the performance of coarse-grained superplastic Al alloys

    NARCIS (Netherlands)

    Chezan, A.R; de Hosson, J.T.M.; Houtte, PV; Kestens, L

    2005-01-01

    Deformed under optimum conditions of temperature and strain rate, coarse-grained aluminum alloys show elongation to failure in excess of 300%. The strain rate sensitivity index and the activation energy point to solute drag creep as the principal mechanism, a mechanism that has virtually no grain

  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

    generations. However, the adoption of such coarse-grained bit-rate granularity with lower flexibility for traffic grooming raises important questions: (1) What repercussions do they have on the overall power consumption and thus operational expenditures (OPEX) compared to legacy fine-grained designs (i...

  5. A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Roghayeh Abedi Karjiban

    2013-01-01

    Full Text Available The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC, dilauroylphosphatidylcholine (DLPC, dimyristoylphosphatidylcholine (DMPC, and distearoylphosphatidylcholine (DSPC in water were investigated using a coarse-grained molecular dynamics (CG-MD simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Statistical mechanics of coarse graining: estimating dynamical speedups from excess entropies.

    Science.gov (United States)

    Armstrong, J A; Chakravarty, C; Ballone, P

    2012-03-28

    The excess entropy of fluids has been shown to play a decisive role in the determination of dynamical properties [Y. Rosenfeld, Phys. Rev. A 15, 2545 (1977)]. We argue that it could play an equally important role in connecting dynamical properties of atomistic and coarse-grained models of molecular fluid systems. Molecular dynamics simulations for an atomistic and a coarse-grained model of water confirm the validity of this conjecture, showing that the sizable enhancement of the diffusion rate upon coarse-graining is a simple function of the difference in the excess entropy of the two models. This empirical observation could ease the way to a first-principles prediction of the relation of dynamical properties estimated from models at different resolution.

  11. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    Science.gov (United States)

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  12. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Rajat Desikan

    pore forming toxins (PFTs) in lipid membranes - Cytolysin A (ClyA), which is an example of an α toxin, and α-hemolysin (AHL) ... out mesoscopic simulations which are required to understand protomer oligomerization, pore formation and leakage. Keywords. ... large heterogeneous systems can elucidate important molecular ...

  13. Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

    International Nuclear Information System (INIS)

    Yang, Delian; Wang, Qiang

    2015-01-01

    We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N m monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N m

  14. Coarse-grained variables for particle-based models: diffusion maps and animal swarming simulations

    Science.gov (United States)

    Liu, Ping; Safford, Hannah R.; Couzin, Iain D.; Kevrekidis, Ioannis G.

    2014-12-01

    As microscopic (e.g. atomistic, stochastic, agent-based, particle-based) simulations become increasingly prevalent in the modeling of complex systems, so does the need to systematically coarse-grain the information they provide. Before even starting to formulate relevant coarse-grained equations, we need to determine the right macroscopic observables—the right variables in terms of which emergent behavior will be described. This paper illustrates the use of data mining (and, in particular, diffusion maps, a nonlinear manifold learning technique) in coarse-graining the dynamics of a particle-based model of animal swarming. Our computational data-driven coarse-graining approach extracts two coarse (collective) variables from the detailed particle-based simulations, and helps formulate a low-dimensional stochastic differential equation in terms of these two collective variables; this allows the efficient quantification of the interplay of "informed" and "naive" individuals in the collective swarm dynamics. We also present a brief exploration of swarm breakup and use data-mining in an attempt to identify useful predictors for it. In our discussion of the scope and limitations of the approach we focus on the key step of selecting an informative metric, allowing us to usefully compare different particle swarm configurations.

  15. 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

    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, Torus...

  16. FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS

    KAUST Repository

    Harmandaris, Vagelis

    2017-10-03

    The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.

  17. 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,

  18. 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.

  19. 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.

  20. 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

  1. 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 can...

  2. 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 standa...

  3. Embrittlement of Intercritically Reheated Coarse Grain Heat-Affected Zone of ASTM4130 Steel

    Science.gov (United States)

    Li, Liying; Han, Tao; Han, Bin

    2018-04-01

    In this investigation, a thermal welding simulation technique was used to investigate the microstructures and mechanical properties of the intercritically reheated coarse grain heat-affected zone (IR CGHAZ) of ASTM4130 steel. The effect of post weld heat treatment (PWHT) on the toughness of IR CGHAZ was also analyzed. The toughness of IR CGHAZ was measured by means of Charpy impact, and it is found that IR CGHAZ has the lowest toughness which is much lower than that of the base metal regardless of whether PWHT is applied or not. The as-welded IR CGHAZ is mainly composed of ferrite, martensite, and many blocky M-A constituents distributing along grain boundaries and subgrain boundaries in a near-connected network. Also, the prior austenite grains are still as coarse as those in the coarse grain heat-affected zone (CGHAZ). The presence of the blocky M-A constituents and the coarsened austenite grains result in the toughness deterioration of the as-welded IR CGHAZ. Most of the blocky M-A constituents are decomposed to granular bainite due to the effect of the PWHT. However, PWHT cannot refine the prior austenite grains. Thus, the low toughness of IR CGHAZ after PWHT can be attributed to two factors, i.e., the coarsened austenite grains, and the presence of the remaining M-A constituents and granular bainite, which are located at grain boundaries and subgrain boundaries in a near-connected network. The absorbed energy of the IR CGHAZ was increased by about 3.75 times, which means that the PWHT can effectively improve the toughness but it cannot be recovered to the level of base metal.

  4. Coarse-grained Monte Carlo simulations of non-equilibrium systems.

    Science.gov (United States)

    Liu, Xiao; Crocker, John C; Sinno, Talid

    2013-06-28

    We extend the scope of a recent method for generating coarse-grained lattice Metropolis Monte Carlo simulations [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012); and J. Chem. Phys. 138, 114104 (2013)] from continuous interaction potentials to non-equilibrium situations. The original method has been shown to satisfy detailed balance at the coarse scale and to provide a good representation of various equilibrium properties in both atomic and molecular systems. However, we show here that the original method is inconsistent with non-equilibrium trajectories generated by full-resolution Monte Carlo simulations, which, under certain conditions, have been shown to correspond to Langevin dynamics. The modified coarse-grained method is generated by simultaneously biasing the forward and backward transition probability for every possible move, thereby preserving the detailed balance of the original method. The resulting coarse-grained Monte Carlo simulations are shown to provide trajectories that are consistent with overdamped Langevin (Smoluchowski) dynamics using a sequence of simple non-equilibrium examples. We first consider the purely diffusional spreading of a Gaussian pulse of ideal-gas particles and then include an external potential to study the influence of drift. Finally, we validate the method using a more general situation in which the particles interact via a Lennard-Jones interparticle potential.

  5. 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.

  6. Effect of cooling rates on the weld heat affected zone coarse grain microstructure

    Directory of Open Access Journals (Sweden)

    Roman Celin

    2018-04-01

    Full Text Available The effect of a cooling rate on the S690Q quenched and tempered steel welded joint coarse grain heat affected zone microstructure was investigated using a dilatometer with controlled heating and cooling fixture. Steel samples were heated to a peak temperature of 1350 °C and cooled at the different cooling time Dt8/5. A dilatometric analysis and hardness measurements of the simulated thermal cycle coarse grain samples were done. Transformation start and finish temperature were determined using dilatation vs. temperature data analysis. The microstructure of the sample with a cooling time 5 s consists of martensite, whereas at cooling time 80 s a bainitic microstructure was observed. The investigated steel cooling cycle using simulation approach makes possible to determine the range of an optimum CG HAZ cooling time for the welding.

  7. 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...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced.......We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...

  8. Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

    Science.gov (United States)

    Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

    2014-05-14

    A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.

  9. Simulating Cellulose Structure, Properties, Thermodynamics, Synthesis, and Deconstruction with Atomistic and Coarse-Grain Models

    Energy Technology Data Exchange (ETDEWEB)

    Crowley, M. F.; Matthews, J.; Beckham, G.; Bomble, Y.; Hynninen, A. P.; Ciesielski, P. F.

    2012-01-01

    Cellulose is still a mysterious polymer in many ways: structure of microfibrils, thermodynamics of synthesis and degradation, and interactions with other plant cell wall components. Our aim is to uncover the details and mechanisms of cellulose digestion and synthesis. We report the details of the structure of cellulose 1-beta under several temperature conditions and report here the results of these studies and connections to experimental measurements and the measurement in-silico the free energy of decrystallization of several morphologies of cellulose. In spatially large modeling, we show the most recent work of mapping atomistic and coarse-grain models into tomographic images of cellulose and extreme coarse-grain modeling of interactions of large cellulase complexes with microfibrils. We discuss the difficulties of modeling cellulose and suggest future work both experimental and theoretical to increase our understanding of cellulose and our ability to use it as a raw material for fuels and materials.

  10. BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

    Science.gov (United States)

    Abrahamsson, Erik; Plotkin, Steven S

    2009-09-01

    Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

  11. 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.

  12. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

    Science.gov (United States)

    Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

    2018-01-01

    We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

  13. 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

  14. Determination of residual stress within complex-shaped coarse-grained cobalt-chrome biomedical castings

    OpenAIRE

    Conroy, Brian P; Tanner, David A

    2016-01-01

    peer-reviewed ASTM F75 femoral knee implant casting components distort during manufacture due to residual stress re-distribution or inducement. These castings pose a number of challenges for residual stress determination methods; they have a complex geometry, their micro-structure is inhomogeneous, they work-harden rapidly and they have a coarse, elastically-anisotropic grain structure. The contour method is anticipated to be the most promising residual stress determination technique. X-ra...

  15. Coarse-grained simulation of a real-time process control network under peak load

    International Nuclear Information System (INIS)

    George, A.D.; Clapp, N.E. Jr.

    1992-01-01

    This paper presents a simulation study on the real-time process control network proposed for the new ANS reactor system at ORNL. A background discussion is provided on networks, modeling, and simulation, followed by an overview of the ANS process control network, its three peak-load models, and the results of a series of coarse-grained simulation studies carried out on these models using implementations of 802.3, 802.4, and 802.5 standard local area networks

  16. Rapid Functional Modelling and Simulation of Coarse Grained Reconfigurable Array Architectures

    OpenAIRE

    Patel, Kunjan; McGettrick, Séamas; Bleakley, Chris J.

    2011-01-01

    Increases in the complexity of Coarse Grained Reconfigurable Array (CGRA) architectures have made implementation of new architectures difficult and time consuming. Due to the large number of design options available, it is difficult for designers to make optimal design decisions in the early stages of the design cycle. This paper proposes a novel functional modelling framework for CGRA architectures which makes the design space exploration process easier and faster. The framework allows archi...

  17. A coarse grained description of time evolution: Irreversible state reduction and time-energy relation

    International Nuclear Information System (INIS)

    Bonifacio, R.; Milan Univ.

    1983-05-01

    We show that a proper coarse-grained description of time evolution leads to a finite difference equation with step tau for the density operator. This implies state reduction to the diagonal form in the energy representation and a quasi ergodic behaviour of quantum mechanical ensemble averages. An intrinsic time-energy relation tauΔE>=(h/2π)/2 is proposed, and its equivalence to a time quantization is discussed. (author)

  18. REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes

    Energy Technology Data Exchange (ETDEWEB)

    Moritsugu, K [University of Heidelberg; Smith, Jeremy C [ORNL

    2008-08-01

    Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all {alpha}), plastocyanin (all {beta}), and dihydrofolate reductase ({alpha}/{beta}) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations.

  19. Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes

    Energy Technology Data Exchange (ETDEWEB)

    Moritsugu, K [University of Heidelberg; Smith, Jeremy C [ORNL

    2008-05-01

    Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all {alpha}), plastocyanin (all {beta}), and dihydrofolate reductase ({alpha}/{beta}) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations.

  20. 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).

  1. Multiscale simulation of thin-film lubrication: free-energy-corrected coarse graining.

    Science.gov (United States)

    Wu, Z-B; Zeng, X C

    2014-09-01

    The quasicontinuum method was previously extended to the nonzero temperature conditions by implementing a free-energy correction on non-nodal atoms in coarse-grained solid systems to avoid the dynamical constraint, [Diestler, Wu, and Zeng, J. Chem. Phys. 121, 9279 (2004)]. In this paper, we combine the extended quasicontinuum method and an atomistic simulation to treat the monolayer film lubrication with elastic (nonrigid) substrates. It is shown that the multiscale method with the coarse-graining local elements in the merging regions between the atomistic and continuous descriptions of the substrates can reasonably predict the shear stress profile, the mean separation curve, and the transverse stress profile in the fully atomistic simulation for the tribological system. Moreover, when the nonlocal elements are placed in the merging regions, the inhomogeneous solid atoms in the near regions covered by the cut-off circles of the nonlocal elements replace the homogeneous ones at the equilibrium configuration for the free-energy correction on the non-nodal atoms. The treatment can cause an unphysical sliding between the near and far regions of the upper substrate. It is shown that if the free-energy correction on the non-nodal atoms in the coarse-grained merging regions is removed, the multiscale method can still well reproduce the shear stress profile, the mean separation curve, and the transverse stress profile obtained from the fully atomistic simulation for the system.

  2. An Information-Theoretic Perspective on Coarse-Graining, Including the Transition from Micro to Macro

    Directory of Open Access Journals (Sweden)

    Kristian Lindgren

    2015-05-01

    Full Text Available An information-theoretic perspective on coarse-graining is presented. It starts with an information characterization of configurations at the micro-level using a local information quantity that has a spatial average equal to a microscopic entropy. With a reversible micro dynamics, this entropy is conserved. In the micro-macro transition, it is shown how this local information quantity is transformed into a macroscopic entropy, as the local states are aggregated into macroscopic concentration variables. The information loss in this transition is identified, and the connection to the irreversibility of the macro dynamics and the second law of thermodynamics is discussed. This is then connected to a process of further coarse-graining towards higher characteristic length scales in the context of chemical reaction-diffusion dynamics capable of pattern formation. On these higher levels of coarse-graining, information flows across length scales and across space are defined. These flows obey a continuity equation for information, and they are connected to the thermodynamic constraints of the system, via an outflow of information from macroscopic to microscopic levels in the form of entropy production, as well as an inflow of information, from an external free energy source, if a spatial chemical pattern is to be maintained.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

    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

  4. Using phase information to enhance speckle noise reduction in the ultrasonic NDE of coarse grain materials

    Science.gov (United States)

    Lardner, Timothy; Li, Minghui; Gachagan, Anthony

    2014-02-01

    Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.

  5. Ensemble Empirical Mode Decomposition based methodology for ultrasonic testing of coarse grain austenitic stainless steels.

    Science.gov (United States)

    Sharma, Govind K; Kumar, Anish; Jayakumar, T; Purnachandra Rao, B; Mariyappa, N

    2015-03-01

    A signal processing methodology is proposed in this paper for effective reconstruction of ultrasonic signals in coarse grained high scattering austenitic stainless steel. The proposed methodology is comprised of the Ensemble Empirical Mode Decomposition (EEMD) processing of ultrasonic signals and application of signal minimisation algorithm on selected Intrinsic Mode Functions (IMFs) obtained by EEMD. The methodology is applied to ultrasonic signals obtained from austenitic stainless steel specimens of different grain size, with and without defects. The influence of probe frequency and data length of a signal on EEMD decomposition is also investigated. For a particular sampling rate and probe frequency, the same range of IMFs can be used to reconstruct the ultrasonic signal, irrespective of the grain size in the range of 30-210 μm investigated in this study. This methodology is successfully employed for detection of defects in a 50mm thick coarse grain austenitic stainless steel specimens. Signal to noise ratio improvement of better than 15 dB is observed for the ultrasonic signal obtained from a 25 mm deep flat bottom hole in 200 μm grain size specimen. For ultrasonic signals obtained from defects at different depths, a minimum of 7 dB extra enhancement in SNR is achieved as compared to the sum of selected IMF approach. The application of minimisation algorithm with EEMD processed signal in the proposed methodology proves to be effective for adaptive signal reconstruction with improved signal to noise ratio. This methodology was further employed for successful imaging of defects in a B-scan. Copyright © 2014. Published by Elsevier B.V.

  6. 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).

  7. 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

  8. Fundamental Pair Interactions and Applications for Colloidal Silica Particles by Coarse-Grained Simulations

    International Nuclear Information System (INIS)

    Lee, Cheng K.; Hua, Chi C.

    2008-01-01

    In the first part of this presentation, we introduce how the fundamental pair interactions for colloidal silica particles may be constracted from a self-consistent mapping procedure and coarse-grained simulation without introducing adjustable parameters. Force fields for silica particles with diameter ranging from 1 nm to 100 nm are reported and tabulated in a simple analytical form. In the second part, we describe how the previously obtained force fields may be utilized for modeling rod-like colloidal systems. Focus is on exploring the effects of force field and particulate aspect ratio on the thermodynamic and rheological properties

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

    Science.gov (United States)

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

    2015-07-28

    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.

  10. Coarse-Grained Dynamics of Protein Synthesis in a Cell-Free System

    Science.gov (United States)

    Karzbrun, Eyal; Shin, Jonghyeon; Bar-Ziv, Roy H.; Noireaux, Vincent

    2011-01-01

    A complete gene expression reaction is reconstituted in a cell-free system comprising the entire endogenous transcription, translation, as well as mRNA and protein degradation machinery of E. coli. In dissecting the major reaction steps, we derive a coarse-grained enzymatic description of biosynthesis and degradation, from which ten relevant rate constants and concentrations are determined. Governed by zeroth-order degradation, protein expression follows a sharp transition from undetectable levels to constant-rate accumulation, without reaching steady state.

  11. 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

    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...

  12. The random phase transducer in ultrasonic NDT of coarse grain stainless steel

    International Nuclear Information System (INIS)

    Bordier, J.M.; Fink, M.; Le Brun, A.; Cohen-Tenoudji, F.

    1993-11-01

    Ultrasonic NDT of cast stainless steel is known to be difficult due to a huge loss of focussing of the ultrasonic beam, and to a high level speckle noise generated by the coarse grain structure. In this paper, we describe the principle of the ultrasonic random phase transducer. Experimental results are compared with those obtained with a standard spatial compound technique. We show that the random phase transducer is a good tool to characterize the multiple scattering process generated by these materials. (authors). 7 figs., 11 refs

  13. 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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)

    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.

  16. 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.

  17. 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

  18. Deformation bands in ⟨120⟩ grains in coarse-grained aluminium

    DEFF Research Database (Denmark)

    Bilde-Sørensen, Jørgen

    1986-01-01

    ](111) and (a/2)[011](111), allowing for glide only, are tilt boundaries with a normal [001] and a rotation axis along [110] and twist boundaries with a normal [100] and a rotation axis along [100]. A consideration of the boundary energies indicates that the twist boundary has a lower energy than the tilt...... to [001], the boundaries between the bands were parallel to [010] and the neighbouring bands were rotated around [100] with respect to one another. Two slip systems in a critical relationship are equally stressed with a Schmid factor of 0.49 in grains with a [120] orientation, namely (a/2...

  19. 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.

  20. Kelp, cobbles, and currents: Biologic reduction of coarse grain entrainment stress

    Science.gov (United States)

    Masteller, Claire C; Finnegan, Noah J; Warrick, Jonathan; Miller, Ian M.

    2015-01-01

    Models quantifying the onset of sediment motion do not typically account for the effect of biotic processes because they are difficult to isolate and quantify in relation to physical processes. Here we investigate an example of the interaction of kelp (Order Laminariales) and coarse sediment transport in the coastal zone, where it is possible to directly quantify and test its effect. Kelp is ubiquitous along rocky coastlines and the impact on ecosystems has been well studied. We develop a physical model to explore the reduction in critical shear stress of large cobbles colonized by Nereocystis luetkeana, or bull kelp. Observations of coarse sediment motion at a site in the Strait of Juan de Fuca (northwest United States–Canada boundary channel) confirm the model prediction and show that kelp reduces the critical stress required for transport of a given grain size by as much as 92%, enabling annual coarse sediment transport rates comparable to those of fluvial systems. We demonstrate that biology is fundamental to the physical processes that shape the coastal zone in this setting.

  1. 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

  2. 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.

  3. Path statistics, memory, and coarse-graining of continuous-time random walks on networks

    Science.gov (United States)

    Manhart, Michael; Kion-Crosby, Willow; Morozov, Alexandre V.

    2015-12-01

    Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs.

  4. 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.

  5. 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.

  6. 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'.

  7. Parameterizing the Morse potential for coarse-grained modeling of blood plasma

    International Nuclear Information System (INIS)

    Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

    2014-01-01

    Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately

  8. Systematic hierarchical coarse-graining with the inverse Monte Carlo method

    International Nuclear Information System (INIS)

    Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.; Laaksonen, Aatto

    2015-01-01

    We outline our coarse-graining strategy for linking micro- and mesoscales of soft matter and biological systems. The method is based on effective pairwise interaction potentials obtained in detailed ab initio or classical atomistic Molecular Dynamics (MD) simulations, which can be used in simulations at less accurate level after scaling up the size. The effective potentials are obtained by applying the inverse Monte Carlo (IMC) method [A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E 52(4), 3730–3737 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. An in-house software package MagiC is developed to obtain the effective potentials for arbitrary molecular systems. In this work we compute effective potentials to model DNA-protein interactions (bacterial LiaR regulator bound to a 26 base pairs DNA fragment) at physiological salt concentration at a coarse-grained (CG) level. Normally the IMC CG pair-potentials are used directly as look-up tables but here we have fitted them to five Gaussians and a repulsive wall. Results show stable association between DNA and the model protein as well as similar position fluctuation profile

  9. 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.

  10. Coarse-grained model for the interconversion between different crystalline cellulose allomorphs

    Energy Technology Data Exchange (ETDEWEB)

    Langan, Paul [ORNL

    2012-01-01

    We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.

  11. 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.

  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. 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.

  14. Coarse-grained molecular dynamics simulation of DNA translocation in chemically modified nanopores.

    Science.gov (United States)

    Ramachandran, Abhijit; Guo, Qingjiang; Iqbal, Samir M; Liu, Yaling

    2011-05-19

    Solid-state nanopores provide a direct means to detect and analyze DNA and proteins. In a typical setup, the DNA molecules travel through a nanopore under electrophoretic voltage bias. The nanopore is sandwiched between two chambers that are filled with ionic solution. A major challenge in using solid-state nanopores for DNA sequencing and gene detection is to improve their selectivity and detection sensitivity. To achieve these goals, one solution is to functionalize the nanopores by chemically modifying the pore walls with silanes or nucleic acids. However, little is known about molecular interactions in functionalized nanopores. This paper presents DNA translocation dynamics and the mechanism of DNA sequencing in a functionalized nanopore through a coarse-grained molecular dynamics model. The DNA nucleotide is coarse-grained into two interaction sites: one site corresponds to the base group and the other encompasses the phosphate and sugar groups. The water molecules are included in the model implicitly through Langevin dynamics. The coarse-grained model immensely improves the computational efficiency while still capturing the essential translocation dynamics. The model characterizes important physical properties of functionalized nanopores such as the effective pore diameter and effect of biasing voltage on the DNA translocation dynamics. The model reveals a nonlinear relationship between translocation speed of DNA and applied voltage. Moreover, DNA translocation in nanopores functionalized with hairpin-loop (HPL) DNA and single-stranded DNA (ss-DNA) shows significant differences: a target DNA is found to translocate through a ss-DNA coated nanopore 9 times faster than through an HPL coated one at a bias of 100 mV, putatively from lower stiffness of ss-DNA than that for HPL. The DNA translocation speed is also largely influenced by interaction potential between the DNA and surface-tethered molecules. The results reveal that such selective translocation

  15. A coarse-grained generalized second law for holographic conformal field theories

    Science.gov (United States)

    Bunting, William; Fu, Zicao; Marolf, Donald

    2016-03-01

    We consider the universal sector of a d\\gt 2 dimensional large-N strongly interacting holographic CFT on a black hole spacetime background B. When our CFT d is coupled to dynamical Einstein-Hilbert gravity with Newton constant G d , the combined system can be shown to satisfy a version of the thermodynamic generalized second law (GSL) at leading order in G d . The quantity {S}{CFT}+\\frac{A({H}B,{perturbed})}{4{G}d} is non-decreasing, where A({H}B,{perturbed}) is the (time-dependent) area of the new event horizon in the coupled theory. Our S CFT is the notion of (coarse-grained) CFT entropy outside the black hole given by causal holographic information—a quantity in turn defined in the AdS{}d+1 dual by the renormalized area {A}{ren}({H}{{bulk}}) of a corresponding bulk causal horizon. A corollary is that the fine-grained GSL must hold for finite processes taken as a whole, though local decreases of the fine-grained generalized entropy are not obviously forbidden. Another corollary, given by setting {G}d=0, states that no finite process taken as a whole can increase the renormalized free energy F={E}{out}-{{TS}}{CFT}-{{Ω }}J, with T,{{Ω }} constants set by {H}B. This latter corollary constitutes a 2nd law for appropriate non-compact AdS event horizons.

  16. Modification of Hazen's equation in coarse grained soils by soft computing techniques

    Science.gov (United States)

    Kaynar, Oguz; Yilmaz, Isik; Marschalko, Marian; Bednarik, Martin; Fojtova, Lucie

    2013-04-01

    Hazen first proposed a Relationship between coefficient of permeability (k) and effective grain size (d10) was first proposed by Hazen, and it was then extended by some other researchers. However many attempts were done for estimation of k, correlation coefficients (R2) of the models were generally lower than ~0.80 and whole grain size distribution curves were not included in the assessments. Soft computing techniques such as; artificial neural networks, fuzzy inference systems, genetic algorithms, etc. and their hybrids are now being successfully used as an alternative tool. In this study, use of some soft computing techniques such as Artificial Neural Networks (ANNs) (MLP, RBF, etc.) and Adaptive Neuro-Fuzzy Inference System (ANFIS) for prediction of permeability of coarse grained soils was described, and Hazen's equation was then modificated. It was found that the soft computing models exhibited high performance in prediction of permeability coefficient. However four different kinds of ANN algorithms showed similar prediction performance, results of MLP was found to be relatively more accurate than RBF models. The most reliable prediction was obtained from ANFIS model.

  17. 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.

  18. Coarse-grained entropy decrease and phase-space focusing in Hamiltonian dynamics

    International Nuclear Information System (INIS)

    Pattanayak, Arjendu K.; Brooks, Daniel W.C.; Fuente, Anton de la; Uricchio, Lawrence; Holby, Edward; Krawisz, Daniel; Silva, Jorge I.

