Stamatakis Michail
2010-04-01
Full Text Available Abstract Background An adaptive coarse-grained (kinetic Monte Carlo (ACGMC simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime. Results Coarse-graining of dimerization, rather than of diffusion, may lead to computational error. It is shown that the ACGMC method is an effective technique to minimize error in diffusion-reaction processes and is superior to the microscopic kinetic Monte Carlo simulation in terms of computational cost while retaining accuracy. The low computational cost enables sensitivity analysis calculations. Sensitivity analysis indicates that it may be possible to retain clusters of receptors over the time scale of minutes under suitable conditions and the cluster lifetime may depend on both receptor density and cluster size. Conclusions The ACGMC method is an ideal platform to resolve large length and time scales in heterogeneous biological systems well beyond the plasma membrane and the EGFR system studied here. Our results demonstrate that cluster size must be considered in conjunction with receptor density, as they synergistically affect EGFR cluster lifetime. Further, the cluster lifetime being of the order of several seconds suggests that any mechanisms responsible for EGFR aggregation must operate on shorter timescales (at most a fraction of a second, to overcome dissipation and produce stable clusters observed experimentally.
Systematic hierarchical coarse-graining with the inverse Monte Carlo method
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
Systematic hierarchical coarse-graining with the inverse Monte Carlo method
Lyubartsev, Alexander P.; Naômé, Aymeric; Vercauteren, Daniel P.; Laaksonen, Aatto
2015-12-01
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.
Systematic hierarchical coarse-graining with the inverse Monte Carlo method
Lyubartsev, Alexander P., E-mail: alexander.lyubartsev@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Naômé, Aymeric, E-mail: aymeric.naome@unamur.be [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Vercauteren, Daniel P., E-mail: daniel.vercauteren@unamur.be [UCPTS Division, University of Namur, 61 Rue de Bruxelles, B 5000 Namur (Belgium); Laaksonen, Aatto, E-mail: aatto@mmk.su.se [Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm (Sweden); Science for Life Laboratory, 17121 Solna (Sweden)
2015-12-28
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.
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Zavadlav, Julija; Praprotnik, Matej, E-mail: praprot@cmm.ki.si [Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Melo, Manuel N.; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl [Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen (Netherlands)
2015-06-28
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties.
A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo
Nikolay Korolev
2014-05-01
Full Text Available Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra- and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1–100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.
Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.
Janner, A
2016-05-01
Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109
A general adaptive modeling algorithm for selection and validation of coarse-grained models of atomistic systems is presented. A Bayesian framework is developed to address uncertainties in parameters, data, and model selection. Algorithms for computing output sensitivities to parameter variances, model evidence and posterior model plausibilities for given data, and for computing what are referred to as Occam Categories in reference to a rough measure of model simplicity, make up components of the overall approach. Computational results are provided for representative applications
Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation
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.
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.
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. PMID:27155649
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Zavadlav, Julija; Melo, Manuel N.; Marrink, Siewert J.; Praprotnik, Matej
2015-01-01
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that
Geneste, Grégory; Bellaiche, L.; Kiat, Jean-Michel
2016-06-01
The radio-frequency dielectric response of the lead-free Ba (Zr0.5Ti0.5)O3 relaxor ferroelectric is simulated using a coarse-grained Hamiltonian. This concept, taken from real-space renormalization group theories, allows us to depict the collective behavior of correlated local modes gathered in blocks. Free-energy barriers for their thermally activated collective hopping are deduced from this ab initio-based approach, and used as input data for kinetic Monte Carlo simulations. The resulting numerical scheme allows us to simulate the dielectric response for external field frequencies ranging from kHz up to a few tens of MHz for the first time and to demonstrate, e.g., that local (electric or elastic) random fields lead to the dielectric relaxation in the radio-frequency range that has been observed in relaxors.
The study of particle coagulation and sintering processes is important in a variety of research studies ranging from cell fusion and dust motion to aerosol formation applications. These processes are traditionally simulated using either Monte-Carlo methods or integro-differential equations for particle number density functions. In this paper, we present a computational technique for cases where we believe that accurate closed evolution equations for a finite number of moments of the density function exist in principle, but are not explicitly available. The so-called equation-free computational framework is then employed to numerically obtain the solution of these unavailable closed moment equations by exploiting (through intelligent design of computational experiments) the corresponding fine-scale (here, Monte-Carlo) simulation. We illustrate the use of this method by accelerating the computation of evolving moments of uni- and bivariate particle coagulation and sintering through short simulation bursts of a constant-number Monte-Carlo scheme.
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.
Tsoumanis, A C
2010-01-01
We address an iterative procedure that can be used to detect coarse-grained hyperbolic unstable equilibria (saddle points) of microscopic simulators when no equations at the macroscopic level are available. The scheme is based on the concept of coarse timestepping [Kevrekidis et al., 2003] incorporating an adaptive mechanism based on the chord method allowing the location of coarse-grained saddle points directly. Ultimately, it can be used in a consecutive manner to trace the coarse-grained open-loop saddle-node bifurcation diagrams. We illustrate the procedure through two indicatively examples including (i) a kinetic Monte Carlo simulation (kMC) of simple surface catalytic reactions and (ii) a simple agent-based model, a financial caricature which is used to simulate the dynamics of buying and selling of a large population of interacting individuals in the presence of mimesis. Both models exhibit coarse-grained regular turning points which give rise to branches of saddle points.
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.
Coarse-graining complex dynamics
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...
Pandey, Ras B.; Heinz, Hendrik; Farmer, Barry L.; Jones, Sharon; Drummy, Lawrence F.