    2005-01-01

    We analyze the behavior of the coarse-grained entropy for classical probabilities in nonlinear Hamiltonians. We focus on the result that if the trajectory dynamics are integrable, the probability ensemble shows transient increases in the coherence, corresponding to an increase in localization of the ensemble and hence the phase-space density of the ensemble. We discuss the connection of these dynamics to the problem of cooling in atomic ensembles. We show how these dynamics can be understood in terms of the behavior of individual trajectories, allowing us to manipulate ensembles to create 'cold' dense final ensembles. We illustrate these results with an analysis of the behavior of particular nonlinear integrable systems, including discussions of the spin-echo effect and the seeming violation of Liouville's theorem

  19. Influences of nanotwin volume fraction on the ballistic performance of coarse-grained metals

    Directory of Open Access Journals (Sweden)

    Q.D. Ouyang

    2017-09-01

    Full Text Available Coarse-grained (CG metals strengthened by nanotwinned (NT regions possess high strength and good ductility. As such, they are very suitable for applications in bullet-proof targets. Here, a numerical model based on the conventional theory of strain gradient plasticity and the Johnson–Cook failure criterion is employed to study the influences of volume fraction of NT regions on their ballistic performance. The results show that in general a relatively small twin spacing (4–10 nm and a moderate volume fraction (7%–20% will lead to excellent limit velocity and that the influences of volume fraction on limit displacement change with the category of impact processes.

  20. Star polymers as unit cells for coarse-graining cross-linked networks

    Science.gov (United States)

    Molotilin, Taras Y.; Maduar, Salim R.; Vinogradova, Olga I.

    2018-03-01

    Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the reduced network. Here we study polymer networks in a good solvent, by considering star polymers as their unit elements, and first quantify the interaction between their centers of masses. We then reduce the complexity of a network by replacing sets of its bridged star polymers by equivalent effective soft particles with dense cores. Our coarse graining allows us to approximate complex polymer networks by much simpler ones, keeping their relevant mechanical properties, as illustrated in computer experiments.

  1. Multiscale Modeling at Nanointerfaces: Polymer Thin Film Materials Discovery via Thermomechanically Consistent Coarse Graining

    Science.gov (United States)

    Hsu, David D.

    Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational

  2. On fast iterative mapping algorithms for stripe based coarse-grained reconfigurable architectures

    Science.gov (United States)

    Mehta, Gayatri; Patel, Krunalkumar; Pollard, Nancy S.

    2015-01-01

    Reconfigurable devices have potential for great flexibility/efficiency, but mapping algorithms onto these architectures is a long-standing challenge. This paper addresses this challenge for stripe based coarse-grained reconfigurable architectures (CGRAs) by drawing on insights from graph drawing. We adapt fast, iterative algorithms from hierarchical graph drawing to the problem of mapping to stripe based architectures. We find that global sifting is 98 times as fast as simulated annealing and produces very compact designs with 17% less area on average, at a cost of 5% greater wire length. Interleaving iterations of Sugiyama and global sifting is 40 times as fast as simulated annealing and achieves somewhat more compact designs with 1.8% less area on average, at a cost of only 1% greater wire length. These solutions can enable fast design space exploration, rapid performance testing, and flexible programming of CGRAs "in the field."

  3. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

    Science.gov (United States)

    Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  4. Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model

    Science.gov (United States)

    Wu, Shuai; Zhan, Hai-yi; Wang, Hong-ming; Ju, Yan

    2012-04-01

    The secondary structure of different Iβ cellulose was analyzed by a molecular dynamics simulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N 4 of 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N 8 of 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.

  5. Computational study of imperfect networks using a coarse-grained model

    Science.gov (United States)

    Sliozberg, Yelena R.; Chantawansri, Tanya L.

    2013-11-01

    The structural and mechanical properties of imperfect entangled polymer networks with various fractions of elastically active chains are studied using a generic coarse-grained model. Network topology is analyzed at various degrees of cross-linking and correlated with the mechanical response under uniaxial deformation at various strain rates. We found excellent agreement between results obtained from the structural analysis and from fitting to stress relaxation data. The relaxation tensile modulus at various engineering strains was also calculated as a function of the fraction of active strands. Results indicate that the mechanical and viscoelastic properties of entangled polymer networks are susceptible to variation in the network structure, where defects can affect the mechanical response especially at low strain rates and the relaxation behavior at long times.

  6. 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.

  7. 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.

  8. Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

    Science.gov (United States)

    Plimpton, Steve

    Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Frank C Pickard

    2014-07-01

    Full Text Available 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.

  11. 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

  12. Design of a rotamer library for coarse-grained models in protein-folding simulations.

    Science.gov (United States)

    Larriva, María; Rey, Antonio

    2014-01-27

    Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, and X-ray and NMR structure validation. However, they usually present too much information and are not always fully compatible with the coarse-grained models of the protein geometry that are frequently used to tackle the protein-folding problem through molecular simulation. In this work, we introduce a new backbone-dependent rotamer library for side chains compatible with low-resolution models in polypeptide chains. We have dispensed with an atomic description of proteins, representing each amino acid side chain by its geometric center (or centroid). The resulting rotamers have been estimated from a statistical analysis of a large structural database consisting of high-resolution X-ray protein structures. As additional information, each rotamer includes the frequency with which it has been found during the statistical analysis. More importantly, the library has been designed with a careful control to ensure that the vast majority of side chains in protein structures (at least 95% of residues) are properly represented. We have tested our library using an independent set of proteins, and our results support a good correlation between the reconstructed centroids from our rotamer library and those in the experimental structures. This new library can serve to improve the definition of side chain centroids in coarse-grained models, avoiding at the same time an excessive additional complexity in a geometric model for the polypeptide chain.

  13. Experimental fossilization of mat-forming cyanobacteria in coarse-grained siliciclastic sediments.

    Science.gov (United States)

    Newman, S A; Klepac-Ceraj, V; Mariotti, G; Pruss, S B; Watson, N; Bosak, T

    2017-07-01

    Microbial fossils and textures are commonly preserved in Ediacaran and early Cambrian coarse-grained siliciclastic sediments that were deposited in tidal and intertidal marine settings. In contrast, the fossilization of micro-organisms in similar marine environments of post-Cambrian age is less frequently reported. Thus, temporal discrepancies in microbial preservation may have resulted from the opening and closing of a unique taphonomic window during the terminal Proterozoic and early Phanerozoic, respectively. Here, we expand upon previous work to identify environmental factors which may have facilitated the preservation of cyanobacteria growing on siliciclastic sand, by experimentally determining the ability of microbial mats to trap small, suspended mineral grains, and precipitate minerals from ions in solution. We show that (i) fine grains coat the sheaths of filamentous cyanobacteria (e.g., Nodosilinea sp.) residing within the mat, after less than 1 week of cell growth under aerobic conditions, (ii) clay minerals do not coat sterile cellulose fibers and rarely coat unsheathed cyanobacterial cells (e.g., Nostoc sp.), (iii) stronger disturbances (where culture jars were agitated at 170 rpm; 3 mm orbital diameter) produce the smoothest and most extensive mineral veneers around cells, compared with those agitated at slower rotational speeds (150 and 0 rpm), and (iv) mineral veneers coating cyanobacterial cells are ~1 μm in width. These new findings suggest that sheathed filamentous cyanobacteria may be preferentially preserved under conditions of high fluid energy. We integrate these results into a mechanistic model that explains the preservation of microbial fossils and textures in Ediacaran sandstones and siltstones, and in fine-grained siliciclastic deposits that contain exceptionally preserved microbial mats. © 2017 John Wiley & Sons Ltd.

  14. 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

  15. 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

  16. 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

    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 atomist...

  17. Deterministic and stochastic dynamics of bed load tracer particles in a coarse grained river

    Science.gov (United States)

    Phillips, C. B.; Martin, R. L.; Jerolmack, D. J.

    2012-12-01

    Understanding the mechanics of a single coarse sediment particle, and the mechanics of sediment transport at the flood scale, is critical to linking event scale bed load transport rates to annual bed load fluxes. We present research on the dynamics of coarse sediment tracer particles tagged with passive radio transponder tags, observing motion resulting from individual floods and the cumulative transport over many floods spanning two years, in the Mameyes River in the Luquillo Mountains of Puerto Rico. This region presents an ideal study area due to the high frequency of coarse sediment mobilizing events, which allows us to field test the applicability of recently-proposed deterministic and stochastic theories for particle motion. Data for each flood are composed of (1) measured 'flight' lengths for each transported particle, (2) the fraction of tagged particles mobilized, and (3) high-resolution river stage measurements. At the single flood scale, measured tracer particle flight lengths are exponentially distributed, and modal flight lengths scale linearly with excess shear velocity. This is in quantitative agreement with recent theory and laboratory experiments, suggesting that moving particles' velocity is determined by momentum balance with the fluid. The fraction of mobile particles per event increases rapidly with flood stage, creating a logistic-like curve whose inflection point is used to empirically define the threshold of motion. This finding is in contrast to the linear relation observed in small-scale experiments and predicted from momentum balance between sediment and fluid; we use a particle Stokes number argument to suggest that a collision cascade from grain-grain interactions is responsible for the nonlinear relation between mobile fraction and fluid stress, in dynamical equivalence with aeolian sand transport. To examine particle dispersion and relate it to transport mechanics, it is necessary to remove the time over which the fluid stress is

  18. 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

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

    International Nuclear Information System (INIS)

    Izvekov, Sergei; Rice, Betsy M.

    2014-01-01

    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

  20. Lipid composition of grains from wild grasses

    Directory of Open Access Journals (Sweden)

    Zydgalo, J. A.

    1995-02-01

    Full Text Available Physicochemical characteristics, fatty acid and sterol composition were studied in grains of Agropyron elongatum, Bromus catharticus, Festuca arundinacea, Stipa hyaline and Panicum maximum. The highest protein level was found in A. elongatum. Linoleic and palmitic acids were the predominant fatty acids in all species, β-sitosterol was by far the most prominent sterol component in all samples, while Δ7-stigmasterol was detected in only trace amounts.

    Se estudió las características físico-químicas, la composición de ácidos grasos y esteroles de Agropyron elongatum, Bromus catharticus, Festuca arundinacea, Stipa hialina y Panicum maximum. Los niveles más altos de proteínas fueron encontrados en A. elongatum. Dentro de los ácidos grasos el linoleico y el palmítico fueron los predominantes. En todas las muestras el β-sitosterol fue el esterol que se presentó en mayor cantidad, mientras que el Δ7-estigmasterol fue detectado en cantidades trazas.

  1. Guided search for hybrid systems based on coarse-grained space abstractions.

    Science.gov (United States)

    Bogomolov, Sergiy; Donzé, Alexandre; Frehse, Goran; Grosu, Radu; Johnson, Taylor T; Ladan, Hamed; Podelski, Andreas; Wehrle, Martin

    Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space ). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search . Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential.

  2. A systematic coarse-graining strategy for semi-dilute copolymer solutions: from monomers to micelles

    Energy Technology Data Exchange (ETDEWEB)

    Capone, Barbara [Computational Physics, University of Vienna, Sensengasse 8, A-1090 Wien (Austria); Coluzza, Ivan [Computational Physics, University of Vienna, Boltzmanngasse 5, A-1090 Wien (Austria); Hansen, Jean-Pierre [University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

    2011-05-18

    A systematic coarse-graining procedure is proposed for the description and simulation of AB diblock copolymers in selective solvents. Each block is represented by a small number, n{sub A} or n{sub B}, of effective segments or blobs, containing a large number of microscopic monomers. n{sub A} and n{sub B} are unequivocally determined by imposing that blobs do not, on average, overlap, even if complete copolymer coils interpenetrate (semi-dilute regime). Ultra-soft effective interactions between blobs are determined by a rigorous inversion procedure in the low concentration limit. The methodology is applied to an athermal copolymer model where A blocks are ideal (theta solvent), B blocks self-avoiding (good solvent), while A and B blocks are mutually avoiding. The model leads to aggregation into polydisperse spherical micelles beyond a critical micellar concentration determined by Monte Carlo simulations for several size ratios f of the two blocks. The simulations also provide accurate estimates of the osmotic pressure and of the free energy of the copolymer solutions over a wide range of concentrations. The mean micellar aggregation numbers are found to be significantly lower than those predicted by an earlier, minimal two-blob representation (Capone et al 2009 J. Phys. Chem. B 113 3629).

  3. A systematic coarse-graining strategy for semi-dilute copolymer solutions: from monomers to micelles

    International Nuclear Information System (INIS)

    Capone, Barbara; Coluzza, Ivan; Hansen, Jean-Pierre

    2011-01-01

    A systematic coarse-graining procedure is proposed for the description and simulation of AB diblock copolymers in selective solvents. Each block is represented by a small number, n A or n B , of effective segments or blobs, containing a large number of microscopic monomers. n A and n B are unequivocally determined by imposing that blobs do not, on average, overlap, even if complete copolymer coils interpenetrate (semi-dilute regime). Ultra-soft effective interactions between blobs are determined by a rigorous inversion procedure in the low concentration limit. The methodology is applied to an athermal copolymer model where A blocks are ideal (theta solvent), B blocks self-avoiding (good solvent), while A and B blocks are mutually avoiding. The model leads to aggregation into polydisperse spherical micelles beyond a critical micellar concentration determined by Monte Carlo simulations for several size ratios f of the two blocks. The simulations also provide accurate estimates of the osmotic pressure and of the free energy of the copolymer solutions over a wide range of concentrations. The mean micellar aggregation numbers are found to be significantly lower than those predicted by an earlier, minimal two-blob representation (Capone et al 2009 J. Phys. Chem. B 113 3629).

  4. A systematic coarse-graining strategy for semi-dilute copolymer solutions: from monomers to micelles

    Science.gov (United States)

    Capone, Barbara; Coluzza, Ivan; Hansen, Jean-Pierre

    2011-05-01

    A systematic coarse-graining procedure is proposed for the description and simulation of AB diblock copolymers in selective solvents. Each block is represented by a small number, nA or nB, of effective segments or blobs, containing a large number of microscopic monomers. nA and nB are unequivocally determined by imposing that blobs do not, on average, overlap, even if complete copolymer coils interpenetrate (semi-dilute regime). Ultra-soft effective interactions between blobs are determined by a rigorous inversion procedure in the low concentration limit. The methodology is applied to an athermal copolymer model where A blocks are ideal (theta solvent), B blocks self-avoiding (good solvent), while A and B blocks are mutually avoiding. The model leads to aggregation into polydisperse spherical micelles beyond a critical micellar concentration determined by Monte Carlo simulations for several size ratios f of the two blocks. The simulations also provide accurate estimates of the osmotic pressure and of the free energy of the copolymer solutions over a wide range of concentrations. The mean micellar aggregation numbers are found to be significantly lower than those predicted by an earlier, minimal two-blob representation (Capone et al 2009 J. Phys. Chem. B 113 3629).

  5. 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.

  6. 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.

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

    International Nuclear Information System (INIS)

    Snodin, Benedict E. K.; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-01-01

    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 + ] = 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

  8. Cooper-Frye Negative Contributions in a Coarse-Grained Transport Approach

    Science.gov (United States)

    Oliinychenko, D.; Huovinen, P.; Petersen, H.

    2015-04-01

    Many models of heavy ion collisions employ relativistic hydrodynamics to describe the system evolution at high densities. The Cooper-Frye formula is applied in most of these models to turn the hydrodynamical fields into particles. However, the number of particles obtained from the Cooper-Frye formula is not always positive-definite. Physically negative contributions of the Cooper-Frye formula are particles that stream backwards into the hydrodynamical region. We quantify the Cooper-Frye negative contributions in a coarse-grained transport approach, which allows to compare them to the actual number of underlying particles crossing the transition hypersurface. It is found that the number of underlying inward crossings is much smaller than the one the Cooper-Frye formula gives under the assumption of equilibrium distribution functions. The magnitude of Cooper-Frye negative contributions is also investigated as a function of hadron mass, collision energy in the range Elab = 5 — 160A GeV, and collision centrality. The largest negative contributions we find are around 13% for the pion yield at midrapidity at Elab = 20A GeV collisions.

  9. Beyond amphiphiles: coarse-grained simulations of star-polyphile liquid crystalline assemblies.

    Science.gov (United States)

    Kirkensgaard, Jacob Judas Kain; Hyde, Stephen

    2009-03-28

    We have simulated the self-assembly of a novel class of three-arm molecules, ABC star-architecture polyphiles, using coarse-grained bead simulations. A number of topologically complex liquid crystalline mesostructures arise that can be related to the better-known bicontinuous mesophases of lyotropic amphiphilic systems. The simulations reveal 3D self-assemblies whose structural variations follow those expected assuming a simple steric molecular packing model as a function of star polyphile splay and relative volumes of each arm in the polyphile. The splay of each arm, characterised by the 3D wedge-shape emanating from the core of each molecule to its exterior induces torsion of the interfaces along the triple lines, whereas differences in the relative volumes of arms induce curvature of the triple lines. Three distinct mesostructures are described, characterised by their micro-domain topologies, which are unknown in simpler amphiphilic systems, but resemble in some respects bicontinuous mesophases. These three- (or more) arm polyphilic systems offer an interesting extension to the better-known self-assembly of (two-arm) amphiphiles in solution.

  10. PSO-Assisted Development of New Transferable Coarse-Grained Water Models.

    Science.gov (United States)

    Bejagam, Karteek K; Singh, Samrendra; An, Yaxin; Berry, Carter; Deshmukh, Sanket A

    2018-02-15

    We have employed two-to-one mapping scheme to develop three coarse-grained (CG) water models, namely, 1-, 2-, and 3-site CG models. Here, for the first time, particle swarm optimization (PSO) and gradient descent methods were coupled to optimize the force-field parameters of the CG models to reproduce the density, self-diffusion coefficient, and dielectric constant of real water at 300 K. The CG MD simulations of these new models conducted with various timesteps, for different system sizes, and at a range of different temperatures are able to predict the density, self-diffusion coefficient, dielectric constant, surface tension, heat of vaporization, hydration free energy, and isothermal compressibility of real water with excellent accuracy. The 1-site model is ∼3 and ∼4.5 times computationally more efficient than 2- and 3-site models, respectively. To utilize the speed of 1-site model and electrostatic interactions offered by 2- and 3-site models, CG MD simulations of 1:1 combination of 1- and 2-/3-site models were performed at 300 K. These mixture simulations could also predict the properties of real water with good accuracy. Two new CG models of benzene, consisting of beads with and without partial charges, were developed. All three water models showed good capacity to solvate these benzene models.

  11. 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.

  12. 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.

  13. 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.

  14. An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.

    Directory of Open Access Journals (Sweden)

    Levan Tsereteli

    Full Text Available Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.

  15. Optimal number of coarse-grained sites in different components of large biomolecular complexes.

    Science.gov (United States)

    Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

    2012-07-26

    The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

  16. Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations.

    Science.gov (United States)

    Hsieh, Meng-Juei; Luo, Ray

    2011-08-01

    We have implemented and evaluated a coarse-grained distributive method for finite-difference Poisson-Boltzmann (FDPB) calculations of large biomolecular systems. This method is based on the electrostatic focusing principle of decomposing a large fine-grid FDPB calculation into multiple independent FDPB calculations, each of which focuses on only a small and a specific portion (block) of the large fine grid. We first analyzed the impact of the focusing approximation upon the accuracy of the numerical reaction field energies and found that a reasonable relative accuracy of 10(-3) can be achieved when the buffering space is set to be 16 grid points and the block dimension is set to be at least (1/6)(3) of the fine-grid dimension, as in the one-block focusing method. The impact upon efficiency of the use of buffering space to maintain enough accuracy was also studied. It was found that an "optimal" multi-block dimension exists for a given computer hardware setup, and this dimension is more or less independent of the solute geometries. A parallel version of the distributive focusing method was also implemented. Given the proper settings, the distributive method was able to achieve respectable parallel efficiency with tested biomolecular systems on a loosely connected computer cluster.

  17. Coarse-grained parallel genetic algorithm applied to a nuclear reactor core design optimization problem

    International Nuclear Information System (INIS)

    Pereira, Claudio M.N.A.; Lapa, Celso M.F.

    2003-01-01

    This work extends the research related to generic algorithms (GA) in core design optimization problems, which basic investigations were presented in previous work. Here we explore the use of the Island Genetic Algorithm (IGA), a coarse-grained parallel GA model, comparing its performance to that obtained by the application of a traditional non-parallel GA. The optimization problem consists on adjusting several reactor cell parameters, such as dimensions, enrichment and materials, in order to minimize the average peak-factor in a 3-enrichment zone reactor, considering restrictions on the average thermal flux, criticality and sub-moderation. Our IGA implementation runs as a distributed application on a conventional local area network (LAN), avoiding the use of expensive parallel computers or architectures. After exhaustive experiments, taking more than 1500 h in 550 MHz personal computers, we have observed that the IGA provided gains not only in terms of computational time, but also in the optimization outcome. Besides, we have also realized that, for such kind of problem, which fitness evaluation is itself time consuming, the time overhead in the IGA, due to the communication in LANs, is practically imperceptible, leading to the conclusion that the use of expensive parallel computers or architecture can be avoided

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

    Directory of Open Access Journals (Sweden)

    Cao Liang

    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 μm CMOS standard cell technology. The core area is about 8.5 mm2, 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.

  19. CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.

    Science.gov (United States)

    Kenzaki, Hiroo; Koga, Nobuyasu; Hori, Naoto; Kanada, Ryo; Li, Wenfei; Okazaki, Kei-Ichi; Yao, Xin-Qiu; Takada, Shoji

    2011-06-14

    For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of one-particle-per-residue, CafeMol equips four structure-based protein models: (1) the off-lattice Go model, (2) the atomic interaction based CG model for native state and folding dynamics, (3) the multiple-basin model for conformational change dynamics, and (4) the elastic network model for quasiharmonic fluctuations around the native structure. Ligands can be treated either explicitly or implicitly. For mimicking functional motions of proteins driven by some external force, CafeMol has various and flexible means to "switch" the energy functions that induce active motions of the proteins. CafeMol can do parallel computation with modest sized PC clusters. We describe CafeMol methods and illustrate it with several examples, such as rotary motions of F1-ATPase and drug exports from a transporter. The CafeMol source code is available at www.cafemol.org .

  20. Fast AdaBoost-Based Face Detection System on a Dynamically Coarse Grain Reconfigurable Architecture

    Science.gov (United States)

    Xiao, Jian; Zhang, Jinguo; Zhu, Min; Yang, Jun; Shi, Longxing

    An AdaBoost-based face detection system is proposed, on a Coarse Grain Reconfigurable Architecture (CGRA) named “REMUS-II”. Our work is quite distinguished from previous ones in three aspects. First, a new hardware-software partition method is proposed and the whole face detection system is divided into several parallel tasks implemented on two Reconfigurable Processing Units (RPU) and one micro Processors Unit (µPU) according to their relationships. These tasks communicate with each other by a mailbox mechanism. Second, a strong classifier is treated as a smallest phase of the detection system, and every phase needs to be executed by these tasks in order. A phase of Haar classifier is dynamically mapped onto a Reconfigurable Cell Array (RCA) only when needed, and it's quite different from traditional Field Programmable Gate Array (FPGA) methods in which all the classifiers are fabricated statically. Third, optimized data and configuration word pre-fetch mechanisms are employed to improve the whole system performance. Implementation results show that our approach under 200MHz clock rate can process up-to 17 frames per second on VGA size images, and the detection rate is over 95%. Our system consumes 194mW, and the die size of fabricated chip is 23mm2 using TSMC 65nm standard cell based technology. To the best of our knowledge, this work is the first implementation of the cascade Haar classifier algorithm on a dynamically CGRA platform presented in the literature.

  1. 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.

  2. 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.

  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. Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization

    Science.gov (United States)

    Luo, Chuanfu; Sommer, Jens-Uwe

    2009-08-01

    We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summaryProgram title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program

  5. A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

    International Nuclear Information System (INIS)

    Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro

    2013-01-01

    This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)

  6. 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.

  7. Fine-grained, local maps and coarse, global representations support human spatial working memory.

    Directory of Open Access Journals (Sweden)

    Mohammad Zia Ul Haq Katshu

    Full Text Available 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.

  8. Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations.

    Science.gov (United States)

    Theisen, Kelly E; Desai, Neha J; Volski, Allison M; Dima, Ruxandra I

    2013-09-28

    We investigate the mechanical behavior of microtubule (MT) protofilaments under the action of bending forces, ramped up linearly in time, to provide insight into the severing of MTs by microtubule associated proteins (MAPs). We used the self-organized polymer model which employs a coarse-grained description of the protein chain and ran Brownian dynamics simulations accelerated on graphics processing units that allow us to follow the dynamics of a MT system on experimental timescales. Our study focused on the role played in the MT depolymerization dynamics by the inter-tubulin contacts a protofilament experiences when embedded in the MT lattice, and the number of binding sites of MAPs on MTs. We found that proteins inducing breaking of MTs must have at least three attachment points on any tubulin dimer from an isolated protofilament. In contrast, two points of contact would suffice when dimers are located in an intact MT lattice, in accord with experimental findings on MT severing proteins. Our results show that confinement of a protofilament in the MT lattice leads to a drastic reduction in the energy required for the removal of tubulin dimers, due to the drastic reduction in entropy. We further showed that there are differences in the energetic requirements based on the location of the dimer to be removed by severing. Comparing the energy of tubulin dimers removal revealed by our simulations with the amount of energy resulting from one ATP hydrolysis, which is the source of energy for all MAPs, we provided strong evidence for the experimental finding that severing proteins do not bind uniformly along the MT wall.

  9. Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

    Energy Technology Data Exchange (ETDEWEB)

    Van Essen, B; Panda, R; Wood, A; Ebeling, C; Hauck, S

    2010-12-01

    Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous

  10. Mori-Zwanzig theory for dissipative forces in coarse-grained dynamics in the Markov limit

    Science.gov (United States)

    Izvekov, Sergei

    2017-01-01

    We derive alternative Markov approximations for the projected (stochastic) force and memory function in the coarse-grained (CG) generalized Langevin equation, which describes the time evolution of the center-of-mass coordinates of clusters of particles in the microscopic ensemble. This is done with the aid of the Mori-Zwanzig projection operator method based on the recently introduced projection operator [S. Izvekov, J. Chem. Phys. 138, 134106 (2013), 10.1063/1.4795091]. The derivation exploits the "generalized additive fluctuating force" representation to which the projected force reduces in the adopted projection operator formalism. For the projected force, we present a first-order time expansion which correctly extends the static fluctuating force ansatz with the terms necessary to maintain the required orthogonality of the projected dynamics in the Markov limit to the space of CG phase variables. The approximant of the memory function correctly accounts for the momentum dependence in the lowest (second) order and indicates that such a dependence may be important in the CG dynamics approaching the Markov limit. In the case of CG dynamics with a weak dependence of the memory effects on the particle momenta, the expression for the memory function presented in this work is applicable to non-Markov systems. The approximations are formulated in a propagator-free form allowing their efficient evaluation from the microscopic data sampled by standard molecular dynamics simulations. A numerical application is presented for a molecular liquid (nitromethane). With our formalism we do not observe the "plateau-value problem" if the friction tensors for dissipative particle dynamics (DPD) are computed using the Green-Kubo relation. Our formalism provides a consistent bottom-up route for hierarchical parametrization of DPD models from atomistic simulations.

  11. 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.

  12. Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array

    International Nuclear Information System (INIS)

    Van Essen, B.; Panda, R.; Wood, A.; Ebeling, C.; Hauck, S.

    2010-01-01

    Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous

  13. 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.

  14. Applying Ultrasonic Phased Array Technology to Examine Austenitic Coarse-Grained Structures for Light Water Reactor Piping

    International Nuclear Information System (INIS)

    Anderson, Michael T.; Cumblidge, Stephen E.; Doctor, Steven R.

    2003-01-01

    Pacific Northwest Laboratory is evaluating the capabilities and limitations of phased array (PA) technology to detect service-type flaws in coarse-grained austenitic piping structures. The work is being sponsored by the U.S. Nuclear Regulatory Commission, Office of Research. This paper presents initial work involving the use of PA technology to determine the effectiveness of detecting and accurately characterizing flaws on the far-side of austenitic piping welds

  15. 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.

  16. 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.

  17. Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

    International Nuclear Information System (INIS)

    Sanyal, Tanmoy; Shell, M. Scott

    2016-01-01

    Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

  18. Effect of Composition and Deformation on Coarse-Grained Austenite Transformation in Nb-Mo Microalloyed Steels

    Science.gov (United States)

    Isasti, N.; Jorge-Badiola, D.; Taheri, M. L.; López, B.; Uranga, P.

    2011-12-01

    Thermomechanical processing of microalloyed steels containing niobium can be performed to obtain deformed austenite prior to transformation. Accelerated cooling can be employed to refine the final microstructure and, consequently, to improve both strength and toughness. This general rule is fulfilled if the transformation occurs on a quite homogeneous austenite microstructure. Nevertheless, the presence of coarse austenite grains before transformation in different industrial processes is a usual source of concern, and regarding toughness, the coarsest high-angle boundary units would determine its final value. Sets of deformation dilatometry tests were carried out using three 0.06 pct Nb microalloyed steels to evaluate the effect of Mo alloying additions (0, 0.16, and 0.31 pct Mo) on final transformation from both recrystallized and unrecrystallized coarse-grained austenite. Continuous cooling transformation (CCT) diagrams were created, and detailed microstructural characterization was achieved through the use of optical microscopy (OM), field emission gun scanning electron microscopy (FEGSEM), and electron backscattered diffraction (EBSD). The resultant microstructures ranged from polygonal ferrite (PF) and pearlite (P) at slow cooling ranges to bainitic ferrite (BF) accompanied by martensite (M) for fast cooling rates. Plastic deformation of the parent austenite accelerated both ferrite and bainite transformation, moving the CCT curves to higher temperatures and shorter times. However, an increase in the final heterogeneity was observed when BF packets were formed, creating coarse high-angle grain boundary units.

  19. 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.

  20. Reaction and relaxation in a coarse-grained fluvial system following catchment-wide disturbance

    Science.gov (United States)

    Tunnicliffe, Jon; Brierley, Gary; Fuller, Ian C.; Leenman, Anya; Marden, Mike; Peacock, Dave

    2018-04-01

    The Waiapu River catchment (drainage area of 1734-km2) is one of the most prolific conveyors of sediment in the world, annually delivering roughly 35 Mt of fine material to the ocean from eroding gullies, hillslopes, and reworked sediment on valley floors. Tectonic and geologic influences, in combination with a dynamic climate influenced by tropical cyclones and clearance of vegetation from steep hillslopes, predisposes this region to high rates of erosion. The bedload sediment regime of the river is strongly influenced by several exceptionally large gullies and gully complexes that produce a coarse-grained, poorly sorted sediment mixture. Rapid abrasion and breakdown leads to high rates of suspended sediment yield. A wave of bedload material, manifesting as elevated bed levels and significant widening of active alluvial fills, has been triggered by large inputs of hillslope material from a few key tributary catchments following Cyclone Bola in 1988. We review the evidence for the relaxation process of the sedimentary system in the subsequent 29 years, appraising some of the legacy effects that may endure, as associated with reworking of the considerable alluvial stores within the Waiapu system. We use Structure-from-Motion (SfM) techniques and archival aerial photos to quantify changes in sediment storage at the base of two major gully systems in recent decades. A record of over 850 cross section surveys at 62 sites on 10 rivers throughout the catchment (1958-2017) indicates recent transition from a trend of continuous accumulation to downcutting and remobilisation of valley-bottom deposits. The channel cross sections provide a minimum estimate of sediment flux from source areas to the lower reaches of the river, giving a rudimentary but spatially extensive picture of the wave of material cascading through the drainage network. The largest impacts occur in the upper steepland rivers, closest to the landslide-derived sediment supply. Transport rates here, as

  1. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Science.gov (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

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

    Energy Technology Data Exchange (ETDEWEB)

    Garrido, J. M. [Departamento de Ingeniería Química, Universidad de Concepción, POB 160-C Concepción (Chile); Algaba, J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Míguez, J. M. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain); Piñeiro, M. M. [Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain)

    2016-04-14

    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

  3. Lower Badenian coarse-grained Gilbert deltas in the southern margin of the Western Carpathian Foredeep basin

    Science.gov (United States)

    Nehyba, Slavomír

    2018-02-01

    Two coarse-grained Gilbert-type deltas in the Lower Badenian deposits along the southern margin of the Western Carpathian Foredeep (peripheral foreland basin) were newly interpreted. Facies characterizing a range of depositional processes are assigned to four facies associations — topset, foreset, bottomset and offshore marine pelagic deposits. The evidence of Gilbert deltas within open marine deposits reflects the formation of a basin with relatively steep margins connected with a relative sea level fall, erosion and incision. Formation, progradation and aggradation of the thick coarse-grained Gilbert delta piles generally indicate a dramatic increase of sediment supply from the hinterland, followed by both relatively continuous sediment delivery and an increase in accommodation space. Deltaic deposition is terminated by relatively rapid and extended drowning and is explained as a transgressive event. The lower Gilbert delta was significantly larger, more areally extended and reveals a more complicated stratigraphic architecture than the upper one. Its basal surface represents a sequence boundary and occurs around the Karpatian/Badenian stratigraphic limit. Two coeval deltaic branches were recognized in the lower delta with partly different stratigraphic arrangements. This different stratigraphic architecture is mostly explained by variations in the sediment delivery and /or predisposed paleotopography and paleobathymetry of the basin floor. The upper delta was recognized only in a restricted area. Its basal surface represents a sequence boundary probably reflecting a higher order cycle of a relative sea level rise and fall within the Lower Badenian. Evidence of two laterally and stratigraphically separated coarse-grained Gilbert deltas indicates two regional/basin wide transgressive/regressive cycles, but not necessarily of the same order. Provenance analysis reveals similar sources of both deltas. Several partial source areas were identified (Mesozoic

  4. 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

  5. Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots

    DEFF Research Database (Denmark)

    Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull

    2017-01-01

    . Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....

  6. Whole-grain and blood lipid changes in apparently healthy adults

    DEFF Research Database (Denmark)

    Hollænder, Pernille Lærke Bjørndal; Ross, Alastair B; Kristensen, Mette Bredal

    2015-01-01

    BACKGROUND: Whole grains are recognized for their potential role in preventing cardiovascular diseases; however, results from randomized controlled studies on blood lipids are inconsistent, potentially because of compositional differences between individual grain types for some nutrients, includi...

  7. Ultrasonic phased array sound field mapping through large-bore coarse grained cast austenitic stainless steel (CASS) piping materials

    Science.gov (United States)

    Cinson, A. D.; Crawford, S. L.; Prowant, M. S.; Diaz, A. A.; Hathaway, J. E.; Anderson, M. T.

    2012-04-01

    A sound field beam mapping exercise was conducted to further understand the effects of coarse-grained microstructures found in cast austenitic stainless steel (CASS) materials on phased array ultrasonic wave propagation. Laboratory measurements were made on three CASS specimens with different microstructures; the specimens were polished and etched to reveal measurable grain sizes, shapes, and orientations. Three longitudinal, phased array probes were fixed on a specimen's outside diameter with the sound field directed toward one end (face) of the pipe segment over a fixed range of angles. A point receiver was raster scanned over the surface of the specimen face generating a sound field image. A slice of CASS material was then removed from the specimen end and the beam mapping exercise repeated. The sound fields acquired were analyzed for spot size, coherency, and beam redirection. Qualitative analyses were conducted between the resulting sound fields and the microstructural characteristics of each specimen.

  8. 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.

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

    Science.gov (United States)

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

    2018-04-01

    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 using contact insecticides. As some chemical insecticides can harm humans and the environment, there is a global tendency to reduce their use by finding alternative eco-friendly approaches. In this study, the natural pest-managing agent pulegone was encapsulated into coarse and nano emulsions. The emulsions were characterized using 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, whereas coarse emulsions showed high efficacy for only 1 week. The developed pulegone-based nano emulsions could serve as a model for an effective alternative method for pest control. Although pulegone is from a natural source, toxicological studies should be performed before the widespread application of pulegone or pulegone-containing essential oils to dry food products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  10. GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.

    Science.gov (United States)

    Boudard, Mélanie; Barth, Dominique; Bernauer, Julie; Denise, Alain; Cohen, Johanne

    2017-08-15

    Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule. We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods. GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/. melanie.boudard@lri.fr or johanne.cohen@lri.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  11. 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.

  12. Coarse-grained Mineral Dust Deposition in Alpine Lake Sediments: Implications for Regional Drought Patterns and Land-use Changes in the Southwest USA

    Science.gov (United States)

    Pedraza, A.; Kingsley, C.; Marchitto, T. M., Jr.; Lora, J. M.; Pollen, A.; Vollmer, T.; Leithold, E. L.; Mitchell, J.; Tripati, A. K.; Bhattacharya, A.

    2017-12-01

    Mineral dust accumulation is often causally associated with aridity. However, the relation might not be as straightforward. Consideration of grain sizes and geochemical fingerprinting of the coarse grain fraction will clearly have an impact on how we interpret the sedimentary record of mineral dust in depositional environments e.g. coarse grain fractions of mineral dust would most certainly be transported over relatively short distances and as such in depositional environments, the depositional rate of coarse grains must be determined in order to reliably understand erosional patterns associated with meteorological events (such as frequency of intense wind events such as tornadoes), climatological phenomenon (such as regional droughts) as well as more recently land-use changes. In this study we separate the two size fractions of mineral dust accumulation- fine fraction (typically 25 microns using grain size analysis from well-studied cores collected from several lake sites distributed across the western southwestern and the Great Plain regions; furthermore we use trace element analysis in each size fraction to identify contributing source regions. We find evidence that the coarser-grain size fraction in the studied lake cores could be of regional origin (and not just local in orgin);. the coarser fraction also appears to be related to intense meteorological events (i.e., the occurrence of cyclones). Analysis is underway to understand the impact of land-use changes on coarse grain fraction

  13. A Coarse-Grained Two-Fluid Model for Gas-Solid Fluidized Beds

    Directory of Open Access Journals (Sweden)

    S. Schneiderbauer

    2014-03-01

    Full Text Available Due to increasing computer power the numerical simulation of fluidized and moving beds has become feasible. However, while kinetic theory based CFD (Computational Fluid Dynamics has become a valuable design tool for modeling pilot plant scale gassolid fluidized bed reactors, a fully resolved simulation of industrial scale reactor is still nearly unfeasible. It is, therefore, common to use sub-grid models to account for the effect of the small unresolved structures on large resolved scales when using coarse grids. It is generally agreed that the influence of these small scales on the drag force is a key parameter in the prediction of the hydrodynamics of fluidized beds. We present a sub-grid drag modification dealing with the influence of heterogeneous structures on the drag force. It is assumed that these structures appear as distinct clusters of particles within an interstitial dilute particle phase. The clusters and the dilute phase itself consist of homogeneously distributed particles enabling the application of a homogenous drag correlation to these structures. In contrast to the established sub-grid drag modification EMMS (Energy-Minimization Multi-Scale Method, the presented model distinguishes between resolved and unresolved clusters by computing the expectation value of the diameter of the unresolved clusters. This reveals a grid and slip velocity dependent drag modification, which recovers the homogenous drag law as the solids volume fraction approaches the maximum packing of frictional spheres. The presented model is validated on the one hand, in case of industrial scale bubbling and turbulent fluidized beds. On the other hand, the model is applied to the coarse grid simulation of a riser flow. The numerical results obtained on a coarse gird demonstrate that our model reveals fairly good agreement with experimental data of bed expansion and solids volume fraction distributions. Thus, the results proof that the presented drag

  14. 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

  15. Modelling of P3HT:PCBM interface using coarse-grained forcefield derived from accurate atomistic forcefield.

    Science.gov (United States)

    To, T T; Adams, S

    2014-03-14

    To understand the morphological evolution of P3HT:PCBM bulk heterojunction during thermal treatment process, we employed coarse-grained Molecular Dynamics (MD) simulations with a forcefield derived from atomistic model and experimental data such as crystal structure and melting temperature. The current study focuses on the differences between interfaces that PCBM forms with various P3HT orientations. Crystallinity analysis suggests that more ordered P3HT is observed near the interface for face-on and amorphous case, while no such trend is observed for edge-on and end-on configurations due to weaker interactions at the interface as evident from the considerably less negative interfacial energy. An analysis of pathways for C60 diffusion into P3HT using both an energy-based and solvent surface approach for amorphous P3HT reveals continuous chain motion-assisted pathways while for crystalline P3HT diffusion pathways remain restricted to grain boundaries. Based on these calculations, we propose a morphological evolution process for P3HT:PCBM bulk-heterojunction, which starts with nucleation crystallisation at the P3HT:PCBM interface, followed by PCBM diffusion along the grain boundaries and amorphous P3HT regions towards PCBM-rich domains.

  16. A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

    Energy Technology Data Exchange (ETDEWEB)

    Li, Tong; Gu, YuanTong, E-mail: yuantong.gu@qut.edu.au

    2014-04-15

    As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grained level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.

  17. A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: Theory and application to microfilaments

    Science.gov (United States)

    Li, Tong; Gu, YuanTong

    2014-04-01

    As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grained level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.

  18. Coarse-grained simulations for flow of complex soft matter fluids in the bulk and in the presence of solid interfaces.

    Science.gov (United States)

    Ahuja, V R; van der Gucht, J; Briels, W J

    2016-11-21

    We present a coarse-grained particle-based simulation technique for modeling flow of complex soft matter fluids such as polymer solutions in the presence of solid interfaces. In our coarse-grained description of the system, we track the motion of polymer molecules using their centers-of-mass as our coarse-grain co-ordinates and also keep track of another set of variables that describe the background flow field. The coarse-grain motion is thus influenced not only by the interactions based on appropriate potentials used to model the particular polymer system of interest and the random kicks associated with thermal fluctuations, but also by the motion of the background fluid. In order to couple the motion of the coarse-grain co-ordinates with the background fluid motion, we use a Galilean invariant, first order Brownian dynamics algorithm developed by Padding and Briels [J. Chem. Phys. 141, 244108 (2014)], which on the one hand draws inspiration from smoothed particle hydrodynamics in a way that the motion of the background fluid is efficiently calculated based on a discretization of the Navier-Stokes equation at the positions of the coarse-grain coordinates where it is actually needed, but also differs from it because of the inclusion of thermal fluctuations by having momentum-conserving pairwise stochastic updates. In this paper, we make a few modifications to this algorithm and introduce a new parameter, viz., a friction coefficient associated with the background fluid, and analyze the relationship of the model parameters with the dynamic properties of the system. We also test this algorithm for flow in the presence of solid interfaces to show that appropriate boundary conditions can be imposed at solid-fluid interfaces by using artificial particles embedded in the solid walls which offer friction to the real fluid particles in the vicinity of the wall. We have tested our method using a model system of a star polymer solution at the overlap concentration.

  19. Interpretation of sedimentological processes of coarse-grained deposits applying a novel combined cluster and discriminant analysis

    Directory of Open Access Journals (Sweden)

    Farics Éva

    2017-10-01

    Full Text Available The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity. The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes.

  20. 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.

  1. 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%.

  2. 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.

  3. Coarse-grained modelling of triglyceride crystallisation: a molecular insight into tripalmitin tristearin binary mixtures by molecular dynamics simulations

    International Nuclear Information System (INIS)

    Pizzirusso, Antonio; De Nicola, Antonio; Milano, Giuseppe; Brasiello, Antonio; Marangoni, Alejandro G

    2015-01-01

    The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined. (paper)

  4. 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

  5. Increasing density leads to generalization in both coarse-grained habitat selection and fine-grained resource selection in a large mammal.

    Science.gov (United States)

    van Beest, Floris M; Uzal, Antonio; Vander Wal, Eric; Laforge, Michel P; Contasti, Adrienne L; Colville, David; McLoughlin, Philip D

    2014-01-01

    Density is a fundamental driver of many ecological processes including habitat selection. Theory on density-dependent habitat selection predicts that animals should be distributed relative to profitability of habitat, resulting in reduced specialization in selection (i.e. generalization) as density increases and competition intensifies. Despite mounting empirical support for density-dependent habitat selection using isodars to describe coarse-grained (interhabitat) animal movements, we know little of how density affects fine-grained resource selection of animals within habitats [e.g. using resource selection functions (RSFs)]. Using isodars and RSFs, we tested whether density simultaneously modified habitat selection and within-habitat resource selection in a rapidly growing population of feral horses (Equus ferus caballus Linnaeus; Sable Island, Nova Scotia, Canada; 42% increase in population size from 2008 to 2012). Among three heterogeneous habitat zones on Sable Island describing population clusters distributed along a west-east resource gradient (west-central-east), isodars revealed that horses used available habitat in a density-dependent manner. Intercepts and slopes of isodars demonstrated a pattern of habitat selection that first favoured the west, which generalized to include central and east habitats with increasing population size consistent with our understanding of habitat quality on Sable Island. Resource selection functions revealed that horses selected for vegetation associations similarly at two scales of extent (total island and within-habitat zone). When densities were locally low, horses were able to select for sites of the most productive forage (grasslands) relative to those of poorer quality. However, as local carrying capacity was approached, selection for the best of available forage types weakened while selection for lower-quality vegetation increased (and eventually exceeded that of grasslands). Isodars can effectively describe coarse-grained

  6. Investigation on the crystallography of the transformation products of reverted austenite in intercritically reheated coarse grained heat affected zone

    International Nuclear Information System (INIS)

    You, Yang; Shang, Chengjia; Chen, Liang; Subramanian, Sundaresa

    2013-01-01

    Highlights: ► Area of reverted austenite is traced out by crystallographic information. ► Bainite and martensite regions were confirmed within it. ► The martensite region is considered as the blocky MA particles. ► Martensite region has high deformation to initiate fracture. ► More uniform transformation of the reverted austenite is good for toughness. -- Abstract: In present study the intercritically reheated coarse grained heat affected zone (ICCGHAZ) showing the worst impact toughness in the heat affected zone of multi-pass welding was simulated by Gleeble-1500, and its microstructure was investigated in detail by means of scanning electron microscope (SEM) and electron backscattering diffraction (EBSD). With the crystallographic information from EBSD scanning the area of a single reverted austenite grain which formed during the thermal cycles of second pass simulation was traced out. Within it two regions with different characteristic both in morphology and crystallography were found out, showing an un-uniform transformation of the reverted austenite. The region I is a bainitic region containing larger bainitic ferrite grains, while the region II is made up of several clusters containing tiny grains. Based on the crystallographic information each cluster was determined as martensite island thereby should be considered as blocky Martensite/Austenite constituent (M/A), which is hard phase and harmful for toughness. Analysis on the level of deformation shows that the region II is much higher deformed than the region I, indicating there is high stress concentration within the region II. The possible influence of the region I and the region II on fracture is discussed under the early proposed M/A’s fracture-initiating mechanisms. It suggests that the main cause of the toughness reduction is the un-uniform transformation of the reverted austenite, and the toughness performance of the ICCGHAZ could be improved if the transformation of the reverted

  7. Coarse-grain parallel solution of few-group neutron diffusion equations

    International Nuclear Information System (INIS)

    Sarsour, H.N.; Turinsky, P.J.

    1991-01-01

    The authors present a parallel numerical algorithm for the solution of the finite difference representation of the few-group neutron diffusion equations. The targeted architectures are multiprocessor computers with shared memory like the Cray Y-MP and the IBM 3090/VF, where coarse granularity is important for minimizing overhead. Most of the work done in the past, which attempts to exploit concurrence, has concentrated on the inner iterations of the standard outer-inner iterative strategy. This produces very fine granularity. To coarsen granularity, the authors introduce parallelism at the nested outer-inner level. The problem's spatial domain was partitioned into contiguous subregions and assigned a processor to solve for each subregion independent of all other subregions, hence, processors; i.e., each subregion is treated as a reactor core with imposed boundary conditions. Since those boundary conditions on interior surfaces, referred to as internal boundary conditions (IBCs), are not known, a third iterative level, the recomposition iterations, is introduced to communicate results between subregions

  8. Multiaxial creep of fine grained 0.5Cr-0.5Mo-0.25V and coarse grained 1Cr-0.5Mo steels

    International Nuclear Information System (INIS)

    Browne, R.J.; Flewitt, P.E.J.; Lonsdale, D.

    1991-01-01

    To explore the multiaxial creep response of materials used for electrical power generating plant, two steels, a fine grained 0.5Cr-0.5Mo-0.25V steel in a normalised and tempered condition with high creep ductility and a coarse grained 1Cr-0.5Mo steel in a quenched and tempered condition with low uniaxial creep ductility, have been selected. A range of multiaxial stress testing techniques which span the stress states that would allow identification of any technique dependent variables has been used. The deformation and failure of the normalised and tempered 0.5Cr-0.5Mo-0.25V steel for a range of multiaxial test techniques and, therefore, stress states may be described by an equivalent stress criterion. The results from the multiaxial tests carried out on the fully bainitic 1Cr-0.5Mo steel show that the multiaxial stress rupture criterion (MSRC) varies with stress state; at high triaxiality (notch), it is controlled by the maximum principal stress, whereas at low triaxiality (shear) it is dependent on both maximum principal stress and equivalent stress. Furthermore, a simple description of stress state based on maximum principal and equivalent stress does not define this uniquely, since the MSRC derived from uniaxial and torsion testing does not describe the failure of notch, tube, or double shear tests. (author)

  9. Archie’s saturation exponent for natural gas hydrate in coarse-grained reservoirs

    Science.gov (United States)

    Cook, Ann E.; Waite, William F.

    2018-01-01

    Accurately quantifying the amount of naturally occurring gas hydrate in marine and permafrost environments is important for assessing its resource potential and understanding the role of gas hydrate in the global carbon cycle. Electrical resistivity well logs are often used to calculate gas hydrate saturations, Sh, using Archie's equation. Archie's equation, in turn, relies on an empirical saturation parameter, n. Though n = 1.9 has been measured for ice‐bearing sands and is widely used within the hydrate community, it is highly questionable if this n value is appropriate for hydrate‐bearing sands. In this work, we calibrate n for hydrate‐bearing sands from the Canadian permafrost gas hydrate research well, Mallik 5L‐38, by establishing an independent downhole Sh profile based on compressional‐wave velocity log data. Using the independently determined Sh profile and colocated electrical resistivity and bulk density logs, Archie's saturation equation is solved for n, and uncertainty is tracked throughout the iterative process. In addition to the Mallik 5L‐38 well, we also apply this method to two marine, coarse‐grained reservoirs from the northern Gulf of Mexico Gas Hydrate Joint Industry Project: Walker Ridge 313‐H and Green Canyon 955‐H. All locations yield similar results, each suggesting n ≈ 2.5 ± 0.5. Thus, for the coarse‐grained hydrate bearing (Sh > 0.4) of greatest interest as potential energy resources, we suggest that n = 2.5 ± 0.5 should be applied in Archie's equation for either marine or permafrost gas hydrate settings if independent estimates of n are not available.

  10. 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.

  11. 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 O1→4-bonded polyglucose chains.

    Science.gov (United States)

    Lubecka, Emilia A; Liwo, Adam

    2017-09-21

    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=140 ° 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 torsional potentials very well

  12. 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

  13. Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

    International Nuclear Information System (INIS)

    Nishizawa, Manami; Nishizawa, Kazuhisa

    2014-01-01

    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 OPLS ). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT 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 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 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) 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 findings may help interpret

  14. 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

  15. 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

  16. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    International Nuclear Information System (INIS)

    Knott, Michael; Best, Robert B.

    2014-01-01

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD

  17. Ultrasonic imaging of defects in coarse-grained steels with the decomposition of the time reversal operator.

    Science.gov (United States)

    Lopez Villaverde, Eduardo; Robert, Sébastien; Prada, Claire

    2016-07-01

    In the present work, the Synthetic Transmit Aperture (STA) imaging is combined with the Decomposition of the Time Reversal Operator (DORT) method to image a coarse grained austenitic-ferritic steel using a contact transducer array. The highly heterogeneous structure of this material produces a strong scattering noise in ultrasound images. Furthermore, the surface waves guided along the array interfere with the bulk waves backscattered by defects. In order to overcome these problems, the DORT method is applied before calculating images with the STA algorithm. The method consists in analyzing in the frequency domain the singular values and singular vectors of the full array transfer matrix. This paper first presents an analysis of the singular values of different waves contained in the data acquisition, which facilitates the identification of the subspace associated with the surface guided waves for filtering operations. Then, a filtered matrix is defined where the contribution of structural noise and guided waves are reduced. Finally, in the time domain, the STA algorithm is applied to this matrix in order to calculate an image with reduced structural noise. Experiments demonstrate that this filtering improves the signal-to-noise ratio by more than 12 dB in comparison with the STA image before filtering.

  18. Interpretation of sedimentological processes of coarse-grained deposits applying a novel combined cluster and discriminant analysis

    Science.gov (United States)

    Farics, Éva; Farics, Dávid; Kovács, József; Haas, János

    2017-10-01

    The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity) in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA) in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity). The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes. In the Buda Hills, we were able to distinguish various sedimentological environments within the area based on the results: fan, intermittent stream or marine.

  19. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

    Science.gov (United States)

    Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

    2018-04-01

    Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

  20. 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.

  1. Systematic investigation of negative Cooper-Frye contributions in heavy ion collisions using coarse-grained molecular dynamics

    Science.gov (United States)

    Oliinychenko, D.; Huovinen, P.; Petersen, H.

    2015-02-01

    In most heavy ion collision simulations involving relativistic hydrodynamics, the Cooper-Frye formula is applied to transform the hydrodynamical fields to particles. In this article the so-called negative contributions in the Cooper-Frye formula are studied using a coarse-grained transport approach. The magnitude of negative contributions is investigated as a function of hadron mass, collision energy in the range of Elab=5 -160 A GeV, collision centrality, and the energy density transition criterion defining the hypersurface. The microscopic results are compared to negative contributions expected from hydrodynamical treatment assuming local thermal equilibrium. The main conclusion is that the number of actual microscopic particles flying inward is smaller than the negative contribution one would expect in an equilibrated scenario. The largest impact of negative contributions is found to be on the pion rapidity distribution at midrapidity in central collisions. For this case negative contributions in equilibrium constitute 8-13% of positive contributions, depending on collision energy, but only 0.5-4% in cascade calculation. The dependence on the collision energy itself is found to be nonmonotonous with a maximum at 10 - 20 A GeV.

  2. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  3. Hysteresis of liquid adsorption in porous media by coarse-grained Monte Carlo with direct experimental validation

    Science.gov (United States)

    Zeidman, Benjamin D.; Lu, Ning; Wu, David T.

    2016-05-01

    The effects of path-dependent wetting and drying manifest themselves in many types of physical systems, including nanomaterials, biological systems, and porous media such as soil. It is desirable to better understand how these hysteretic macroscopic properties result from a complex interplay between gasses, liquids, and solids at the pore scale. Coarse-Grained Monte Carlo (CGMC) is an appealing approach to model these phenomena in complex pore spaces, including ones determined experimentally. We present two-dimensional CGMC simulations of wetting and drying in two systems with pore spaces determined by sections from micro X-ray computed tomography: a system of randomly distributed spheres and a system of Ottawa sand. Results for the phase distribution, water uptake, and matric suction when corrected for extending to three dimensions show excellent agreement with experimental measurements on the same systems. This supports the hypothesis that CGMC can generate metastable configurations representative of experimental hysteresis and can also be used to predict hysteretic constitutive properties of particular experimental systems, given pore space images.

  4. String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

    Science.gov (United States)

    Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

    2018-03-01

    Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.

  5. 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.

  6. Diffusion maps and coarse-graining: A unified framework for dimensionality reduction, graph partitioning, and data set parameterization.

    Science.gov (United States)

    Lafon, Stéphane; Lee, Ann B

    2006-09-01

    We provide evidence that nonlinear dimensionality reduction, clustering, and data set parameterization can be solved within one and the same framework. The main idea is to define a system of coordinates with an explicit metric that reflects the connectivity of a given data set and that is robust to noise. Our construction, which is based on a Markov random walk on the data, offers a general scheme of simultaneously reorganizing and subsampling graphs and arbitrarily shaped data sets in high dimensions using intrinsic geometry. We show that clustering in embedding spaces is equivalent to compressing operators. The objective of data partitioning and clustering is to coarse-grain the random walk on the data while at the same time preserving a diffusion operator for the intrinsic geometry or connectivity of the data set up to some accuracy. We show that the quantization distortion in diffusion space bounds the error of compression of the operator, thus giving a rigorous justification for k-means clustering in diffusion space and a precise measure of the performance of general clustering algorithms.

  7. Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

    Science.gov (United States)

    Devaurs, Didier; Antunes, Dinler A; Papanastasiou, Malvina; Moll, Mark; Ricklin, Daniel; Lambris, John D; Kavraki, Lydia E

    2017-01-01

    Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a single conformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins.

  8. Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model.

    Science.gov (United States)

    Lenoci, Leonardo; Camp, Philip J

    2006-08-09

    The self-assembly of model peptides is studied using Brownian dynamics computer simulations. A coarse-grained, bead-spring model is designed to mimic silaffins, small peptides implicated in the biomineralization of certain silica diatom skeletons and observed to promote the formation of amorphous silica nanospheres in vitro. The primary characteristics of the silaffin are a 15 amino acid hydrophilic backbone and two modified lysine residues near the ends of the backbone carrying long polyamine chains. In the simulations, the model peptides self-assemble to form spherical clusters, networks of strands, or bicontinuous structures, depending on the peptide concentration and effective temperature. The results indicate that over a broad range of volume fractions (0.05-25%) the characteristic structural lengthscales fall in the range 12-45 nm. On this basis, we suggest that self-assembled structures act as either nucleation points or scaffolds for the deposition of 10-100 nm silica-peptide building blocks from which diatom skeletons and synthetic nanospheres are constructed.

  9. 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.

  10. Colloid-associated plutonium aged at room temperature: evaluating its transport velocity in saturated coarse-grained granites.

    Science.gov (United States)

    Xie, Jinchuan; Lin, Jianfeng; Wang, Yu; Li, Mei; Zhang, Jihong; Zhou, Xiaohua; He, Yifeng

    2015-01-01

    The fate and transport of colloidal contaminants in natural media are complicated by physicochemical properties of the contaminants and heterogeneous characteristics of the media. Size and charge exclusion are two key microscopic mechanisms dominating macroscopic transport velocities. Faster velocities of colloid-associated actinides than that of (3)H2O were consistently indicated in many studies. However, dissociation/dissolution of these sorbed actinides (e.g., Pu and Np), caused by their redox reactions on mineral surfaces, possibly occurred under certain chemical conditions. How this dissolution is related to transport velocities remains unanswered. In this study, aging of the colloid-associated Pu (pseudo-colloid) at room temperature and transport through the saturated coarse-grained granites were performed to study whether Pu could exhibit slower velocity than that of (3)H2O (UPu/UT colloidal granite particles took place during the aging period. The relative velocity of UPu/UT declined from 1.06 (unaged) to 0.745 (135 d) over time. Size exclusion limited to the uncharged nano-sized particles could not explain such observed UPu/UT colloid-associated Pu(IV) was observed in the aged suspensions. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. 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.

  12. 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.

  13. Bifidogenic effect of grain larvae extract on serum lipid, glucose and ...

    Indian Academy of Sciences (India)

    Keywords. Bifidogenic effect; blood lipid; cecal microflora; grain larvae; IgG; organic acid ... grain larvae ethanol extract (GLE) had a bifidogenic effect in normal rats. Male Sprague–Dawley rats were divided into a negative control group (CO) and GLE orally administered (5.0, 7.0 and 9.0 mg/100 g body weight) groups.

  14. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

    International Nuclear Information System (INIS)

    Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo

    2006-01-01

    Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases

  15. 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.

  16. 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.

  17. 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.

  18. A novel numerical model to predict the morphological behavior of magnetic liquid marbles using coarse grained molecular dynamics concepts

    Science.gov (United States)

    Polwaththe-Gallage, Hasitha-Nayanajith; Sauret, Emilie; Nguyen, Nam-Trung; Saha, Suvash C.; Gu, YuanTong

    2018-01-01

    Liquid marbles are liquid droplets coated with superhydrophobic powders whose morphology is governed by the gravitational and surface tension forces. Small liquid marbles take spherical shapes, while larger liquid marbles exhibit puddle shapes due to the dominance of gravitational forces. Liquid marbles coated with hydrophobic magnetic powders respond to an external magnetic field. This unique feature of magnetic liquid marbles is very attractive for digital microfluidics and drug delivery systems. Several experimental studies have reported the behavior of the liquid marbles. However, the complete behavior of liquid marbles under various environmental conditions is yet to be understood. Modeling techniques can be used to predict the properties and the behavior of the liquid marbles effectively and efficiently. A robust liquid marble model will inspire new experiments and provide new insights. This paper presents a novel numerical modeling technique to predict the morphology of magnetic liquid marbles based on coarse grained molecular dynamics concepts. The proposed model is employed to predict the changes in height of a magnetic liquid marble against its width and compared with the experimental data. The model predictions agree well with the experimental findings. Subsequently, the relationship between the morphology of a liquid marble with the properties of the liquid is investigated. Furthermore, the developed model is capable of simulating the reversible process of opening and closing of the magnetic liquid marble under the action of a magnetic force. The scaling analysis shows that the model predictions are consistent with the scaling laws. Finally, the proposed model is used to assess the compressibility of the liquid marbles. The proposed modeling approach has the potential to be a powerful tool to predict the behavior of magnetic liquid marbles serving as bioreactors.

  19. 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.

  20. 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.

  1. Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials

    International Nuclear Information System (INIS)

    Toth, Gergely

    2007-01-01

    The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car-Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions (Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well. We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method

  2. Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids.

    Science.gov (United States)

    Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek

    2017-10-25

    We study the mechanical response of cellulose and β-amyloid microfibrils to three types of deformation: tensile, indentational, and shear. The cellulose microfibrils correspond to the allomorphs Iα or Iβ whereas the β-amyloid microfibrils correspond to the polymorphs of either two- or three-fold symmetry. This response can be characterized by three elastic moduli, namely, Y L , Y T , and S. We use a structure-based coarse-grained model to analyze the deformations in a unified manner. We find that each of the moduli is almost the same for the two allomorphs of cellulose but Y L is about 20 times larger than Y T (140 GPa vs. 7 GPa), indicating the existence of significant anisotropy. For cellulose we note that the anisotropy results from the involvement of covalent bonds in stretching. For β-amyloid, the sense of anisotropy is opposite to that of cellulose. In the three-fold symmetry case, Y L is about half of Y T (3 vs. 7) whereas for two-fold symmetry the anisotropy is much larger (1.6 vs. 21 GPa). The S modulus is derived to be 1.2 GPa for three-fold symmetry and one half of it for the other symmetry and 3.0 GPa for cellulose. The values of the moduli reflect deformations in the hydrogen-bond network. Unlike in our theoretical approach, no experiment can measure all three elastic moduli with the same apparatus. However, our theoretical results are consistent with various measured values: typical Y L for cellulose Iβ ranges from 133 to 155 GPa, Y T from 2 to 25 GPa, and S from 1.8 to 3.8 GPa. For β-amyloid, the experimental values of S and Y T are about 0.3 GPa and 3.3 GPa respectively, while the value of Y L has not been reported.

  3. 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.

  4. 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.

  5. Coarse-Grain Molecular Dynamics Simulations to Investigate the Bulk Viscosity and Critical Micelle Concentration of the Ionic Surfactant Sodium Dodecyl Sulfate (SDS) in Aqueous Solution.

    Science.gov (United States)

    Ruiz-Morales, Yosadara; Romero-Martínez, Ascencion

    2018-03-13

    The first critical micelle concentration (CMC) of the ionic surfactant sodium dodecyl sulfate (SDS), in diluted aqueous solution, has been determined at room temperature from the investigation of the bulk viscosity, at several concentrations of SDS, by means of coarse grain molecular dynamics simulations. The coarse-grained model molecules at the mesoscale level are adopted. The bulk viscosity of SDS was calculated at several millimolar concentrations of SDS in water using the MARTINI force field by means of NVT shear Mesocite molecular dynamics. The definition of each bead in the MARTINI force field is established, as well as their radius, volume, and mass. The effect of the size of the simulation box on the obtained CMC has been investigated as well as the effect of the number of SDS molecules, in the simulations, on the formation of aggregates. The CMC, which was obtained from a graph of the calculated viscosities versus concentration, is in good agreement with reported experimental data, and do not depend on the size of the box used in the simulation. The formation of a spherical micelle-like aggregate is observed, where the dodecyl sulfate tails point inwards and the heads point outwards the aggregation micelle, in accordance with experimental observations. The advantage of using coarse grain molecular dynamics is the possibility of treating explicitly charged beads, applying a shear flow for viscosity calculation, as well as to process much larger spatial and temporal scales than atomistic molecular dynamics can. Furthermore, the CMC of SDS obtained with the coarse-grained model is in much better agreement with the experimental value than the value obtained with atomistic simulations.

  6. Effect of isothermal loading temperature on reversible inelastic strain in coarse-grained Ti49.7Ni50.7

    Science.gov (United States)

    Zhapova, Dorzhima; Lotkov, Aleksander; Grishkov, Victor; Timkin, Victor; Gembuh, Lev; Melnik, Andrey

    2017-12-01

    The paper presents experimental research results on the temperature dependence of reversible inelastic strain (superelasticity and shape memory effect) in coarse-grained Ti49.3Ni50.7 specimens (at %) under torsion. The experiments demonstrate that its value can measure up to ˜18% against minimum plastic strain accumulation in the material in martensitic and austenitic states with low martensite shear stresses.

  7. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  8. 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.

  9. 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.

  10. 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

  11. 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.

    2018-02-01

    This work presents the analysis of non-equilibrium energy transfer and dissociation of nitrogen molecules (N2(g+1Σ) ) 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(g+1Σ ) -N2(g+1Σ ) 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

  12. Microstructure and Impact Toughness of the Intercritically Reheated Coarse-grained Heat Affected Zone of 13MnNiMoR Steel

    Science.gov (United States)

    Han, Yang; Jinbo, Qu

    The microstructure and impact toughness of intercritically reheated coarse-grained heat affected zone (ICCGHAZ) of 13MnNiMoR and the effect of post-welding heat treatment (PWHT) process were investigated by means of welding thermal simulation test. The result shows that after the first welding thermal cycle, the microstructure of the coarse-grained heat affected zone (CGHAZ) mainly consists of granular bainite and lath bainite, with good impact toughness. After the second thermal cycle with a peak temperature of 650 to 700°C, the CGHAZ microstructure experiences a tempering process and its impact toughness improves due to the precipitation of carbides and reduction of dislocations. With a second peak temperature of 750 to 850°C, part of the CGHAZ microstructure retransforms to austenite and during cooling, martensite-austenite (MA) constituents forms along grain boundaries in the ICCGHAZ microstructure, leading to a sharp drop of toughness. When the second thermal cycle peak temperature is up to 900°C, the CGHAZ microstructure is fully austenitized, and the final microstructure mainly consists of ferrite and granular bainite. After a PWHT process in the temperature range of 560 to 640°C, the impact toughness of ICCGHAZ is markedly improved, primarily due to the decomposition of MA constituents.

  13. 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.

  14. 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.

  15. 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.

  16. 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 region...... 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....

  17. Estimation of a noise level using coarse-grained entropy of experimental time series of internal pressure in a combustion engine

    International Nuclear Information System (INIS)

    Litak, Grzegorz; Taccani, Rodolfo; Radu, Robert; Urbanowicz, Krzysztof; HoIyst, Janusz A.; Wendeker, MirosIaw; Giadrossi, Alessandro

    2005-01-01

    We report our results on non-periodic experimental time series of pressure in a single cylinder spark ignition engine. The experiments were performed for different levels of loading. We estimate the noise level in internal pressure calculating the coarse-grained entropy from variations of maximal pressures in successive cycles. The results show that the dynamics of the combustion is a non-linear multidimensional process mediated by noise. Our results show that so defined level of noise in internal pressure is not monotonous function of loading

  18. 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.

  19. Effect of inter-critically reheating temperature on microstructure and properties of simulated inter-critically reheated coarse grained heat affected zone in X70 steel

    International Nuclear Information System (INIS)

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

    2014-01-01

    This study investigated the influence of the inter-critical reheating temperature on the microstructure and mechanical properties of a coarse grained heat affected zone (CGHAZ) in an API 5L grade X70 pipeline steel seam weld. A Gleeble 3500 thermo-mechanical simulator was employed to duplicate particular weld thermal cycles in order to accurately assess specific regions of the weld HAZ. Detailed microstructural analysis, including investigation of the martensite–austenite (M–A) constituent, was performed using optical microscope (OM), scanning electron microscope (SEM) and selective etching techniques. It is shown that the fracture toughness of the CGHAZ is significantly reduced following exposure to a subsequent inter-critical thermal cycle. Fracture toughness gradually improves as the inter-critical temperature is increased, but does not return to the value of the original CGHAZ due to the presence of isolated large M–A particles and coarse microstructure. Significance of M–A particles to the HAZ fracture toughness is first related to the location of particles along prior austenite grain boundaries, followed by the size of individual M–A particles

  20. Relation between the grafting density of liquid crystal macromolecule and the symmetry of self-assembled bulk phase: coarse-grained molecular dynamics study

    Directory of Open Access Journals (Sweden)

    J.M. Ilnytskyi

    2013-01-01

    Full Text Available I consider a generic coarse-grained model suitable for the study of bulk self-assembly of liquid crystal (LC macromolecules. The cases include LC dendrimers, gold nanoparticles modified by polymer chains with terminating LC groups and oth. The study is focused on the relation between a number of grafted chains, Nch, and the symmetry of the self-assembled bulk phases. Simple space-filling arguments are used first to estimate stability intervals for a rod-like, disc-like and spherulitic conformations in terms of Nch. These are followed by coarse-grained molecular dynamics simulations for both spontaneous and aided self-assembly of LC macromolecules into bulk phases. In spontaneous self-assembly runs, essential coexistence of rod-like and disc-like conformations is observed (via analysis of the histograms for the molecular asphericity in a broad interval of Nch, which prevents formation of defect-free structures. The use of uniaxial and planar aiding fields is found to improve self-assembly into monodomain phases by promoting conformations of respective symmetry. Strong shape-phase relation, observed experimentally, is indicated also by the simulations by the coincidence of the stability intervals for the respective conformations with those for the bulk phases.

  1. Lipid Structure in Triolein Lipid Droplets

    DEFF Research Database (Denmark)

    Chaban, Vitaly V; Khandelia, Himanshu

    2014-01-01

    Lipid droplets (LDs) are primary repositories of esterified fatty acids and sterols in animal cells. These organelles originate on the lumenal or cytoplasmic side of endoplasmic reticulum (ER) membrane and are released to the cytosol. In contrast to other intracellular organelles, LDs are composed...... of a mass of hydrophobic lipid esters coved by phospholipid monolayer. The small size and unique architecture of LDs makes it complicated to study LD structure by modern experimental methods. We discuss coarse-grained molecular dynamics (MD) simulations of LD formation in systems containing 1-palmitoyl-2...... to coarse-grained simulations, the presence of PE lipids at the interface has a little impact on distribution of components and on the overall LD structure. (4) The thickness of the lipid monolayer at the surface of the droplet is similar to the thickness of one leaflet of a bilayer. Computer simulations...

  2. 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 a...... 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.......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...

  3. Modulation of the activities of membrane enzymes by cereal grain resorcinolic lipids.

    Science.gov (United States)

    Kozubek, A; Nietubyc, M; Sikorski, A F

    1992-01-01

    Resorcinolic lipids, amphiphilic compounds from cereal grains show strong effects upon the activity of membrane enzymes. The concentrations for 50% inhibition of erythrocyte membrane acetylcholinesterase were in the range of 18-90 microM and were dependent on the length of the aliphatic side chain of the homologue and on the modification of hydroxyl groups in the benzene ring. Sulfonation of OH groups resulted in a drastic decrease of the inhibitory potency. The effect of resorcinolic lipids on the activity of Ca2+(calmodulin)-ATPase was the opposite. Up to concentrations of 50 microM alk(en)ylresorcinols stimulated the activity of this enzyme and only slight inhibition (approx. 30%) was observed above 100 microM. The results suggest that the effect of resorcinolic lipids might depend on their ability to alter the bilayer properties. Most probably these compounds decrease the mobility of membrane phospholipid molecules.

  4. 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.

    2018-02-01

    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

  5. Source and depositional processes of coarse-grained limestone event beds in Frasnian slope deposits (Kostomłoty-Mogiłki quarry, Holy Cross Mountains, Poland)

    Science.gov (United States)

    Vierek, Aleksandra

    2010-10-01

    The Kostomłoty-Mogiłki succession is situated in the Kostomłoty transitional zone between the shallow-water Kielce stromatoporoid-coral platform and the deeper Łysogóry basin. In the Kostomłoty-Mogiłki quarry, the upper part of the Szydłówek Beds and Kostomłoty Beds are exposed. The Middle-Upper Frasnian Kostomłoty Beds are composed of shales, micritic and nodular limestones with abundant intercalations of detrital limestones. The dark shales and the micritic and nodular limestones record background sedimentation. The interbedded laminated and detrital limestones reflect high-energy deposition (= event beds). These event beds comprise laminated calcisiltites, fine-grained calcarenites, coarse-grained grain-supported calcirudites fabrics, and matrix-supported calcirudites. The material of these event beds was supplied by both erosion of the carbonate-platform margin and cannibalistic erosion of penecontemporaneous detrital limestones building the slope of this platform. Storms and the tectonic activity were likely the main causes of erosion. Combined and gravity flows were the transporting mechanisms involved in the reworking and redeposition.

  6. 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.

  7. Whole grains, bran, and germ in relation to homocysteine and markers of glycemic control, lipids, and inflammation 1

    DEFF Research Database (Denmark)

    Jensen, Majken K; Koh-Banerjee, Pauline; Franz, Mary

    2006-01-01

    BACKGROUND: Intake of whole grains is inversely associated with risk of diabetes and ischemic heart disease in observational studies. The lower risk associated with high whole-grain intakes may be mediated through improvements in glycemic control, lipid profiles, or reduced inflammation. OBJECTIV...

  8. Lateral pressure profiles in lipid monolayers

    NARCIS (Netherlands)

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2010-01-01

    We have used molecular dynamics simulations with coarse-grained and atomistic models to study the lateral pressure profiles in lipid monolayers. We first consider simple oil/air and oil/water interfaces, and then proceed to lipid monolayers at air/water and oil/water interfaces. The results are

  9. Mineralogy and origin of coarse-grained segregations in the pyrometallurgical Zn-Pb slags from Katowice-Wełnowiec (Poland)

    Science.gov (United States)

    Warchulski, R.; Gawęda, A.; Janeczek, J.; Kądziołka-Gaweł, M.

    2016-10-01

    The unique among pyrometallurgical slags, coarse-grained (up to 2.5 cm) segregations (up to 40 cm long) rimmed by "aplitic" border zones occur within holocrystalline historical Zn-smelting slag in Katowice, S Poland. Slag surrounding the segregations consists of olivine, spinel series, melilite, clinopyroxene, leucite, nepheline and sulphides. Ca-olivines, kalsilite and mica compositionally similar to oxykinoshitalite occur in border zones in addition to olivine, spinel series and melilite. Miarolitic and massive pegmatite-like segregations are built of subhedral crystals of melilite, leucite, spinel series, clinopyroxene and hematite. Melilite, clinopyroxenes and spinels in the segregations are enriched in Zn relatively to original slag and to fine-grained border zones. The segregations originated as a result of crystallization from residual melt rich in volatiles (presumably CO2). The volatile-rich melt was separated during fractional crystallization of molten slag under the cover of the overlying hot (ca. 1250 °C) vesicular slag, preventing the escape of volatiles. That unique slag system is analogous to natural magmatic systems.

  10. 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

    The IRSL and post-IR IRSL (pIRIR) signal characteristics of polymineral fine grains are investigated and compared with those of K- and Na-rich feldspar extracts. TL signal loss after IR and pIRIR stimulations occurs mainly at around 320 °C for polymineral and Na-feldspar samples and around 410 °C...... for K-feldspar samples, when a preheat temperature of 250 °C for 60 s is used. After preheating to a higher temperature (320 °C for 60 s) all samples show a TL reduction around 410 °C in the blue detection window. Pulse annealing experiments for IRSL and pIRIR signals for preheats between 320 °C and 500...... °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...

  11. Brownian dynamics simulations of lipid bilayer membrane with hydrodynamic interactions in LAMMPS

    Science.gov (United States)

    Fu, Szu-Pei; Young, Yuan-Nan; Peng, Zhangli; Yuan, Hongyan

    Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiency has been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4 6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane (such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity). In this work we implement such interaction potential in LAMMPS to simulate large-scale lipid systems such as vesicles and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for red blood cell (RBC) dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. We focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with varying enclosed volume; 2. RBC shape transitions with different enclosed volume.

  12. 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

  13. 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

  14. Monte Carlo tests of small-world architecture for coarse-grained networks of the United States railroad and highway transportation systems

    Science.gov (United States)

    Aldrich, Preston R.; El-Zabet, Jermeen; Hassan, Seerat; Briguglio, Joseph; Aliaj, Enela; Radcliffe, Maria; Mirza, Taha; Comar, Timothy; Nadolski, Jeremy; Huebner, Cynthia D.

    2015-11-01

    Several studies have shown that human transportation networks exhibit small-world structure, meaning they have high local clustering and are easily traversed. However, some have concluded this without statistical evaluations, and others have compared observed structure to globally random rather than planar models. Here, we use Monte Carlo randomizations to test US transportation infrastructure data for small-worldness. Coarse-grained network models were generated from GIS data wherein nodes represent the 3105 contiguous US counties and weighted edges represent the number of highway or railroad links between counties; thus, we focus on linkage topologies and not geodesic distances. We compared railroad and highway transportation networks with a simple planar network based on county edge-sharing, and with networks that were globally randomized and those that were randomized while preserving their planarity. We conclude that terrestrial transportation networks have small-world architecture, as it is classically defined relative to global randomizations. However, this topological structure is sufficiently explained by the planarity of the graphs, and in fact the topological patterns established by the transportation links actually serve to reduce the amount of small-world structure.

  15. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.

    Science.gov (United States)

    Spill, Yannick G; Pasquali, Samuela; Derreumaux, Philippe

    2011-05-10

    The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.

  16. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

    International Nuclear Information System (INIS)

    Dunn, Nicholas J. H.; Noid, W. G.

    2016-01-01

    This work investigates the promise of a “bottom-up” extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative “structure” within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.

  17. 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.

  18. Effect of solvent on the structure of a protein (H3.1) with a coarse-grained model with knowledge-based interactions

    Science.gov (United States)

    Pandey, Ras; Farmer, Barry

    2013-03-01

    Quality of solvent plays a critical role in modulating the structure of a protein along with the temperature. Using a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV) we examine the structure and dynamics of a histone (H3.1). The empty lattice sites constitute the effective solvent medium in which the protein is embedded. Residue-solvent characteristic interaction is based on the hydropathy index while the residue-residue interaction is used from the knowledge-based contact matrices derived from ensembles of protein structures in the protein data bank. Large scale simulations are performed to analyze the structure of protein for a range of residue-solvent interaction strength, a measure of the solvent quality with each potential. Unlike the monotonic thermal response, the radius of gyration of the protein exhibits non-monotonic dependence of the solvent strength. Quantitative comparison of the structure and dynamics emerging from three knowledge-based potentials will be presented in this talk. This work is supported by Air Force Research Laboratory.

  19. Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation.

    Science.gov (United States)

    Calero-Rubio, Cesar; Paik, Bradford; Jia, Xinqiao; Kiick, Kristi L; Roberts, Christopher J

    2016-10-01

    This report focuses on the molecular-level processes and thermodynamics of unfolding of a series of helical peptides using a coarse-grained (CG) molecular model. The CG model was refined to capture thermodynamics and structural changes as a function of temperature for a set of published peptide sequences. Circular dichroism spectroscopy (CD) was used to experimentally monitor the temperature-dependent conformational changes and stability of published peptides and new sequences introduced here. The model predictions were quantitatively or semi-quantitatively accurate in all cases. The simulations and CD results showed that, as expected, in most cases the unfolding of helical peptides is well described by a simply 2-state model, and conformational stability increased with increased length of the helices. A notable exception in a 19-residue helix was when two Ala residues were each replaced with Phe. This stabilized a partly unfolded intermediate state via hydrophobic contacts, and also promoted aggregates at higher peptide concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

    Science.gov (United States)

    Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary

    2018-03-01

    A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.

  1. Climatic impact on isovolumetric weathering of a coarse-grained schist in the northern Piedmont Province of the central Atlantic states

    Science.gov (United States)

    Cleaves, E.T.

    1993-01-01

    The possible impact of periglacial climates on the rate of chemical weathering of a coarse-grained plagioclase-muscovite-quartz schist has been determined for a small watershed near Baltimore, Maryland. The isovolumetric chemical weathering model formulated from the geochemical mass balance study of the watershed shows that the weathering front advances at a velocity of 9.1 m/m.y., if the modern environmental parameters remain the same back through time. However, recent surficial geological mapping demonstrates that periglacial climates have impacted the area. Such an impact significantly affects two key chemical weathering parameters, the concentration of CO2 in the soil and groundwater moving past the weathering front. Depending upon the assumptions used in the model, the rate of saprolitization varies from 2.2 to 5.3 m/m.y. The possible impact of periglacial processes suggested by the chemical weathering rates indicates a need to reconsider theories of landscape evolution as they apply to the northern Piedmont Province of the mid-Atlantic states. I suggest that from the Late Miocene to the present that the major rivers have become incised in their present locations; this incision has enhanced groundwater circulation and chemical weathering such that crystalline rocks beneath interfluvial areas remain mantled by saprolite; and the saprolite mantle has been partially stripped as periglacial conditions alternate with humid-temperate conditions. ?? 1993.

  2. Microphase separation and the formation of ion conductivity channels in poly(ionic liquid)s: A coarse-grained molecular dynamics study

    Science.gov (United States)

    Weyman, Alexander; Bier, Markus; Holm, Christian; Smiatek, Jens

    2018-05-01

    We study generic properties of poly(ionic liquid)s (PILs) via coarse-grained molecular dynamics simulations in bulk solution and under confinement. The influence of different side chain lengths on the spatial properties of the PIL systems and on the ionic transport mechanism is investigated in detail. Our results reveal the formation of apolar and polar nanodomains with increasing side chain length in good agreement with previous results for molecular ionic liquids. The ion transport numbers are unaffected by the occurrence of these domains, and the corresponding values highlight the potential role of PILs as single-ion conductors in electrochemical devices. In contrast to bulk behavior, a pronounced formation of ion conductivity channels in confined systems is initiated in close vicinity to the boundaries. We observe higher ion conductivities in these channels for increasing PIL side chain lengths in comparison with bulk values and provide an explanation for this effect. The appearance of these domains points to an improved application of PILs in modern polymer electrolyte batteries.

  3. Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method

    Science.gov (United States)

    Ardham, Vikram Reddy; Deichmann, Gregor; van der Vegt, Nico F. A.; Leroy, Frédéric

    2015-12-01

    We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion WSL calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of WSL that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and WSL is elucidated through a detailed study of the energy and entropy components of WSL. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of WSL. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.

  4. Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method

    Energy Technology Data Exchange (ETDEWEB)

    Ardham, Vikram Reddy; Leroy, Frédéric, E-mail: vandervegt@csi.tu-darmstadt.de, E-mail: f.leroy@theo.chemie.tu-darmstadt.de [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt (Germany); Deichmann, Gregor; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de, E-mail: f.leroy@theo.chemie.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt (Germany)

    2015-12-28

    We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion W{sub SL} calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of W{sub SL} that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and W{sub SL} is elucidated through a detailed study of the energy and entropy components of W{sub SL}. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of W{sub SL}. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.

  5. Temporal coarse graining of CO2 and N2 diffusion in zeolite NaKA: from the quantum scale to the macroscopic.

    Science.gov (United States)

    Mace, Amber; Leetmaa, Mikael; Laaksonen, Aatto

    2015-10-13

    The kinetic CO2-over-N2 sieving capabilities in narrow pore zeolites are dependent on the free-energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately compute the energy barriers, whereas it is desirable to predict the macroscopic scale diffusion for industrial applications. Using ab initio molecular dynamics on the picosecond time scale, the free-energy barriers of diffusion can be predicted for different local pore properties in order to identify those that are rate-determining for the pore-to-pore diffusion. Specifically, we investigate the effects of the Na(+)-to-K(+) exchange at the different cation sites and the CO2 loading in Zeolite NaKA. These computed energy barriers are then used as input for the Kinetic Monte Carlo method, coarse graining the dynamic simulation steps to the pore-to-pore diffusion. With this approach, we simulate how the identified rate-determining properties as well as the application of skin-layer surface defects affect the diffusion driven uptake in a realistic Zeolite NaKA powder particle model on a macroscopic time scale. Lastly, we suggest a model by combining these effects, which provides an excellent agreement with the experimental CO2 and N2 uptake behaviors presented by Liu et al. (Chem. Commun. 2010, 46, 4502-4504).

  6. Whole grains, bran, and germ in relation to homocysteine and markers of glycemic control, lipids, and inflammation 1

    DEFF Research Database (Denmark)

    Jensen, Majken K; Koh-Banerjee, Pauline; Franz, Mary

    2006-01-01

    : The aim was to examine whether the intake of whole grains, bran, and germ is related to homocysteine, plasma markers of glycemic control (fasting insulin, hemoglobin A1c, C-peptide, and leptin), lipids (total cholesterol, triacylglycerol, HDL cholesterol, and LDL cholesterol), and inflammation (C......-reactive protein, fibrinogen, and interleukin 6). DESIGN: This was a cross-sectional study of the relations of whole grains, bran, and germ intakes with homocysteine and markers of glycemic control, lipids, and inflammation in 938 healthy men and women. RESULTS: Whole-grain intake was inversely associated...... with homocysteine and markers of glycemic control. Compared with participants in the bottom quintile of whole-grain intake, participants in the highest quintile had 17%, 14%, 14%, and 11% lower concentrations of homocysteine (P

  7. Preferred carbon precursors for lipid labelling in the heterotrophic endosperm of developing oat (Avena sativa L.) grains.

    Science.gov (United States)

    Grimberg, Åsa

    2014-10-01

    Oat (Avena sativa L.) is unusual among the cereal grains in storing high amounts of oil in the endosperm; up to 90% of total grain oil. By using oat as a model species for oil metabolism in the cereal endosperm, we can learn how to develop strategies to redirect carbon from starch to achieve high-oil yielding cereal crops. Carbon precursors for lipid synthesis were compared in two genetically close oat cultivars with different endosperm oil content (about 6% and 10% of grain dw, medium-oil; MO, and high-oil; HO cultivar, respectively) by supplying a variety of (14)C-labelled substrates to the grain from both up- and downstream parts of glycolysis, either through detached oat panicles in vitro or by direct injection in planta. When supplied by direct injection, (14)C from acetate was identified to label the lipid fraction of the grain to the highest extent among substrates tested; 46% of net accumulated (14)C, demonstrating its applicability as a marker for lipids in the endosperm. Time course analyses of injected (14)C acetate during grain development suggested a more efficient transfer of fatty acids from polar lipids to triacylglycerol in the HO as compared to the MO cultivar, and turnover of triacylglycerol was suggested to not play a major role for the final oil content of oat grain endosperm despite the low amount of protective oleosins in this tissue. Moreover, availability of light was shown to drastically affect grain net carbon accumulation from (14)C-sucrose when supplied through detached panicles for the HO cultivar. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  8. Spontaneous Buckling of Lipid Bilayer and Vesicle Budding Induced by Antimicrobial Peptide Magainin 2: A Coarse-Grained Simulation Study

    Science.gov (United States)

    2011-05-30

    nonspherical (such as prolate) shapes develop narrowing necks and evolve into dumbbell and necklace-shaped objects when exposed to increasing concentrations...changes into shapes such as dumbbells or necklaces are not directly accessible, it is expected that the poration process will occur locally on the

  9. Curvature function and coarse graining

    International Nuclear Information System (INIS)

    Diaz-Marin, Homero; Zapata, Jose A.

    2010-01-01

    A classic theorem in the theory of connections on principal fiber bundles states that the evaluation of all holonomy functions gives enough information to characterize the bundle structure (among those sharing the same structure group and base manifold) and the connection up to a bundle equivalence map. This result and other important properties of holonomy functions have encouraged their use as the primary ingredient for the construction of families of quantum gauge theories. However, in these applications often the set of holonomy functions used is a discrete proper subset of the set of holonomy functions needed for the characterization theorem to hold. We show that the evaluation of a discrete set of holonomy functions does not characterize the bundle and does not constrain the connection modulo gauge appropriately. We exhibit a discrete set of functions of the connection and prove that in the abelian case their evaluation characterizes the bundle structure (up to equivalence), and constrains the connection modulo gauge up to ''local details'' ignored when working at a given scale. The main ingredient is the Lie algebra valued curvature function F S (A) defined below. It covers the holonomy function in the sense that expF S (A)=Hol(l=∂S,A).

  10. 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.

  11. 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.

  12. 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.

  13. 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 (T m ) 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 (T a ) 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 T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2015-08-11

    Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

  1. Hydrodynamically Coupled Brownian Dynamics: A coarse-grain particle-based Brownian dynamics technique with hydrodynamic interactions for modeling self-developing flow of polymer solutions

    Science.gov (United States)

    Ahuja, V. R.; van der Gucht, J.; Briels, W. J.

    2018-01-01

    We present a novel coarse-grain particle-based simulation technique for modeling self-developing flow of dilute and semi-dilute polymer solutions. The central idea in this paper is the two-way coupling between a mesoscopic polymer model and a phenomenological fluid model. As our polymer model, we choose Responsive Particle Dynamics (RaPiD), a Brownian dynamics method, which formulates the so-called "conservative" and "transient" pair-potentials through which the polymers interact besides experiencing random forces in accordance with the fluctuation dissipation theorem. In addition to these interactions, our polymer blobs are also influenced by the background solvent velocity field, which we calculate by solving the Navier-Stokes equation discretized on a moving grid of fluid blobs using the Smoothed Particle Hydrodynamics (SPH) technique. While the polymers experience this frictional force opposing their motion relative to the background flow field, our fluid blobs also in turn are influenced by the motion of the polymers through an interaction term. This makes our technique a two-way coupling algorithm. We have constructed this interaction term in such a way that momentum is conserved locally, thereby preserving long range hydrodynamics. Furthermore, we have derived pairwise fluctuation terms for the velocities of the fluid blobs using the Fokker-Planck equation, which have been alternatively derived using the General Equation for the Non-Equilibrium Reversible-Irreversible Coupling (GENERIC) approach in Smoothed Dissipative Particle Dynamics (SDPD) literature. These velocity fluctuations for the fluid may be incorporated into the velocity updates for our fluid blobs to obtain a thermodynamically consistent distribution of velocities. In cases where these fluctuations are insignificant, however, these additional terms may well be dropped out as they are in a standard SPH simulation. We have applied our technique to study the rheology of two different

  2. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.

    Science.gov (United States)

    Sieradzan, Adam K; Niadzvedtski, Andrei; Scheraga, Harold A; Liwo, Adam

    2014-05-13

    Continuing our effort to introduce d-amino-acid residues in the united residue (UNRES) force field developed in our laboratory, in this work the C α ··· C α ··· C α backbone-virtual-bond-valence-angle (θ) potentials for systems containing d-amino-acid residues have been developed. The potentials were determined by integrating the combined energy surfaces of all possible triplets of terminally blocked glycine, alanine, and proline obtained with ab initio molecular quantum mechanics at the MP2/6-31G(d,p) level to calculate the corresponding potentials of mean force (PMFs). Subsequently, analytical expressions were fitted to the PMFs to give the virtual-bond-valence potentials to be used in UNRES. Alanine represented all types of amino-acid residues except glycine and proline. The blocking groups were either the N -acetyl and N ', N '-dimethyl or N -acetyl and pyrrolidyl group, depending on whether the residue next in sequence was an alanine-type or a proline residue. A total of 126 potentials (63 symmetry-unrelated potentials for each set of terminally blocking groups) were determined. Together with the torsional, double-torsional, and side-chain-rotamer potentials for polypeptide chains containing d-amino-acid residues determined in our earlier work (Sieradzan et al. J. Chem. Theory Comput. , 2012 , 8, 4746), the new virtual-bond-angle (θ) potentials now constitute the complete set of physics-based potentials with which to run coarse-grained simulations of systems containing d-amino-acid residues. The ability of the extended UNRES force field to reproduce thermodynamics of polypeptide systems with d-amino-acid residues was tested by comparing the experimentally measured and the calculated free energies of helix formation of model KLALKLALxxLKLALKLA peptides, where x denotes any d- or l- amino-acid residue. The obtained results demonstrate that the UNRES force field with the new potentials reproduce the changes of free energies of helix formation upon d

  3. Whole grain products, fish and bilberries alter glucose and lipid metabolism in a randomized, controlled trial: the Sysdimet study.

    Directory of Open Access Journals (Sweden)

    Maria Lankinen

    Full Text Available Due to the growing prevalence of type 2 diabetes, new dietary solutions are needed to help improve glucose and lipid metabolism in persons at high risk of developing the disease. Herein we investigated the effects of low-insulin-response grain products, fatty fish, and berries on glucose metabolism and plasma lipidomic profiles in persons with impaired glucose metabolism.Altogether 106 men and women with impaired glucose metabolism and with at least two other features of the metabolic syndrome were included in a 12-week parallel dietary intervention. The participants were randomized into three diet intervention groups: (1 whole grain and low postprandial insulin response grain products, fatty fish three times a week, and bilberries three portions per day (HealthyDiet group, (2 Whole grain enriched diet (WGED group, which includes principally the same grain products as group (1, but with no change in fish or berry consumption, and (3 refined wheat breads (Control. Oral glucose tolerance, plasma fatty acids and lipidomic profiles were measured before and after the intervention. Self-reported compliance with the diets was good and the body weight remained constant. Within the HealthyDiet group two hour glucose concentration and area-under-the-curve for glucose decreased and plasma proportion of (n-3 long-chain PUFAs increased (False Discovery Rate p-values <0.05. Increases in eicosapentaenoic acid and docosahexaenoic acid associated curvilinearly with the improved insulin secretion and glucose disposal. Among the 364 characterized lipids, 25 changed significantly in the HealthyDiet group, including multiple triglycerides incorporating the long chain (n-3 PUFA.The results suggest that the diet rich in whole grain and low insulin response grain products, bilberries, and fatty fish improve glucose metabolism and alter the lipidomic profile. Therefore, such a diet may have a beneficial effect in the efforts to prevent type 2 diabetes in high risk

  4. Effects of whole grain, fish and bilberries on serum metabolic profile and lipid transfer protein activities: a randomized trial (Sysdimet.

    Directory of Open Access Journals (Sweden)

    Maria Lankinen

    Full Text Available We studied the combined effects of wholegrain, fish and bilberries on serum metabolic profile and lipid transfer protein activities in subjects with the metabolic syndrome.Altogether 131 subjects (40-70 y, BMI 26-39 kg/m(2 with impaired glucose metabolism and features of the metabolic syndrome were randomized into three groups with 12-week periods according to a parallel study design. They consumed either: a wholegrain and low postprandial insulin response grain products, fatty fish 3 times a week, and bilberries 3 portions per day (HealthyDiet, b wholegrain and low postprandial insulin response grain products (WGED, or c refined wheat breads as cereal products (Control. Altogether 106 subjects completed the study. Serum metabolic profile was studied using an NMR-based platform providing information on lipoprotein subclasses and lipids as well as low-molecular-weight metabolites.There were no significant differences in clinical characteristics between the groups at baseline or at the end of the intervention. Mixed model analyses revealed significant changes in lipid metabolites in the HealthyDiet group during the intervention compared to the Control group. All changes reflected increased polyunsaturation in plasma fatty acids, especially in n-3 PUFAs, while n-6 and n-7 fatty acids decreased. According to tertiles of changes in fish intake, a greater increase of fish intake was associated with increased concentration of large HDL particles, larger average diameter of HDL particles, and increased concentrations of large HDL lipid components, even though total levels of HDL cholesterol remained stable.The results suggest that consumption of diet rich in whole grain, bilberries and especially fatty fish causes changes in HDL particles shifting their subclass distribution toward larger particles. These changes may be related to known protective functions of HDL such as reverse cholesterol transport and could partly explain the known protective

  5. Modern dispersal patterns of fine and coarse-grained sediments on the continental shelf off the Mekong River delta, South China Sea - insights from mineralogy, geochemistry and sediment budget

    Science.gov (United States)

    Jagodziński, R.; Sternal, B.; Szczucinski, W.; Stattegger, K.

    2016-02-01

    The Mekong River is one of the major suppliers of sediments to the ocean. The river delivers both fine- and coarse-grained sediment fraction, which may be distributed on the adjacent continental shelf in various ways and the objective of the study is to provide evidence of their dominating transport directions, sedimentation mode, as well as the sediment budget. Szczuciński et al. (2013) provided evidence of sediment dispersal of fine-grained sediments. They confirmed that a major portion of the supplied sediments is accumulated in the subaqueous delta front, which progrades directly off the river mouths and also forms at a distance of more than 200 km westward, next to the Camau Peninsula, provided evidence for the existence of a Mekong-fed prodelta further offshore and presented a quantitative assessment of the modern fluvial-derived fine-grained sediment dispersal on the continental shelf. This study extends the previous work and focus on dispersal of coarse-grained sediments. It presents insights from analyses of about 200 river bed sediment and marine surface sediment samples and short sediment cores collected from the delta front, prodelta, as well as from continental shelf further offshore. The sediments were analyzed for grain-size composition, bulk geochemistry and heavy minerals. Sediment accumulation rates were analysed with 210Pb and 137Cs. Dispersal pattern was interpreted mostly from statistical analyses of heavy mineral assemblages in various grain size fractions. They showed that the major transport direction is westward, along the delta front. Most of the deposits retain on the delta front with only a very minor portion stored in the prodelta. So, it differs from the fine-grained sediment budget calculation, which reveals that the subaqueous delta front stores approximately 50%, while roughly one-fourth of the sediments are retained in the subaerial region of the delta, and approximately 25% accumulates on the shelf around the Camau Peninsula

  6. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

    Science.gov (United States)

    Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S; Blood, Philip; Scheraga, Harold A

    2010-03-09

    We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.

  7. ATR-FTIR spectroscopy reveals involvement of lipids and proteins of intact pea pollen grains to heat stress tolerance

    Directory of Open Access Journals (Sweden)

    Rachid eLahlali

    2014-12-01

    Full Text Available With climate change, pea will be more frequently subjected to heat stress in semi-arid regions like Saskatchewan during flowering. The pollen germination percentage of two pea cultivars was reduced by heat stress (36°C with an important decrease in cultivar ‘CDC Golden’ compared to ‘CDC Sage’. Lipids, protein and other pollen coat compositions of whole intact pollen grains of both pea cultivars were investigated using mid infrared (mid-IR Attenuated Total Reflectance (ATR-Fourier Transform Infrared (FTIR spectroscopy. Curve-fitting of ATR absorbance spectra in the protein region enabled estimation and comparison of different protein secondary structures between the two cultivars. CDC Sage had relatively greater amounts of α-helical structures (48.6-43.6%; band at 1654 cm-1 and smaller amounts of β-sheets (41.3-46% than CDC Golden. The CDC Golden had higher amounts of β-sheets (46.3-51.7% compared to α-helical structures (35.3-36.2%. Further, heat stress resulted in prominent changes in the symmetrical and asymmetrical CH2 bands from lipid acyl chain, ester carbonyl band, and carbohydrate region. The intensity of asymmetric and symmetric CH2 vibration of heat stressed CDC Golden was reduced considerably in comparison to the control and the decrease was higher compared to CDC sage. In addition, CDC Golden showed an increase in intensity at the oxidative band of 3015 cm-1. These results reveal that the whole pollen grains of both pea cultivars responded differently to heat stress. The tolerance of CDC Sage to heat stress (expressed as pollen germination percentage may be due to its protein richness with α-helical structures which would protect against the destructive effects of dehydration due to heat stress. The low pollen germination percentage of CDC Golden after heat stress may be also due to its sensitivity to lipid changes due to heat stress.

  8. ATR-FTIR spectroscopy reveals involvement of lipids and proteins of intact pea pollen grains to heat stress tolerance.

    Science.gov (United States)

    Lahlali, Rachid; Jiang, Yunfei; Kumar, Saroj; Karunakaran, Chithra; Liu, Xia; Borondics, Ferenc; Hallin, Emil; Bueckert, Rosalind

    2014-01-01

    With climate change, pea will be more frequently subjected to heat stress in semi-arid regions like Saskatchewan during flowering. The pollen germination percentage of two pea cultivars was reduced by heat stress (36°C) with an important decrease in cultivar 'CDC Golden' compared to 'CDC Sage.' Lipids, protein and other pollen coat compositions of whole intact pollen grains of both pea cultivars were investigated using mid infrared (mid-IR) attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy. Curve fitting of ATR absorbance spectra in the protein region enabled estimation and comparison of different protein secondary structures between the two cultivars. CDC Sage had relatively greater amounts of α-helical structures (48.6-43.6%; band at 1654 cm(-1)) and smaller amounts of β-sheets (41.3-46%) than CDC Golden. The CDC Golden had higher amounts of β-sheets (46.3-51.7%) compared to α-helical structures (35.3-36.2%). Further, heat stress resulted in prominent changes in the symmetrical and asymmetrical CH2 bands from lipid acyl chain, ester carbonyl band, and carbohydrate region. The intensity of asymmetric and symmetric CH2 vibration of heat stressed CDC Golden was reduced considerably in comparison to the control and the decrease was higher compared to CDC Sage. In addition, CDC Golden showed an increase in intensity at the oxidative band of 3015 cm(-1). These results reveal that the whole pollen grains of both pea cultivars responded differently to heat stress. The tolerance of CDC Sage to heat stress (expressed as pollen germination percentage) may be due to its protein richness with α-helical structures which would protect against the destructive effects of dehydration due to heat stress. The low pollen germination percentage of CDC Golden after heat stress may be also due to its sensitivity to lipid changes due to heat stress.

  9. Intermonolayer friction and surface shear viscosity of lipid bilayer membranes

    NARCIS (Netherlands)

    den Otter, Wouter K.; Shkulipa, S.

    2007-01-01

    The flow behavior of lipid bilayer membranes is characterized by a surface viscosity for in-plane shear deformations, and an intermonolayer friction coefficient for slip between the two leaflets of the bilayer. Both properties have been studied for a variety of coarse-grained double-tailed model

  10. Bifidogenic effect of grain larvae extract on serum lipid, glucose and ...

    Indian Academy of Sciences (India)

    2015-07-19

    Jul 19, 2015 ... Grain larvae are described in the Dictionary of. Chinese Medicine, a comprehensive dictionary of Chinese pharmaceutical raw materials, to be effective for blood cleansing and reducing fever and are described in the. Sungje Chongrok as a remedy for insatiable appetite. The. Boncho Gangmok from the ...

  11. Bifidogenic effect of grain larvae extract on serum lipid, glucose and ...

    Indian Academy of Sciences (India)

    2015-07-19

    Jul 19, 2015 ... The main objective of this study was to investigate whether orally administered Korean grain larvae ethanol extract. (GLE) had a bifidogenic effect in normal rats. Male Sprague–Dawley rats were divided into a negative control group. (CO) and GLE orally administered (5.0, 7.0 and 9.0 mg/100 g body weight) ...

  12. The effects of moderate whole grain consumption on fasting glucose and lipids, gastrointestinal symptoms, and microbiota

    Science.gov (United States)

    This study was designed to determine if providing wheat, corn, and rice as whole (WG) or refined grains (RG) under free-living conditions will change parameters of health over a six-week intervention in healthy, habitual non-WG consumers. Measurements of body composition, fecal microbiota, fasting ...

  13. Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

    International Nuclear Information System (INIS)

    Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard

    2016-01-01

    In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock

  14. Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals

    Science.gov (United States)

    Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard

    2016-02-01

    In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock.

  15. The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota.

    Science.gov (United States)

    Cooper, Danielle N; Kable, Mary E; Marco, Maria L; De Leon, Angela; Rust, Bret; Baker, Julita E; Horn, William; Burnett, Dustin; Keim, Nancy L

    2017-02-21

    This study was designed to determine if providing wheat, corn, and rice as whole (WG) or refined grains (RG) under free-living conditions will change parameters of health over a six-week intervention in healthy, habitual non-WG consumers. Measurements of body composition, fecal microbiota, fasting blood glucose, total cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), and triglycerides were made at baseline and post intervention. Subjects were given adequate servings of either WG or RG products based on their caloric need and asked to keep records of grain consumption, bowel movements, and GI symptoms weekly. After six weeks, subjects repeated baseline testing. Significant decreases in total, LDL, and non-HDL cholesterol were seen after the WG treatments but were not observed in the RG treatment. During Week 6, bowel movement frequency increased with increased WG consumption. No significant differences in microbiota were seen between baseline and post intervention, although, abundance of order Erysipelotrichales increased in RG subjects who ate more than 50% of the RG market basket products. Increasing consumption of WGs can alter parameters of health, but more research is needed to better elucidate the relationship between the amount consumed and the health-related outcome.

  16. The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota

    Directory of Open Access Journals (Sweden)

    Danielle N. Cooper

    2017-02-01

    Full Text Available This study was designed to determine if providing wheat, corn, and rice as whole (WG or refined grains (RG under free-living conditions will change parameters of health over a six-week intervention in healthy, habitual non-WG consumers. Measurements of body composition, fecal microbiota, fasting blood glucose, total cholesterol, high density lipoprotein (HDL, low density lipoprotein (LDL, and triglycerides were made at baseline and post intervention. Subjects were given adequate servings of either WG or RG products based on their caloric need and asked to keep records of grain consumption, bowel movements, and GI symptoms weekly. After six weeks, subjects repeated baseline testing. Significant decreases in total, LDL, and non-HDL cholesterol were seen after the WG treatments but were not observed in the RG treatment. During Week 6, bowel movement frequency increased with increased WG consumption. No significant differences in microbiota were seen between baseline and post intervention, although, abundance of order Erysipelotrichales increased in RG subjects who ate more than 50% of the RG market basket products. Increasing consumption of WGs can alter parameters of health, but more research is needed to better elucidate the relationship between the amount consumed and the health-related outcome.

  17. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

    NARCIS (Netherlands)

    Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

    2007-01-01

    We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

  18. Systematic coarse-graining in nucleation theory

    NARCIS (Netherlands)

    Schweizer, M.; Sagis, L.M.C.

    2015-01-01

    In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 - 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem.

  19. Systematic coarse-graining in nucleation theory

    Energy Technology Data Exchange (ETDEWEB)

    Schweizer, M., E-mail: marco.schweizer@math.ethz.ch [Department of Materials, Polymer Physics, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich (Switzerland); Sagis, L. M. C., E-mail: leonard.sagis@wur.nl [Department of Materials, Polymer Physics, ETH Zurich, Vladimir-Prelog-Weg 5, 8093 Zurich (Switzerland); Food Physics Group, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen (Netherlands)

    2015-08-21

    In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.

  20. Systematic coarse-graining in nucleation theory

    Science.gov (United States)

    Schweizer, M.; Sagis, L. M. C.

    2015-08-01

    In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 - 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.

  1. Effects of short-term consumption of bread obtained by an old Italian grain variety on lipid, inflammatory, and hemorheological variables: an intervention study.

    Science.gov (United States)

    Sofi, Francesco; Ghiselli, Lisetta; Cesari, Francesca; Gori, Anna Maria; Mannini, Lucia; Casini, Alessandro; Vazzana, Concetta; Vecchio, Vincenzo; Gensini, Gian Franco; Abbate, Rosanna; Benedettelli, Stefano

    2010-06-01

    The aim of this study was to evaluate the influence of short-term dietary intake of bread obtained by a selected variety of old grain grown in Tuscany, Italy on some parameters related to the atherosclerotic process. Twenty healthy subjects (median age, 39.5 years) followed for 10 weeks a diet containing bread (150 g/day) made from the test grain (test period) and for the same period a diet containing commercially available bread of the same quantity (control period). Lipid, inflammatory, and hemorheological profiles before and after dietary intervention were evaluated. The test period showed a significant (P bread obtained from an old grain variety seems to impose a favorable status with regard to lower circulating levels of markers of atherosclerosis.

  2. Combined effects of headgroup charge and tail unsaturation of lipids on lateral organization and diffusion of lipids in model biomembranes

    International Nuclear Information System (INIS)

    Chen Xiao-Jie; Liang Qing

    2017-01-01

    Lateral organization and dynamics of lipids in plasma membranes are crucial for several cellular processes such as signal transduction across the membrane and still remain elusive. In this paper, using coarse-grained molecular dynamics simulation, we theoretically study the combined effects of headgroup charge and tail unsaturation of lipids on the lateral organization and diffusion of lipids in ternary lipid bilayers. In neutral ternary lipid bilayers composed of saturated lipids, unsaturated lipids, and cholesterols, under the conditions of given temperature and components, the main factor for the phase separation is the unsaturation of unsaturated lipids and the bilayers can be separated into liquid-ordered domains enriched in saturated lipids and cholesterols and liquid-disordered domains enriched in unsaturated lipids. Once the headgroup charge is introduced, the electrostatic repulsion between the negatively charged lipid headgroups will increase the distance between the charged lipids. We find that the lateral organization and diffusion of the lipids in the (partially) charged ternary lipid bilayers are determined by the competition between the headgroup charge and the unsaturation of the unsaturated lipids. In the bilayers containing unsaturated lipids with lower unsaturation, the headgroup charge plays a crucial role in the lateral organization and diffusion of lipids. The headgroup charge may make the lipid domains unstable and even can suppress phase separation of the lipids in some systems. However, in the bilayers containing highly unsaturated lipids, the lateral organization and diffusion of lipids are mainly dominated by the unsaturation of the unsaturated lipids. This work may provide some theoretical insights into understanding the formation of nanosized domains and lateral diffusion of lipids in plasma membranes. (paper)

  3. Interfacial Tension and Surface Pressure of High Density Lipoprotein, Low Density Lipoprotein, and Related Lipid Droplets

    DEFF Research Database (Denmark)

    Ollila, O. H. S.; Lamberg, A.; Lehtivaara, M.

    2012-01-01

    Lipid droplets play a central role in energy storage and metabolism on a cellular scale. Their core is comprised of hydrophobic lipids covered by a surface region consisting of amphiphilic lipids and proteins. For example, high and low density lipoproteins (HDL and LDL, respectively....... Here we use coarse-grained molecular-dynamics simulations to consider a number of related issues by calculating the interfacial tension in protein-free lipid droplets, and in HDL and LDL particles mimicking physiological conditions. First, our results suggest that the curvature dependence...

  4. Nutrients and certain lipid soluble bioactive components in dehusked whole grains (gota) and dehusked splits (dhal) from pigeon pea (Cajanus cajan) and their cooking characteristics.

    Science.gov (United States)

    Jayadeep, Padmanabhan A; Sashikala, Vadakkoot B; Pratape, Vishwas M

    2009-01-01

    The nutritional quality of dehusked whole grains (gota) and dehusked splits (dhal) in red and white varieties of pigeon pea regarding proximate composition and certain lipid-soluble bioactive components was investigated. A decrease in fat and crude fiber was noticed when gota was converted to dhal. The lipid profile of gota and dhal from red and white husk pigeon pea types indicated that essential fatty acids were greater in gota than in their respective dhals. Gota from white husk variety contained more tocopherols than the red variety. Dhal contained less tocopherols than gota. A decrease in the content of gamma and alpha tocopherols, vitamin E activity and total antioxidant activity also indicates loss of bioactive components on splitting gota into dhal. Cooking time and dispersed solids on cooking indicated good cooking quality of gotta. The results indicated the nutritional superiority of gota over dhal and its similarity with dhal in cooking characteristics.

  5. 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

  6. Effect of dietary fiber of "Rihane" barley grains and azoxymethane on serum and liver lipid variables in Wistar rats.

    Science.gov (United States)

    Lahouar, Lamia; Ghrairi, Fatma; El Felah, Mouldi; Salem, Hichem Ben; Miled, Abdel Hedi; Hammami, Mohamed; Achour, Lotfi

    2011-03-01

    The aim of the present study is to evaluate the effects of diet enriched with dietary fiber of barley variety "Rihane" and azoxymethane on serum and liver lipid variables in male rats. Forty male rats were divided into four groups and fed on control diet or experimental diet that contained control enriched with dietary fiber of barley variety "Rihane". Animals were injected with saline (controls) or azoxymethane (20 mg/kg body weight s.c.) at 7 and 8 weeks of age. The experimental diet significantly decreased cholesterol level compared with the control diet. Rats fed with BR diet significantly increased the serum high-density lipoprotein (HDL) cholesterol and significantly decreased low-density lipoprotein (LDL) cholesterol concentrations. The experimental diet decreased the atherogenic index (p liver lipid, serum LDL and triglyceride concentrations, but it caused a significant reduction of HDL. Consequently, the ratio of HDL/TC decreased significantly compared with the control (p dietary fiber of barley variety "Rihane" could be effective in decreasing the atherogenic risk factors in rats whereas the use of the azoxymethane as colon-specific carcinogen substance altered the lipid metabolism.

  7. Extruded whole grain diets based on brown, soaked and germinated rice. Effects on the lipid profile and antioxidant status of growing Wistar rats. Part II.

    Science.gov (United States)

    Albarracín, Micaela; Weisstaub, Adriana R; Zuleta, Angela; Drago, Silvina R

    2016-06-15

    The influence of whole grain (WG) rice based diets on the lipid profile and antioxidant status was evaluated. Thirty-two male Wistar rats were fed with Control (C), extruded Brown rice (B), extruded Soaked whole rice (S) and extruded Germinated whole rice (G) diets for 60 days. Triacylglycerols (TAGs), cholesterol and malondialdehyde equivalent (MDA eq.) in serum and liver were determined. Catalase (CAT), Glutathione Reductase (GR) and Glutathione Peroxidase (GPx) enzyme activities and Glutathione Reduced (GSH) and Oxidized (GSSG) in the liver were analyzed. Animals consuming B and S diets presented lower body weight gain. All WG diets reduced TAGs in serum and MDA eq. content in liver in comparison with the C diet. WG rice diets improved the redox status in animals mainly fed G due to their higher GR activity and GSH/GSSG ratio.

  8. Computer Simulations of Lipid Nanoparticles

    Directory of Open Access Journals (Sweden)

    Xavier F. Fernandez-Luengo

    2017-12-01

    Full Text Available Lipid nanoparticles (LNP are promising soft matter nanomaterials for drug delivery applications. In spite of their interest, little is known about the supramolecular organization of the components of these self-assembled nanoparticles. Here, we present a molecular dynamics simulation study, employing the Martini coarse-grain forcefield, of self-assembled LNPs made by tripalmitin lipid in water. We also study the adsorption of Tween 20 surfactant as a protective layer on top of the LNP. We show that, at 310 K (the temperature of interest in biological applications, the structure of the lipid nanoparticles is similar to that of a liquid droplet, in which the lipids show no nanostructuration and have high mobility. We show that, for large enough nanoparticles, the hydrophilic headgroups develop an interior surface in the NP core that stores liquid water. The surfactant is shown to organize in an inhomogeneous way at the LNP surface, with patches with high surfactant concentrations and surface patches not covered by surfactant.

  9. Influences of the Structure of Lipids on Thermal Stability of Lipid Membranes

    International Nuclear Information System (INIS)

    Hai Nan-Nan; Zhou Xin; Li Ming

    2015-01-01

    The binding free energy (BFE) of lipid to lipid bilayer is a critical factor to determine the thermal or mechanical stability of the bilayer. Although the molecular structure of lipids has significant impacts on BFE of the lipid, there lacks a systematic study on this issue. In this paper we use coarse-grained molecular dynamics simulation to investigate this problem for several typical phospholipids. We find that both the tail length and tail unsaturation can significantly affect the BFE of lipids but in opposite way, namely, BFE decreases linearly with increasing length, but increases linearly with addition of unsaturated bonds. Inspired by the specific structure of cholesterol which is a crucial component of biomembrane, we also find that introduction of carbo-ring-like structures to the lipid tail or to the bilayer may greatly enhance the stability of the bilayer. Our simulation also shows that temperature can influence the bilayer stability and this effect can be significant when the bilayer undergoes phase transition. These results may be helpful to the design of liposome or other self-assembled lipid systems. (paper)

  10. Etude de synergie des effets chimiques et biologiques des lipides de réserve et des huiles essentielles des fruits et graines saisonniers de la sous-région Afrique Centrale

    OpenAIRE

    Ngakegni-Limbili, Adolphe Christian

    2012-01-01

    La composition en huiles essentielles et en lipides de réserve des graines et fruits saisonniers de quatre espèces végétales d’origine congolaise (Aframomum stipulatum (Gagnep) K. Schum, Aframomum giganteum (Oliv. and Hand) K. Schum, Spondias mombin L. et Nephelium lappaceum L.), a été déterminée par l’utilisation du couplage chromatographie en phase gazeuse/spectrométrie de masse. Les résultats obtenus ont permis de comprendre la bioaccumulation des huiles essentielles et des lipides de rése...

  11. Orimulsion penetration and retention in coarse sediments

    International Nuclear Information System (INIS)

    Harper, J.R.; Ward, S.; Brown, T.; Sergy, G.; Dempsey, M.

    2002-01-01

    Orimulsion is a fuel alternative composed of 70 per cent bitumen in 30 per cent water. It is shipped from Venezuela to New Brunswick where it is used as fuel oil for power plants. While there have not been any major spills of Orimulsion, it is recognized that very little is known regarding the dispersal and weathering processes of Orimulsion, or the behaviour and cleanup of the product on both rocky and course sediment shorelines. For that reason, this study was conducted to evaluate Orimulsion penetration and retention in coarse sediments. The objectives were to develop a standardized method to apply dispersed and coalesced bitumen to the coarse grained sediment test substrates and to estimate the quantity of bitumen retained on and in the substrate. Another objective was to evaluate how the two forms of bitumen interact with coarse sediments in terms of penetration and retention characteristics. The impact of tides and temperature on penetration and retention in coarse sediments was also evaluated. The results were interpreted in terms of potential response options and cleanup options for coarse sediment shorelines. It was determined that spilled Orimulsion would be stranded in the form of tar balls. Initial penetration of coalesced bitumen would be limited in granules and pebbles, Penetration of more than 30 cm would occur in cobbles within 4 tidal cycles. Penetration is temperature sensitive. Cold temperatures would limit penetration in cobbles. No washing method was identified for removal of coalesced bitumen, but coalesced bitumen remains buoyant after penetration. The retention of dispersed bitumen is less than 50 mg of bitumen per kg of sediment. 4 refs., 5 tabs., 12 figs

  12. Impact of synthetic antioxidants on lipid peroxidation of distiller's dried grains with solubles and distiller's corn oil stored under high temperature and humidity conditions.

    Science.gov (United States)

    Hanson, A R; Urriola, P E; Johnston, L J; Shurson, G C

    2015-08-01

    This experiment evaluated the effect of antioxidants, oil content in distiller's dried grains with solubles (DDGS), quality of distiller's corn oil, and storage time on lipid peroxidation. A source of low-oil DDGS (LO-DDGS; 5.0% ether extract [EE], as-fed basis), high-oil DDGS (HO-DDGS; 13.0% EE, as-fed basis), and 2 sources of distiller's corn oil (DCO; 1.20, 0.08, and 0.48% moisture, insoluble impurities, and unsaponifiables [MIU], respectively [DCO-1], and 1.20, 0.01, and 0.10% MIU, respectively [DCO-2]) were obtained. Each of the 4 ingredients was divided into 18 representative subsamples (approximately 908 g for DDGS or 2 kg of DCO). Six subsamples of each ingredient were mixed with either no supplemental antioxidants (CON), Rendox-CQ (REN; 1,000 mg/kg EE; Kemin, Industries, Des Moines, IA), or Santoquin-Q4T (SAN; 1,500 mg/kg EE; Novus International, St. Louis, MO). Each mixture ( = 72) was split into thirds, and 1 portion was immediately frozen at -20°C (d 0). Two portions were stored under hot (38.6 ± 0.1°C) and humid conditions (94.0 ± 0.3% relative humidity) for 14 or 28 d. The MIXED procedure of SAS was used to evaluate the effects of ingredient, antioxidant, storage time, and interactions, with d-0 values used as a covariate. From d 14 to 28, peroxide value (PV), -anisidine value (AnV), and thiobarbituric acid reactive substances (TBARS) of DCO and DDGS increased by 3- to 4-fold ( oil, respectively) exceeded ( oil, respectively). Adding REN or SAN ( oil and AnV = 6.5 ± 0.2) over the entire period (mean of d 14 and 28), but TBARS and AnV did not differ ( > 0.05) between antioxidants (TBARS = 6.1 ± 0.2 and 5.9 ± 0.2 mg malondialdehyde Eq/kg oil, respectively, and AnV = 1.9 ± 0.2 and 1.8 ± 0.2 for REN and SAN, respectively). The PV on d 14 and 28 and overall was less ( oil for SAN and REN, respectively). In summary, antioxidants reduced peroxidation of DDGS and DCO by approximately 50% during 28 d of storage at 38.6°C and 94.0% relative humidity

  13. Milestoning with coarse memory

    Science.gov (United States)

    Hawk, Alexander T.

    2013-04-01

    Milestoning is a method used to calculate the kinetics of molecular processes occurring on timescales inaccessible to traditional molecular dynamics (MD) simulations. In the method, the phase space of the system is partitioned by milestones (hypersurfaces), trajectories are initialized on each milestone, and short MD simulations are performed to calculate transitions between neighboring milestones. Long trajectories of the system are then reconstructed with a semi-Markov process from the observed statistics of transition. The procedure is typically justified by the assumption that trajectories lose memory between crossing successive milestones. Here we present Milestoning with Coarse Memory (MCM), a generalization of Milestoning that relaxes the memory loss assumption of conventional Milestoning. In the method, milestones are defined and sample transitions are calculated in the standard Milestoning way. Then, after it is clear where trajectories sample milestones, the milestones are broken up into distinct neighborhoods (clusters), and each sample transition is associated with two clusters: the cluster containing the coordinates the trajectory was initialized in, and the cluster (on the terminal milestone) containing trajectory's final coordinates. Long trajectories of the system are then reconstructed with a semi-Markov process in an extended state space built from milestone and cluster indices. To test the method, we apply it to a process that is particularly ill suited for Milestoning: the dynamics of a polymer confined to a narrow cylinder. We show that Milestoning calculations of both the mean first passage time and the mean transit time of reversal—which occurs when the end-to-end vector reverses direction—are significantly improved when MCM is applied. Finally, we note the overhead of performing MCM on top of conventional Milestoning is negligible.

  14. Organization of lipids in the tear film: a molecular-level view.

    Directory of Open Access Journals (Sweden)

    Alicja Wizert

    Full Text Available Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film.

  15. Organization of Lipids in the Tear Film: A Molecular-Level View

    Science.gov (United States)

    Wizert, Alicja; Iskander, D. Robert; Cwiklik, Lukasz

    2014-01-01

    Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD) simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film. PMID:24651175

  16. Understanding carbon nanotube channel formation in the lipid membrane

    Science.gov (United States)

    Choi, Moon-ki; Kim, Hyunki; Lee, Byung Ho; Kim, Teayeop; Rho, Junsuk; Kim, Moon Ki; Kim, Kyunghoon

    2018-03-01

    Carbon nanotubes (CNTs) have been considered a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for a biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in a lipid membrane for a long period, which has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both the lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT channel. Also, simulation elucidated that a lipid coating on the surface of the CNT prevents the CNT from burrowing into the lipid membrane and the vertical channel is stabilized by the repulsion force between the lipids in the coating and membrane. Our study provides an essential understanding of how CNTs can form stable and vertical channels in the membrane, which is important for designing new types of artificial channels as biosensors for bio-fluidic studies.

  17. Comparison of coarse-grained (MARTINI) and atomistic molecular ...

    Indian Academy of Sciences (India)

    Rajat Desikan

    Abstract. Pore forming toxins (PFTs) are virulent proteins whose primary goal is to lyse target cells by unregulated pore formation. Molecular dynamics simulations can potentially provide molecular insights on the properties of the pore complex as well as the underlying pathways for pore formation. In this manuscript we.

  18. Morphing methods to visualize coarse-grained protein dynamics.

    Science.gov (United States)

    Weiss, Dahlia R; Koehl, Patrice

    2014-01-01

    Morphing was initially developed as a cinematic effect, where one image is seamlessly transformed into another image. The technique was widely adopted by biologists to visualize the transition between protein conformational states, generating an interpolated pathway from an initial to a final protein structure. Geometric morphing seeks to create visually suggestive movies that illustrate structural changes between conformations but do not necessarily represent a biologically relevant pathway, while minimum energy path (MEP) interpolations aim at describing the true transition state between the crystal structure minima in the energy landscape.

  19. Vesicles and vesicle fusion: coarse-grained simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    of vesicles that is crucial for this transport is their ability to fuse to target membranes and release their contents to the distal side. In industry, some personal care products contain vesicles to help transport reagents across the skin, and research on drug formulation shows that packaging active...

  20. 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

  1. 7 CFR 457.113 - Coarse grains crop insurance provisions.

    Science.gov (United States)

    2010-01-01

    ..., Winkler, Ector, Upton, Reagan, Sterling, Coke, Tom Green, Concho, McCulloch, San Saba, Mills, Hamilton...; Nevada; North Carolina; and South Carolina; and El Paso, Hudspeth, Culberson, Reeves, Loving, Winkler...

  2. Generalization of the swelling method to measure the intrinsic curvature of lipids

    Science.gov (United States)

    Barragán Vidal, I. A.; Müller, M.

    2017-12-01

    Via computer simulation of a coarse-grained model of two-component lipid bilayers, we compare two methods of measuring the intrinsic curvatures of the constituting monolayers. The first one is a generalization of the swelling method that, in addition to the assumption that the spontaneous curvature linearly depends on the composition of the lipid mixture, incorporates contributions from its elastic energy. The second method measures the effective curvature-composition coupling between the apposing leaflets of bilayer structures (planar bilayers or cylindrical tethers) to extract the spontaneous curvature. Our findings demonstrate that both methods yield consistent results. However, we highlight that the two-leaflet structure inherent to the latter method has the advantage of allowing measurements for mixed lipid systems up to their critical point of demixing as well as in the regime of high concentration (of either species).

  3. Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field

    DEFF Research Database (Denmark)

    Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena

    2013-01-01

    is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field...... the MARTINI force field, is primarily due to the interactions between the coarse-grained molecules, i.e., the beads, rather than due to the differences between the conformations of saturated and unsaturated lipid acyl chains, namely entropy driven....

  4. Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective.

    Science.gov (United States)

    Moore, Timothy C; Iacovella, Christopher R; Leonhard, Anne C; Bunge, Annette L; McCabe, Clare

    2018-03-29

    The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Giant grains

    International Nuclear Information System (INIS)

    Leitch-Devlin, M.A.; Millar, T.J.; Williams, D.A.

    1976-01-01

    Infrared observations of the Orion nebula have been interpreted by Rowan-Robinson (1975) to imply the existence of 'giant' grains, radius approximately 10 -2 cm, throughout a volume about a parsec in diameter. Although Rowan-Robinson's model of the nebula has been criticized and the presence of such grains in Orion is disputed, the proposition is accepted, that they exist, and in this paper situations in which giant grains could arise are examined. It is found that, while a giant-grain component to the interstellar grain density may exist, it is difficult to understand how giant grains arise to the extent apparently required by the Orion nebula model. (Auth.)

  6. 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...

  7. Structure formation of lipid membranes: Membrane self-assembly and vesicle opening-up to octopus-like micelles

    Science.gov (United States)

    Noguchi, Hiroshi

    2013-02-01

    We briefly review our recent studies on self-assembly and vesicle rupture of lipid membranes using coarse-grained molecular simulations. For single component membranes, lipid molecules self-assemble from random gas states to vesicles via disk-shaped clusters. Clusters aggregate into larger clusters, and subsequently the large disks close into vesicles. The size of vesicles are determined by kinetics than by thermodynamics. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle called bicelle can be formed. When both surfactants have negligibly low critical micelle concentration, it is found that bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and spontaneous curvature of the membrane monolayer.

  8. Experimental investigation of coarse particles-water mixture flow in horizontal and inclined pipes

    Czech Academy of Sciences Publication Activity Database

    Vlasák, Pavel; Chára, Zdeněk; Krupička, Jan; Konfršt, Jiří

    2014-01-01

    Roč. 62, č. 3 (2014), s. 241-247 ISSN 0042-790X R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : hydraulic pipelining * coarse-grained slurry * pressure drops * pipe inclination * concentration distribution Subject RIV: BK - Fluid Dynamics Impact factor: 1.486, year: 2014

  9. 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.

  10. 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.

  11. The grain-size lineup: A test of a novel eyewitness identification procedure.

    Science.gov (United States)

    Horry, Ruth; Brewer, Neil; Weber, Nathan

    2016-04-01

    When making a memorial judgment, respondents can regulate their accuracy by adjusting the precision, or grain size, of their responses. In many circumstances, coarse-grained responses are less informative, but more likely to be accurate, than fine-grained responses. This study describes a novel eyewitness identification procedure, the grain-size lineup, in which participants eliminated any number of individuals from the lineup, creating a choice set of variable size. A decision was considered to be fine-grained if no more than 1 individual was left in the choice set or coarse-grained if more than 1 individual was left in the choice set. Participants (N = 384) watched 2 high-quality or low-quality videotaped mock crimes and then completed 4 standard simultaneous lineups or 4 grain-size lineups (2 target-present and 2 target-absent). There was some evidence of strategic regulation of grain size, as the most difficult lineup was associated with a greater proportion of coarse-grained responses than the other lineups. However, the grain-size lineup did not outperform the standard simultaneous lineup. Fine-grained suspect identifications were no more diagnostic than suspect identifications from standard lineups, whereas coarse-grained suspect identifications carried little probative value. Participants were generally reluctant to provide coarse-grained responses, which may have hampered the utility of the procedure. For a grain-size approach to be useful, participants may need to be trained or instructed to use the coarse-grained option effectively. (c) 2016 APA, all rights reserved).

  12. 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.

  13. 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.

  14. Learning to Play Efficient Coarse Correlated Equilibria

    KAUST Repository

    Borowski, Holly P.

    2018-03-10

    The majority of the distributed learning literature focuses on convergence to Nash equilibria. Coarse correlated equilibria, on the other hand, can often characterize more efficient collective behavior than even the best Nash equilibrium. However, there are no existing distributed learning algorithms that converge to specific coarse correlated equilibria. In this paper, we provide one such algorithm, which guarantees that the agents’ collective joint strategy will constitute an efficient coarse correlated equilibrium with high probability. The key to attaining efficient correlated behavior through distributed learning involves incorporating a common random signal into the learning environment.

  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. 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.

  18. 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

  19. Effect of ultrafine grain on tensile behaviour and corrosion resistance of the duplex stainless steel.

    Science.gov (United States)

    Jinlong, Lv; Tongxiang, Liang; Chen, Wang; Limin, Dong

    2016-05-01

    The ultrafine grained 2205 duplex stainless steel was obtained by cold rolling and annealing. The tensile properties were investigated at room temperature. Comparing with coarse grained stainless steel, ultrafine grained sample showed higher strength and plasticity. In addition, grain size changed deformation orientation. The strain induced α'-martensite was observed in coarse grained 2205 duplex stainless steel with large strain. However, the grain refinement inhibited the transformation of α'-martensite;nevertheless, more deformation twins improved the strength and plasticity of ultrafine grained 2205 duplex stainless steel. In addition, the grain refinement improved corrosion resistance of the 2205 duplex stainless steel in sodium chloride solution. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. 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.

  1. 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...

  2. Coarse fraction components in a red-clay sedimemt core, Central Indian Ocean Basin: Their occurrence and significance

    Digital Repository Service at National Institute of Oceanography (India)

    Iyer, S.D.; Fernandes, G.Q.; Mahender, K.

    Coarse Fractions Components of a sediment core (268 cm from a water depth of 5120 m) collected at 18 degrees S and 80 degrees E from the red clay domain in the Central Indian Ocean Basin (CIOB), comprises mineral grains, basaltic fragments...

  3. 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.

  4. Poisson's ratio and Young's modulus of lipid bilayers in different phases

    Directory of Open Access Journals (Sweden)

    Tayebeh eJadidi

    2014-04-01

    Full Text Available A general computational method is introduced to estimate the Poisson's ratio for membranes with small thickness.In this method, the Poisson's ratio is calculated by utilizing a rescaling of inter-particle distancesin one lateral direction under periodic boundary conditions. As an example for the coarse grained lipid model introduced by Lenz and Schmid, we calculate the Poisson's ratio in the gel, fluid, and interdigitated phases. Having the Poisson's ratio, enable us to obtain the Young's modulus for the membranes in different phases. The approach may be applied to other membranes such as graphene and tethered membranes in orderto predict the temperature dependence of its Poisson's ratio and Young's modulus.

  5. 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 ...

  6. Competing Grain Boundary and Interior Deformation Mechanisms with Varying Sizes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Wei [University of Tennessee (UT); Gao, Yanfei [ORNL; Nieh, T. G. [University of Tennessee, Knoxville (UTK)

    2018-01-01

    In typical coarse-grained alloys, the dominant plastic deformations are dislocation gliding or climbing, and material strengths can be tuned by dislocation interactions with grain boundaries, precipitates, solid solutions, and other defects. With the reduction of grain size, the increase of material strengths follows the classic Hall-Petch relationship up to nano-grained materials. Even at room temperatures, nano-grained materials exhibit strength softening, or called the inverse Hall-Petch effect, as grain boundary processes take over as the dominant deformation mechanisms. On the other hand, at elevated temperatures, grain boundary processes compete with grain interior deformation mechanisms over a wide range of the applied stress and grain sizes. This book chapter reviews and compares the rate equation model and the microstructure-based finite element simulations. The latter explicitly accounts for the grain boundary sliding, grain boundary diffusion and migration, as well as the grain interior dislocation creep. Therefore the explicit finite element method has clear advantages in problems where microstructural heterogeneities play a critical role, such as in the gradient microstructure in shot peening or weldment. Furthermore, combined with the Hall-Petch effect and its breakdown, the above competing processes help construct deformation mechanism maps by extending from the classic Frost-Ashby type to the ones with the dependence of grain size.

  7. Lipid Profile

    Science.gov (United States)

    ... Known As Coronary Risk Panel Formal Name Lipid Profile This article was last reviewed on June 29, ... phospholipid molecules. The particles measured with a lipid profile are classified by their density into high-density ...

  8. Dependency of annealing behaviour on grain size in Al–TiC ...

    Indian Academy of Sciences (India)

    This work investigates the effect of grain size on annealing behaviour in both coarse-grained and ultrafinegrained Al–TiC composite processed by accumulative roll bonding (ARB). Microstructural analysis indicates that annealingbehaviour of the specimens are essentially determined by the level of strain accumulation or ...

  9. 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

    Chinese loess, thus pointing to a potential worldwide phenomenon. While age underestimation is often attributed to signal saturation problems, this is not the case for fine grain material, which saturates at higher doses than coarse grains, yet begins to underestimate true ages earlier. Here we examine...

  10. Eyewitness Recall: Regulation of Grain Size and the Role of Confidence

    Science.gov (United States)

    Weber, Nathan; Brewer, Neil

    2008-01-01

    Eyewitness testimony plays a critical role in Western legal systems. Three experiments extended M. Goldsmith, A. Koriat, and A. Weinberg-Eliezer's (2002) framework of the regulation of grain size (precision vs. coarseness) of memory reports to eyewitness memory. In 2 experiments, the grain size of responses had a large impact on memory accuracy.…

  11. Symmetries and the coarse-mesh method

    International Nuclear Information System (INIS)

    Makai, M.

    1980-10-01

    This report approaches the basic problem of the coarse-mesh method from a new side. Group theory is used for the determination of the space dependency of the flux. The result is a method called ANANAS after the analytic-analytic solution. This method was tested on two benchmark problems: one given by Melice and the IAEA benchmark. The ANANAS program is an experimental one. The method was intended for use in hexagonal geometry. (Auth.)

  12. 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

    Sustainable agricultural production on coarse sandy soil is constrained by the restricted growth of roots, and poor water and nutrient retention. Amending the soil with biochar can reduce these problems, but the processes involved are not known in detail. We investigated in the laboratory...... 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...

  13. Experimental investigation of coarse particles-water mixture flow in horizontal and inclined pipes

    Directory of Open Access Journals (Sweden)

    Vlasák Pavel

    2014-09-01

    Full Text Available The effect of solid concentration and mixture velocity on the flow behaviour, pressure drops, and concentration distribution of coarse particle-water mixtures in horizontal, vertical, and inclined smooth stainless steel pipes of inner diameter D = 100 mm was experimentally investigated. Graded basalt pebbles were used as solid particles. The study revealed that the coarse-grained particle-water mixtures in the horizontal and inclined pipes were significantly stratified. The solid particles moved principally in a layer close to the pipe invert; however for higher and moderate flow velocities, particle saltation became the dominant mode of particle conveyance. Frictional pressure drops in the horizontal pipe were found to be markedly higher than in the vertical pipe, while the frictional pressure drops in the ascending pipe increased with inclination angle up to about 30°.

  14. Refinement of grain structure in 20 MnNiMo (SA508C) steel

    International Nuclear Information System (INIS)

    Sheng Zhongqi; Xiao Hong; Peng Feng; Zou Min

    1997-04-01

    The size of prior austenite grains and bainitic colonies of 20 MnNiMo (SA508C) steel (a reactor pressure vessel steel) after normal heat treatment is measured and its controlling factors are discussed. Results show that low aluminium content can induce serious mixed structure with fine and coarse grains in prior austenite. Fast cooling rate can promote refinement of bainitic colonies. Further refinement of grains can be obtained by inter-critical quenching. (5 figs., 1 tab.)

  15. 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.

  16. Lipid somersaults

    DEFF Research Database (Denmark)

    Günther-Pomorski, Thomas; Menon, Anant K.

    2016-01-01

    Membrane lipids diffuse rapidly in the plane of the membrane but their ability to flip spontaneously across a membrane bilayer is hampered by a significant energy barrier. Thus spontaneous flip-flop of polar lipids across membranes is very slow, even though it must occur rapidly to support diverse...... aspects of cellular life. Here we discuss the mechanisms by which rapid flip-flop occurs, and what role lipid flipping plays in membrane homeostasis and cell growth. We focus on conceptual aspects, highlighting mechanistic insights from biochemical and in silico experiments, and the recent, ground......-breaking identification of a number of lipid scramblases....

  17. 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.

  18. Lipid membrane-mediated attraction between curvature inducing objects

    Science.gov (United States)

    van der Wel, Casper; Vahid, Afshin; Šarić, Anđela; Idema, Timon; Heinrich, Doris; Kraft, Daniela J.

    2016-09-01

    The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (-3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles.

  19. An experimental study of grain sorting effect on braided pattern

    Science.gov (United States)

    Leduc, Pauline; Recking, Alain; Naaim, Mohamed

    2013-04-01

    Braided rivers are characterized by complex morphologies comprising several channels, and their dynamic is still poorly understood. A better understanding of the braiding response to different river equilibrium states (equilibrium, erosion or aggradation) is essential for a sustainable river management. We conducted a series of laboratory experiments to study the effects of sediment supply conditions (particle size distribution and feeding rates) on braided river morphology. Two series of experiments were carried out, the first with uniform sediments (0.5 to 1.5 mm with an average diameter of 0.7 mm), and the second with a bimodal distribution consisting of a mixture of coarse and fine sands, ranging between 1.5 mm to 3 mm with a mean diameter of 1.8 mm. Both sands had different colours in order to facilitate visual observations of grain sorting and to measure the spatial distribution of different grain sizes. Hydro-sedimentary conditions were maintained constant in both cases throughout the experiment. Successive bed topographies were measured using the Moiré method. Both sets of experiments showed different mechanisms. The experiments with uniform sediments suggest that bars morphology is controlled by the continuous propagation of sedimentary lobes. The lobe deposit creates various morphological units including "sedimentary" border and large scour areas. The experiment with non-uniform sediments showed the importance of segregation in the braiding process, with coarse deposits controlling the bed roughness, and as a consequence, the direction of the main flow and paths taken by the coarse and fine grains. Selective depositions produce heterogeneous bed surface grain sizes. The geometry of the confluence of two active channels also depends on the grain size range. Indeed, the depth of the confluence area seems smaller with heterogeneous sediment: coarse sediments are attracted in the pool, limiting thereby erosion. These observations give us keys for

  20. 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...

  1. Sliding wear characteristics of ultrafine-grained non-strain-hardening aluminum-magnesium alloys

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Y.S.; Ha, J.S. [School of Advanced Materials Engineering, Kookmin Univ., Seoul (Korea); Shin, D.H. [Dept. of Metallurgy and Materials Science, Hanyang Univ., Ansan (Korea)

    2005-07-01

    Coarse grains of commercial 5052 Al and 5083 Al alloys were refined by the accumulative roll bonding (ARB) process. Average grain size of the refined microstructure was 200 nm. The 5083 Al alloy that has higher Mg content required more deformation for the refinement. Dry sliding wear behavior of the ultra-fine grained (UFG) Al alloys was investigated using a pin-on-disk wear tester at room temperature. The UFG microstructure of the processed alloys hardly increased the wear resistance of the Al alloys in spite of the increased strength and hardness. Wear rate of the UFG Al alloys was higher than that of the non-processed coarse-grained starting alloys. The SEM observation of worn surfaces revealed that surface deformation controlled the wear. The low wear resistance of the UFG Al alloys was attributed to non-equilibrium and unstable grain boundaries and low strain hardening capability of the alloys. (orig.)

  2. The accumulation of radiocesium in coarse marine sediment: Effects of mineralogy and organic matter

    International Nuclear Information System (INIS)

    Kim, Yeongkyoo; Kim, Kangjoo; Kang, Hee-Dong; Kim, Wan; Doh, Si-Hong; Kim, Do-Sung; Kim, Byoung-Ki

    2007-01-01

    The controlling factors affecting the accumulation of 137 Cs in marine sediment have not been investigated in detail, especially in coarse grained sediment. Eighty eight coarse marine sediment samples near Wuljin, Korea, were characterized by quantitative X-ray-diffraction (XRD), gamma-ray, and total organic carbon (TOC) analysis. Those factors were then compared. The grain size was in the range of -0.48 to 3.6 Mdφ corresponding to sand grains. TOC content was in the range of 0.06-1.75%, and the concentration of 137 Cs was 137 Cs activity, which was first reported here, probably due to the weathered frayed edge site of biotite produced by a release of K. The samples with low TOC contents showed even better correlation between biotite content and 137 Cs activity. For the entire samples, however, the TOC content showed better correlation with 137 Cs activity than other single factors, indicating that biotite and organic carbon are the most important factors controlling 137 Cs fixation. The combined effect of biotite and TOC for 137 Cs fixation was also confirmed by multiple regression analysis ( 137 Cs activity = 1.712 . TOC (wt%) + 0.202 . biotite (wt%) - 0.097; R 2 = 0.819). The regressed slopes indicated that the 137 Cs-adsorption capacity of TOC was about 8.5 times higher than that of biotite. However, the amount of 137 Cs adsorbed onto biotite was 30% more than that adsorbed onto TOC due to much greater biotite content in the sediment. The role of biotite in fixing 137 Cs becomes more important in sediment with coarser grains, containing little TOC

  3. 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.

  4. Management of Coarse Sediment in Regulated Rivers of California

    OpenAIRE

    Kondolf, G. Mathias; Matthews, W.V. Graham

    1991-01-01

    There are significant problems in the management of coarse sediment (sand and gravels) in regulated rivers of California. Unfortunately, these have been generally treated (or ignored) on a case-by-case basis, however, the effects are pervasive and profound, with substantial costs and severe environmental impacts. Problems arise due to the human manipulation of coarse sediment through reservoir construction, which blocks the movement of coarse sediment down the river, and through instream grav...

  5. Influence of grain size in the near-micrometre regime on the deformation microstructure in aluminium

    International Nuclear Information System (INIS)

    Le, G.M.; Godfrey, A.; Hansen, N.; Liu, W.; Winther, G.; Huang, X.

    2013-01-01

    The effect of grain size on deformation microstructure formation in the near-micrometre grain size regime has been studied using samples of aluminium prepared using a spark plasma sintering technique. Samples in a fully recrystallized grain condition with average grain sizes ranging from 5.2 to 0.8 μm have been prepared using this technique. Examination in the transmission electron microscope of these samples after compression at room temperature to approximately 20% reduction reveals that grains larger than 7 μm are subdivided by cell block boundaries similar to those observed in coarse-grained samples, with a similar dependency on the crystallographic orientation of the grains. With decreasing grain size down to approx. 1 μm there is a gradual transition from cell block structures to cell structures. At even smaller grain sizes of down to approx. 0.5 μm the dominant features are dislocation bundles and random dislocations, although at a larger compressive strain of 30% dislocation rotation boundaries may also be found in the interior of grains of this size. A standard 〈1 1 0〉 fibre texture is found for all grain sizes, with a decreasing sharpness with decreasing grain size. The structural transitions with decreasing grain size are discussed based on the general principles of grain subdivision by deformation-induced dislocation boundaries and of low-energy dislocation structures as applied to the not hitherto explored near-micrometre grain size regime

  6. Key molecular requirements for raft formation in lipid/cholesterol membranes.

    Directory of Open Access Journals (Sweden)

    Davit Hakobyan

    Full Text Available The lipid mixture of DPPC (saturated lipid/DUPC (unsaturated lipid/CHOL (cholesterol is studied with respect to its ability to form liquid-ordered and liquid-disordered phases. We employ coarse-grained simulations with MARTINI force field. All three components are systematically modified in order to explore the relevant molecular properties, leading to phase separation. Specifically, we show that the DPPC/DUPC/CHOL system unmixes due to enthalpic DPPC-DPPC and DPPC-CHOL interactions. The phase separation remains unchanged, except for the formation of a gel phase at long times after decreasing the conformational degrees of freedom of the unsaturated DUPC. In contrast, the phase separation can be suppressed by softening the DPPC chains. In an attempt to mimic the ordering and unmixing effect of CHOL the latter is replaced by a stiff and shortened DPPC-like lipid. One still observes phase separation, suggesting that it is mainly the rigid and planar structure of CHOL which is important for raft formation. Addition of an extra bead to the head of CHOL has no notable impact on the phase separation of the system, supporting the irrelevance of the Umbrella model for the phase separation. Reduction of the conformational entropy of CHOL by stiffening its last bead results in a significant increase of the order of the DPPC/CHOL domain. This suggests that the conformational entropy of CHOL is important to prohibit the gelation process. The interleaflet interactions as mediated by the terminal molecular groups seem to have a strong impact on the possibility of a subsequent gelation process after phase separation.

  7. An Apparatus for Bed Material Sediment Extraction From Coarse River Beds in Large Alluvial Rivers

    Science.gov (United States)

    Singer, M. B.; Adam, H.; Cooper, J.; Cepello, S.

    2005-12-01

    Grain size distributions of bed material sediment in large alluvial rivers are required in applications ranging from habitat mapping, calibration of sediment transport models, high resolution sediment routing, and testing of existing theories of longitudinal and cross steam sediment sorting. However, characterizing bed material sediment from coarse river beds is hampered by difficulties in sediment extraction, a challenge that is generally circumvented via pebble counts on point bars, even though it is unclear whether the bulk grain size distribution of bed sediments is well represented by pebble counts on bars. We have developed and tested a boat-based sampling apparatus and methodology for extracting bulk sediment from a wide range of riverbed materials. It involves the use of a 0.4 x 0.4 x 0.2 meter stainless steel toothed sampler, called the Cooper Scooper, which is deployed from and dragged downstream by the weight of a jet boat. The design is based on that of a river anchor such that a rotating center bar connected to a rope line in the boat aligns the sampler in the downstream direction, the teeth penetrate the bed surface, and the sampler digs into the bed. The sampler is fitted with lead weights to keep it from tipping over. The force of the sampler `biting' into the bed can be felt on the rope line held by a person in the boat at which point they let out slack. The boat then motors to the spot above the embedded sampler, which is hoisted to the water surface via a system of pulleys. The Cooper Scooper is then clipped into a winch and boom assembly by which it is brought aboard. This apparatus improves upon commonly used clamshell dredge samplers, which are unable to penetrate coarse or mixed bed surfaces. The Cooper Scooper, by contrast, extracts statistically representative bed material sediment samples of up to 30 kilograms. Not surprisingly, the sampler does not perform well in very coarse or armored beds (e.g. where surface material size is on the

  8. 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

  9. 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.

  10. 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.

  11. The role of geology in sediment supply and bedload transport patterns in coarse-grained streams

    Science.gov (United States)

    Sandra E. Ryan

    2007-01-01

    This paper compares gross differences in rates of bedload sediment moved at bankfull discharges in 19 channels on national forests in the Middle and Southern Rocky Mountains. Each stream has its own "bedload signal," in that the rate and size of materials transported at bankfull discharge largely reflect the nature of flow and sediment particular to that...

  12. 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....

  13. Probabilistic Equilibrium Sampling of Protein Structures from SAXS Data and a Coarse Grained Debye Formula

    DEFF Research Database (Denmark)

    Andreetta, Christian

    ) is also provided. Empowered by data available from SAXS experiments, by this protocol as a forward model for Markov Chain Monte Carlo (MCMC) simulations, by a continuous model of the peptide bond (TorusDBN) and the conformations of side chains (COMPAS and BasiliskDBN), we are able to propose ensembles...... 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...

  14. Coarse-Grain Bandwidth Estimation Scheme for Large-Scale Network

    Science.gov (United States)

    Cheung, Kar-Ming; Jennings, Esther H.; Sergui, John S.

    2013-01-01

    A large-scale network that supports a large number of users can have an aggregate data rate of hundreds of Mbps at any time. High-fidelity simulation of a large-scale network might be too complicated and memory-intensive for typical commercial-off-the-shelf (COTS) tools. Unlike a large commercial wide-area-network (WAN) that shares diverse network resources among diverse users and has a complex topology that requires routing mechanism and flow control, the ground communication links of a space network operate under the assumption of a guaranteed dedicated bandwidth allocation between specific sparse endpoints in a star-like topology. This work solved the network design problem of estimating the bandwidths of a ground network architecture option that offer different service classes to meet the latency requirements of different user data types. In this work, a top-down analysis and simulation approach was created to size the bandwidths of a store-and-forward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. These techniques were used to estimate the WAN bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network. A new analytical approach, called the "leveling scheme," was developed to model the store-and-forward mechanism of the network data flow. The term "leveling" refers to the spreading of data across a longer time horizon without violating the corresponding latency requirement of the data type. Two versions of the leveling scheme were developed: 1. A straightforward version that simply spreads the data of each data type across the time horizon and doesn't take into account the interactions among data types within a pass, or between data types across overlapping passes at a network node, and is inherently sub-optimal. 2. Two-state Markov leveling scheme that takes into account the second order behavior of the store-and-forward mechanism, and the interactions among data types within a pass. The novelty of this approach lies in the modeling of the store-and-forward mechanism of each network node. The term store-and-forward refers to the data traffic regulation technique in which data is sent to an intermediate network node where they are temporarily stored and sent at a later time to the destination node or to another intermediate node. Store-and-forward can be applied to both space-based networks that have intermittent connectivity, and ground-based networks with deterministic connectivity. For groundbased networks, the store-and-forward mechanism is used to regulate the network data flow and link resource utilization such that the user data types can be delivered to their destination nodes without violating their respective latency requirements.

  15. Coarse-Grain Bandwidth Estimation Techniques for Large-Scale Space Network

    Science.gov (United States)

    Cheung, Kar-Ming; Jennings, Esther

    2013-01-01

    In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-andforward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.

  16. A Coarse-grain Force Field for RDX: Density Dependent and Eergy Conserving.

    Czech Academy of Sciences Publication Activity Database

    Moore, J.D.; Barnes, B.C.; Izvekov, S.; Lísal, Martin; Sellers, M.S.; Taylor, D.E.; Brennan, J.K.

    2016-01-01

    Roč. 144, č. 10 (2016), s. 104501 ISSN 0021-9606 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : dissipative particle dynamics * cyclotrimethylele-trinitramine * biomolecular systems Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.965, year: 2016

  17. Coarse-Grained Potential for Interaction with a Spherical Colloidal Particle and Planar Wall

    Czech Academy of Sciences Publication Activity Database

    Předota, Milan; Nezbeda, Ivo; Pařez, Stanislav

    2010-01-01

    Roč. 75, č. 5 (2010), s. 527-545 ISSN 0010-0765 R&D Projects: GA ČR GA203/08/0094; GA AV ČR IAA400720802 Institutional research plan: CEZ:AV0Z40720504 Keywords : spherical colloidal particles * surface interaction * molecular simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.853, year: 2010

  18. Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations

    NARCIS (Netherlands)

    Catte, Andrea; Patterson, James C.; Bashtovyy, Denys; Jones, Martin K.; Gu, Feifei; Li, Ling; Rampioni, Aldo; Sengupta, Durba; Vuorela, Timo; Niemela, Perttu; Karttunen, Mikko; Marrink, Siewert Jan; Vattulainen, Ilpo; Segrest, Jere P.

    2008-01-01

    Spheroidal high-density lipoprotein (HDL) particles circulating in the blood are formed through an enzymatic process activated by apoA-1, leading to the esterification of cholesterol, which creates a hydrophobic core of cholesteryl ester molecules in the middle of the discoidal phospholipid bilayer.

  19. Coarse-grain bandwidth estimation techniques for large-scale network

    Science.gov (United States)

    Cheung, Kar-Ming; Jennings, E.

    In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-and-forward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.

  20. 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

  1. Stresses in non-equilibrium fluids: Exact formulation and coarse-grained theory

    Science.gov (United States)

    Krüger, Matthias; Solon, Alexandre; Démery, Vincent; Rohwer, Christian M.; Dean, David S.

    2018-02-01

    Starting from the stochastic equation for the density operator, we formulate the exact (instantaneous) stress tensor for interacting Brownian particles and show that its average value agrees with expressions derived previously. We analyze the relation between the stress tensor and forces due to external potentials and observe that, out of equilibrium, particle currents give rise to extra forces. Next, we derive the stress tensor for a Landau-Ginzburg theory in generic, non-equilibrium situations, finding an expression analogous to that of the exact microscopic stress tensor, and discuss the computation of out-of-equilibrium (classical) Casimir forces. Subsequently, we give a general form for the stress tensor which is valid for a large variety of energy functionals and which reproduces the two mentioned cases. We then use these relations to study the spatio-temporal correlations of the stress tensor in a Brownian fluid, which we compute to leading order in the interaction potential strength. We observe that, after integration over time, the spatial correlations generally decay as power laws in space. These are expected to be of importance for driven confined systems. We also show that divergence-free parts of the stress tensor do not contribute to the Green-Kubo relation for the viscosity.

  2. Automatic identification of microcracks observed on microscopic images of coarse-grained sandstone

    Czech Academy of Sciences Publication Activity Database

    Obara, B.; Kožušníková, Alena; Ščučka, Jiří

    2011-01-01

    Roč. 48, č. 4 (2011), s. 681-686 ISSN 1365-1609 Institutional research plan: CEZ:AV0Z30860518 Keywords : image analysis * microcracks * optical fluorescence microscopy Subject RIV: DB - Geology ; Mineralogy Impact factor: 1.272, year: 2011 http://www.sciencedirect.com/science/article/pii/S136516091100030X

  3. Second harmonic generation and dielectric study of the fine and coarse grain PMN-35PT ceramics

    Czech Academy of Sciences Publication Activity Database

    Kroupa, Jan; Bovtun, Viktor; Nuzhnyy, Dmitry; Savinov, Maxim; Vaněk, Přemysl; Kamba, Stanislav; Petzelt, Jan; Holc, J.; Kosec, M.; Amorin, H.; Alguero, M.

    2008-01-01

    Roč. 81, 11-12 (2008), s. 1059-1064 ISSN 0141-1594 R&D Projects: GA ČR(CZ) GA202/06/0403; GA MŠk OC 101 Institutional research plan: CEZ:AV0Z10100520 Keywords : relaxor ferroelectrics * phase transitions * PMN-PT * SHG * dielectric Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.201, year: 2008

  4. 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

    design (e.g. [1] and [2]) is the effects of diameter on the initial part of the p-y curves. This part is especially important in connection with the serviceability limit state and fatigue. The effects of diameter on the p-y curves can be investigated by means of either numerical analyses or physical...... 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...

  5. Coarse-grained molecular dynamics simulation of transport through the nuclear pore complex

    NARCIS (Netherlands)

    Ghavami, Ali

    2014-01-01

    Dit proefschrift is gewijd aan het mechanisme van Nucleo - cytoplasmatisch transport openbaren door grofkorrelige moleculaire dynamica simulaties van ontvouwen eiwitten in de nucleaire porie complex (NPC) . NPC's zijn zeer selectief poorten, die alle transporten over nucleaire envelop controleren .

  6. 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.

  7. Coarse-Grain model Simulations of Nonequilibrium Dynamics in Heterogeneous Materials

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin; Moore, J.D.; Izvekov, S.; Schweigert, I.V.; Larentzos, J.P.

    2014-01-01

    Roč. 5, č. 12 (2014), s. 2144-2149 ISSN 1948-7185 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : dissipative particle dynamics * energy-conservation * molecular-dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.458, year: 2014

  8. Electro-Acoustic Behavior of the Mitotic Spindle: A Semi-Classical Coarse-Grained Model

    Czech Academy of Sciences Publication Activity Database

    Havelka, Daniel; Kučera, Ondřej; Deriu, M.A.; Cifra, Michal

    2014-01-01

    Roč. 9, č. 1 (2014), e86501 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP102/11/0649 Institutional support: RVO:67985882 Keywords : electric fields * tubulin * chromosomes Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.234, year: 2014

  9. A coarse-grained model based on core-softened potentials for ...

    Indian Academy of Sciences (India)

    -scale cores oftened potential, we investigate how the system properties evolve inasmuch as particles are put together to form polymers whose chain size varies from 4 up to 32 monomers. We observed that the density and diffusionanomaly ...

  10. Synchronization of faulty processors in coarse-grained TMR protected partially reconfigurable FPGA designs

    International Nuclear Information System (INIS)

    Kretzschmar, U.; Gomez-Cornejo, J.; Astarloa, A.; Bidarte, U.; Ser, J. Del

    2016-01-01

    The expansion of FPGA technology in numerous application fields is a fact. Single Event Effects (SEE) are a critical factor for the reliability of FPGA based systems. For this reason, a number of researches have been studying fault tolerance techniques to harden different elements of FPGA designs. Using Partial Reconfiguration (PR) in conjunction with Triple Modular Redundancy (TMR) is an emerging approach in recent publications dealing with the implementation of fault tolerant processors on SRAM-based FPGAs. While these works pay great attention to the repair of erroneous instances by means of reconfiguration, the essential step of synchronizing the repaired processors is insufficiently addressed. In this context, this paper poses four different synchronization approaches for soft core processors, which balance differently the trade-off between synchronization speed and hardware overhead. All approaches are assessed in practice by synchronizing TMR protected PicoBlaze processors implemented on a Virtex-5 FPGA. Nevertheless all methods are of a general nature and can be applied for different processor architectures in a straightforward fashion. - Highlights: • Four different synchronization methods for faulty processors are proposed. • The methods balance between synchronization speed and hardware overhead. • They can be applied to TMR-protected reconfigurable FPGA designs. • The proposed schemes are implemented and tested in real hardware.

  11. Designing coarse grained-and atom based-potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Tobi Dror

    2010-11-01

    Full Text Available Abstract Background Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results Using a linear programming (LP technique, we developed two types of potentials: (i Side chain-based and (ii Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys, based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked structure, a potential energy lower than those of any of the non-native (misdocked structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atom-based potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.

  12. 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 individual program tasks and the data dependencies among these. This paper introduces two compiler directives which let programmers annotate source code with data dependencies among tasks. Compiler analysis overapproximates the actual dependencies among tasks. The directives help eliminate potential data...... dependencies that do not occur at runtime. This lets tools compute more accurate task graphs from the annotated code. The correct use of the directives cannot be verified at compile time. Therefore, the check for correct use is done at runtime—not unlike dynamic array bounds checking in many languages...

  13. 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.

  14. Coarse-graining time series data: Recurrence plot of recurrence plots and its application for music

    Science.gov (United States)

    Fukino, Miwa; Hirata, Yoshito; Aihara, Kazuyuki

    2016-02-01

    We propose a nonlinear time series method for characterizing two layers of regularity simultaneously. The key of the method is using the recurrence plots hierarchically, which allows us to preserve the underlying regularities behind the original time series. We demonstrate the proposed method with musical data. The proposed method enables us to visualize both the local and the global musical regularities or two different features at the same time. Furthermore, the determinism scores imply that the proposed method may be useful for analyzing emotional response to the music.

  15. Probabilistic Equilibrium Sampling of Protein Structures from SAXS Data and a Coarse Grained Debye Formula

    DEFF Research Database (Denmark)

    Andreetta, Christian

    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-likelihood ......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...... 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...

  16. 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.

    2017-08-01

    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 (g+1Σ) molecules due to interaction with N (S4u ) 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.

  17. 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

  18. Pretreatment of turkey fat-containing wastewater in coarse sand and gravel/coarse sand bioreactors.

    Science.gov (United States)

    Gaur, Rashmi Singh; Cai, Ling; Tuovinen, Olli H; Mancl, Karen M

    2010-02-01

    Fat, oil and grease in wastewater can be difficult to treat because of their slow decomposition. Traditional pretreatment facilities to remove fat, oil and grease from wastewater are increasingly costly. The hypothesis in this study was that pretreatment of animal fat-containing wastewater in sand and sand/gravel filters facilitates the conversion of slowly degradable organic matter measured as the difference between chemical oxygen demand (COD) and 5-day biochemical oxygen demand (BOD(5)) for subsequent biological treatment. The pretreatment was evaluated using simulated turkey-processing wastewater and coarse sand and sand/gravel filters at a constant hydraulic loading rate of 132L/m(2)/day. Two types of fixed media reactors were employed: (i) one set with a varying depth of coarse sand, and (ii) the second was similar but with an additional pea gravel cap. The results indicated that the relative removal of COD was slightly improved in the sand bioreactors with a pea gravel cap irrespective of the depth of coarse sand, but partial conversion to BOD(5) was not consistently demonstrated. Pea gravel may act as a sieve to entrap organic matter including fat globules from the wastewater. Multiple dosing at the same daily loading rate slightly improved the treatment efficiency of the sand bioreactors. The ratios of influent-COD/effluent-COD were always greater than 1.0 following a change in the dosing frequency after a rest period, suggesting that organic matter, specifically fat globules in this case, was retained by the column matrix.

  19. 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.

  20. 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

  1. The Effect of Grain Size on the Strain Hardening Behavior for Extruded ZK61 Magnesium Alloy

    Science.gov (United States)

    Zhang, Lixin; Zhang, Wencong; Chen, Wenzhen; Duan, Junpeng; Wang, Wenke; Wang, Erde

    2017-12-01

    The effects of grain size on the tensile and compressive strain hardening behaviors for extruded ZK61 alloys have been investigated by uniaxial tensile and compressive tests along the extrusion directions. Cylindrical tension and compression specimens of extruded ZK61 alloys with various sized grain were fabricated by annealing treatments. Tensile and compressive tests at ambient temperature were conducted at a strain rate of 0.5 × 10-3 s-1. The results indicate that both tensile strain hardening and compressive strain hardening of ZK61 alloys with different grain sizes have an athermal regime of dislocation accumulation in early deformation. The threshold stress value caused dynamic recovery is predominantly related to grain size in tensile strain hardening, but the threshold stress values for different grain sizes are almost identical in compressive strain hardening. There are obvious transition points on the tensile strain hardening curves which indicate the occurrence of dynamic recrystallization (DRX). The tensile strain hardening rate of the coarse-grained alloy obviously decreases faster than that of fine-grained alloys before DRX and the tensile strain hardening curves of different grain sizes basically tend to parallel after DRX. The compressive strain hardening rate of the fine-grained alloy obviously increases faster than that of coarse-grained alloy for twin-induced strain hardening, but compressive strain hardening curves also tend to parallel after twinning is exhausted.

  2. Marketing Farm Grain Crops.

    Science.gov (United States)

    Ridenour, Harlan E.

    This vocational agriculture curriculum on grain marketing contains three parts: teacher guide, student manual, and student workbook. All three are coordinated and cross-referenced. The course is designed to give students of grain marketing a thorough background in the subject and provide practical help in developing grain marketing strategies for…

  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. Multilevel Algorithms for Generic Coarse Grids for Multigrid Methods

    Science.gov (United States)

    2001-05-09

    Multilevel Algorithms For Generic Coarse Grids For Multigrid Methods Technical Report Department of Computer Science and Engineering University of... Methods Irene Moulitsas and George Karypis May 09, 2001 MULTILEVEL ALGORITHMS FOR GENERATING COARSEGRIDS FOR MULTIGRID METHODS Irene Moulitsas and...the Minnesota Supercomputing Institute.1 Serial Multilevel Coarse Grid Construction1 IntroductionGeometric Multigrid methods have gained widespread

  5. 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 ...

  6. Environmental monitoring of Columbia River sediments: Grain-size distribution and contaminant association

    International Nuclear Information System (INIS)

    Blanton, M.L.; Gardiner, W.W.; Dirkes, R.L.

    1995-04-01

    Based on the results of this study and literature review, the following conclusions can be made: Sediment grain size and TOC (total organic carbon) influence contaminant fate and transport (in general, sediments with higher TOC content and finer grain-size distribution can have higher contaminant burdens than sediments from a given river section that have less TOC and greater amounts of coarse-grained sediments). Physiochemical sediment characteristics are highly variable among monitoring sites along the Columbia River. Sediment grain characterization and TOC analysis should be included in interpretations of sediment-monitoring data

  7. Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their potential as drug delivery vehicles

    Science.gov (United States)

    Shen, Zhiqiang; Loe, David T.; Awino, Joseph K.; Kröger, Martin; Rouge, Jessica L.; Li, Ying

    2016-08-01

    Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and

  8. Coarsely resolved topography along protein folding pathways

    Science.gov (United States)

    Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

    2000-03-01

    The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

  9. 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.

  10. Production of Al-Ti-C grain refiners with the addition of elemental carbon

    International Nuclear Information System (INIS)

    Gezer, Berke Turgay; Toptan, Fatih; Daglilar, Sibel; Kerti, Isil

    2010-01-01

    Grain refining process used in aluminium alloys, has an important role for preventing columnar, coarse grains and encouraging fine, equiaxed grain formation. Al-Ti-B grain refiners are widely used as aluminium grain refiners despite the problems in application Al-Ti-C refiners have an increasing demand in recent years. In the present work, Al-Ti-C grain refiners with different Ti:C ratios were produced by insitu method with the addition of elemental carbon. Microstructures were characterised by optic microscope and scanning electron microscope equipped with energy dispersive spectroscopy. The effects of temperature, holding time and Ti:C ratio on the grain refinement process were investigated and optimum conditions were determined.

  11. 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.

  12. 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.

  13. Triglyceride Blisters in Lipid Bilayers: Implications for Lipid Droplet Biogenesis and the Mobile Lipid Signal in Cancer Cell Membranes

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Duelund, Lars; Pakkanen, Kirsi Inkeri

    2010-01-01

    aggregates of unknown function present in malignant cells, and to the early biogenesis of lipid droplets accommodated between the two leaflets of the endoplasmic reticulum membrane. The TO aggregates give the bilayer a blister-like appearance, and will hinder the formation of multi-lamellar phases in model......Triglycerides have a limited solubility, around 3%, in phosphatidylcholine lipid bilayers. Using millisecond-scale course grained molecular dynamics simulations, we show that the model lipid bilayer can accommodate a higher concentration of triolein (TO) than earlier anticipated, by sequestering...... triolein molecules to the bilayer center in the form of a disordered, isotropic, mobile neutral lipid aggregate, at least 17 nm in diameter, which forms spontaneously, and remains stable on at least the microsecond time scale. The results give credence to the hotly debated existence of mobile neutral lipid...

  14. WORLD GRAIN TRADE

    Directory of Open Access Journals (Sweden)

    Emilia Mary Bălan

    2017-04-01

    Full Text Available Grain is part of agricultural commodities and is of utmost importance for world agriculture,since it is the essential element of food and animal feed. Against this background, grain trade among countries of the world is dynamic and represents about 10% of global trade in food products.This article examines global grain trade both in terms of quantitative and qualitative developments, and highlights the most important competitor countries in this sector. It also details the patterns of grain trade for the world's main exporters and importers of such commodities.Two distinct sections of the research relate to the evolution of the primary grain quotations(wheat, corn, barley, rice and sorghum at the most representative international agricultural commodities markets (Chicago Board of Trade, based on a comprehensive statistical analysis, and the short-term forecasts for global grain trade, respectively.

  15. 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 ...

  16. Nonlinear Multigrid solver exploiting AMGe Coarse Spaces with Approximation Properties

    DEFF Research Database (Denmark)

    Christensen, Max la Cour; Villa, Umberto; Engsig-Karup, Allan Peter

    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), 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 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...... are compared to FAS on a nonlinear saddle point problem with applications to porous media flow. 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...

  17. Non-Steady Oscillatory Flow in Coarse Granular Materials

    DEFF Research Database (Denmark)

    Andersen, O. H.; Gent, M. R. A. van; Meer, J. W. van der

    1992-01-01

    Stationary and oscillatory flow through coarse granular materials have been investigated experimentally at Delft Hydraulics in their oscillating water tunnel with the objective of determining the coefficients of the extended Forchheimer equation. Cylinders, spheres and different types of rock have...

  18. 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.

  19. 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.

  20. Influence of grain size in the near-micrometre regime on the deformation microstructure in aluminium

    DEFF Research Database (Denmark)

    Le, G.M.; Godfrey, A.; Hansen, Niels

    2013-01-01

    .8μm have been prepared using this technique. Examination in the transmission electron microscope of these samples after compression at room temperature to approximately 20% reduction reveals that grains larger than 7μm are subdivided by cell block boundaries similar to those observed in coarse...

  1. 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...

  2. 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...

  3. Estimating the shear strength of concrete with coarse aggregate replacement

    OpenAIRE

    Folagbade Olusoga Peter ORIOLA; George MOSES; Jacob Oyeniyi AFOLAYAN; John Engbonye SANI

    2017-01-01

    For economic, environmental and practical reasons, it is desirable to replace the constituents of concrete with wastes and cheaper alternative materials. However, it is best when such replacements are done at optimum replacement levels. In view of this, a laboratory investigative test was carried out to evaluate the shear strength of concrete with coarse aggregate replacement by Coconut Shell and by Waste Rubber Tyre. The coarse aggregate replacement was done at recommended optimum proportion...

  4. Origins of discontinuous grain growth during liquid phase sintering of WC-Co cemented carbides

    Energy Technology Data Exchange (ETDEWEB)

    Schreiner, M.; Schmitt, T.; Lux, B.; Lassner, E.

    1984-07-01

    The origins of discontinuous grain growth of fine grained WC powders (about 1 ..mu..m average grain size) with Co binder occurring during liquid phase sintering were studied. The results indicate that small amounts of coarse grained WC powder added to fine grained WC-Co mixtures, which otherwise do not show local grain coarsening during liquid phase sintering, produce enhanced local grain growth of the WC crystals. Effects of milling conditions and sintering temperature on microstructure and mechanical properties, such as transverse rupture strength and hardness, were determined. As already observed in previous studies trace elements in blue oxide can have an important effect on the average grain size and grain size distribution of the WC-powder. Also the considerable influence on the sintering behaviour of such powders described here can be traced back to such impurities. It is shown that phosphorus decreases the melting temperature of the WC-Co system and a heterogeneous distribution of it promotes discontinuous grain growth. Contrary to this, carbon heterogeneities in fine grained WC powders did not cause any discontinuous grain growth at all.

  5. Presolar Grains in Indarch

    Science.gov (United States)

    Gao, X.; Nittler, L. R.; Swan, P. D.; Walker, R. M.

    1995-09-01

    We report results for the EH(4) Indarch. Earlier work [1] found 20 micrometers clumps of sub-micron SiC whose presolar nature was inferred from step-wise combustion, noble gas [2], and ion probe isotopic measurements. Our results indicate that the clumps were an artifact of sample preparation. Our sample was first cleaned using 6N HCl, and water and isopropanol rinses, then powdered and reacted with HCl-HF/HCl, KOH, and H3BO3-HCl/HCl giving a C-rich residue 1.14 wt.% of the original. X-ray mapping showed SiC grains and 5x as many Si3N4 grains, but no fine-grained clumps. Large (6 micrometers to 20 micrometers) C-rich spheroids were also present. The sample was further treated with KOH/HNO3 and NH3H2O; attempts to do density-separates were unsuccessful. An aliquot was treated with perchloric acid and separated into 1 micrometer fractions. SEM-EDS measurements of 73 (1 micrometer) grains with the addition of 2 spinel and one Al2O3 grains. The whole rock concentration of SiC was 5.8 ppm, higher than previous determinations [1,3,9]. Confirming earlier suggestions [1,2], we find that SiC in Indarch is much finer-grained than in Murchison; about 2/3 of the mass is in grains size-sorting in the nebula or selective destruction of fine-grained material. Ion probe measurements of 22 (1-3 micrometers) grains gave isotopic results in the range previously measured for Murchison SiCs [4]. Several normal Si3N4 grains (>1 micron) were measured; probably exsolution products similar to those in Qingzhen [7]. Ion mapping was used to search for presolar oxide grains using previously developed techniques [5]. Seven candidate grains out of ~1000 were found. Multiple imaging confirmed an ^(16)O/^(18)O anomaly in one spinel grain - the first presolar oxide found in an E chondrite. Although the proportion of oxide grains relative to SiC is smaller, the fraction of anomalous oxide grains is not strikingly different in Indarch than in Murchison (1/1000) or Tieschitz (1/300). Prior ion probe

  6. Bake hardening of ultra-fine grained low carbon steel produced by constrained groove pressing

    International Nuclear Information System (INIS)

    Alihosseini, H.; Dehghani, K.

    2012-01-01

    Highlights: ► BH of UFG low carbon steel sheets was studied. ► Three passes of CGP are used for producing of UFG sheets. ► Maximum BH was achieved to the UFG specimen pre-strained 8% by baking at 250 °C. - Abstract: In the present work, the bake hardening of ultra-fine grained low carbon steel was compared with that of its coarse-grain counterpart. The ultra-fine grained sheets were produced by applying three passes of constrained groove pressing resulting the grains of 260–270 nm. The microstructure of ultra-fine grain specimens were characterized using electron back-scatter diffraction technique. Then, the bake hardenability of ultra-fine grain and coarse-grain samples were compared by pre-straining to 4, 6 and 8% followed by baking at 150 °C and 250 °C for 20 min. The results show that in case of baking at 250 °C, there was an increase about 108%, 93%, and 72% in the bake hardening for 4%, 6% and 8% pre-strain, respectively. As for baking at 150 °C, these values were 170%, 168%, and 100%, respectively for 4%, 6% and 8% pre-strain. The maximum in bake hardenability (103 MPa) and final yield stress (563 MPa) were pertaining to the ultra-fine grain specimen pre-strained 8% followed by baking at 250 °C.

  7. Grains and Starchy Vegetables

    Science.gov (United States)

    ... Every time you choose to eat a starchy food, make it count! Leave the processed white flour-based products, especially the ones with added ... wheat grain is ground up. "Refined" flours like white and enriched wheat flour include only ... whole grain foods can be a challenge. Some foods only contain ...

  8. Seed lipids.

    Science.gov (United States)

    Wolff, I A

    1966-12-02

    Many of the newly discovered seedoil acids have reactive or unusual functional groups or other facets of molecular structure that permit their ready differentiation from oleic, linoleic, linolenic, and the other most prevalent saturated and unsaturated long-chain fatty acids. The recognition and availability of the new acids, coupled with methods that make detection and determination easy, will help studies of lipid biosynthesis in the plant and of lipid metabolism and utilization in animals, and will stimulate more studies in depth on the fine points of seedlipid structure. Correlations of structural patterns in seed lipids of particular groups of plants with classical taxonomic categories will permit clarifications, raise needed questions concerning classifications, and accelerate research in chemotaxonomy and phylogenetics. Seed lipids are particularly well suited for establishing relationships among plants because of their great variety in structure compared to the more limited structural types of amino acids, sugars, purines, and many other plant substances. The newly characterized seed oils are potentially important industrial raw materials whenever they come from agronomically promising plant species. The molecular structures of seed triglycerides have major influence on their physical properties and therefore advances in knowledge in that sphere have practical implications. For example, the unusual characteristics of cocoa butter that make it so valuable for food and confectionery use are attributed to the specific arrangement of fatty acids it its triglycerides. The glycerides are almost all 2-oleic-1,3-disaturated acid triglycerides. The physical characteristics of lard are advantageously changed by catalytically rearranging fatty acyl groups among the glycerides initially in the fat to achieve a more nearly random distribution, followed sometimes by further fractionation to remove more saturated glycerides. Through this change of glyceride structures a

  9. Load relaxation behavior of ultra-fine grained Ti-6Al-4V alloy

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Y.G.; Kim, J.H.; Lee, C.S. [Dept. of Materials Science and Engineering, Pohang Univ. of Science and Technology, Pohang (Korea); Shin, D.H. [Dept. of Metallurgy and Materials Science, Hanyang Univ., Ansan, Gyeonggi-do (Korea); Semiatin, S.L. [Air Force Research Lab., Materials and Mfg. Directorate Wright-Patterson AFB, OH (United States)

    2005-07-01

    In this study, superplastic deformation behavior of ultrafine-grained Ti-6Al-4V alloy was investigated on the basis of the inelastic deformation theory which consists of grain matrix deformation and grain boundary sliding. Specimens with coarse equiaxed grains (11 {mu}m in diameter) were significantly refined ({approx}0.3 {mu}m in diameter) with high angle boundaries after 4 times of isothermal equal channel angular (ECA) pressing at 600 C. Load relaxation test was performed at 600{proportional_to}700 C to enlighten the deformation mechanisms operating at specific temperature and to find optimum superplastic forming conditions for ultrafine-grained structures. Main efforts were devoted to analyze quantitatively the relative amount of each deformation mode, i.e., dislocation glide and grain boundary sliding operating at specific temperature. (orig.)

  10. 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%.

  11. 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.

  12. Ultrastructure of Withania Somnifera (L.) Dunal pollen grains

    International Nuclear Information System (INIS)

    Alwadie, H.M.

    2002-01-01

    Light, scanning and transmission electron microscopy were used to study the morphology and ultrastructure of Withania Somnifera (L.) Dunall pollen grains. Light microscopic examination revealed that the pollen grains are tri- or tetrazonocoplate grains, approximately as long as broad, measuring 29-um. Scanning electron microscopic observation showed that surface sculpturing of the pollen is scarbate-granulate. Ultrathin sections as examined by transmission electron microscope showed that the pollen contained numerous starch grains, lipid droplets, endoplasmic reticulum and vesicles of dictyosomes. Two layers of the pollen wall were also distinguished, the outer wall (exine) divided into ektexine and endexine as well as the inner layer (intine). The nutritive values of Withania pollen are discussed. The importance of studying the ultrastructure of pollen grains as a new tool in palynology is also discussed. (author)

  13. All About the Grains Group

    Science.gov (United States)

    ... Grains All about the Grains Group Print Share What foods are in the Grains Group? Any food made ... Whole Grains Food Gallery Take the Grains Quiz What Is MyPlate? Food Guide History MyPlate, MyWins Fruits All About the ...

  14. [Effect of grain-bean package, grain-bean package dietary fiber and single whole grain dietary fiber on dyslipidemia rats].

    Science.gov (United States)

    Liu, Yang; Zhai, Chengkai; Sun, Guiju; Zhang, Hong; Jiang, Mingxia; Zhang, Haifeng; Guo, Junling; Lan, Xi

    2014-05-01

    To observe and compare the effects of grain-bean package, dietary fiber (DF) extracted from grain-bean package, and DF from grain corn on the blood lipids and fatty acid synthase (FAS) activity in high-fat, high-cholesterol feeding induced dyslipidemia rats, and observe its effects on regulation of sterol regulatory element protein-1c (SREBP-1c) mRNA expression in rat liver. Consolidation 50 SD rats of clean grade feeding adaptation for one week, randomly assigned into normal control group, hyperlipidemia model group, grain-bean package group, grain-bean package DF group and grain corn group. Feed with corresponding diets for 8 weeks, and measure the total cholesterol (TC), triglyceridaemia (TG), high density lipoprotein cholesterol (HDL-C), fasting blood glucose (FBG), FAS, SREBP-1c mRNA of all groups. Compared with control group, TC, TG, FBG levels of hyperlipidemia model group were significantly increased (P dietary fiber can improve blood lipids levels of dyslipidemia rats, and decrease FAS activity and SREBP-1c mRNA expression.

  15. 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.

  16. Effect of grain structure on Charpy impact behavior of copper.

    Science.gov (United States)

    Liang, Ningning; Zhao, Yonghao; Wang, Jingtao; Zhu, Yuntian

    2017-03-17

    Nanostructured (NS) and ultrafine-grained (UFG) materials have high strength and relatively low ductility. Their toughness has not been comprehensively investigated. Here we report the Charpy impact behavior and the corresponding microstructural evolutions in UFG Cu with equi-axed and elongated grains which were prepared by equal channel angular pressing (ECAP) for 2 and 16 passes at room temperature. It is found that their impact toughness (48 J/cm 2 ) is almost comparable to that of coarse grained (CG) Cu: 55 J/cm 2 . The high strain rate during the Charpy impact was found to enhance the strain hardening capability of the UFG Cu due to the suppression of dynamic dislocation recovery. The crack in the CG Cu was blunted by dislocation-slip mediated plastic deformation, while the cracks in the UFG Cu were formed at grain boundaries and triple junctions due to their limited plasticity. Near the crack surfaces the elongated grains in ECAP-2 sample were refined by recrystallization, while equi-axed grains in the ECAP-16 sample grew larger.

  17. Changes in the Nutrient Composition of Brewery Spent Grain ...

    African Journals Online (AJOL)

    BSN

    The enhancement of the crude protein contents of the grains makes them potential cheap sources of protein for feeding ruminants and monogastric animals. The increase in the Total. Lipid content means more calories for animal using the fermented substrates as feed or feed supplement. Though fermentation reduced the.

  18. Interstellar grain chemistry

    International Nuclear Information System (INIS)

    Buch, V.

    1990-01-01

    This chapter discusses the chemical evolution and composition of dust in dense interstellar clouds. Studies use observations in the infrared, visible and ultraviolet spectral regions. These grains are thought to be made largely of highly disordered and/or composite materials. Recently acquired data on Halley's comet and on the structure, composition and spectral properties of interplanetary dust particles (IDP) are used to study grain chemistry. These substances are though to be similar to dense cloud dust. Dense clouds are thought to contain minerals, poorly crystallized carbonaceous/organic polymers, coating mineral grains and dirty ice mantles and the chemistry of these substances is considered. (UK)

  19. Kansas Agents Study Grain Marketing

    Science.gov (United States)

    Schoeff, Robert W.

    1973-01-01

    Author is an extension specialist in feed and grain marketing for Kansas State University. He describes a tour set up to educate members of the Kansas Grain and Feed Dealers' Association in the area of grain marketing and exporting. (GB)

  20. 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.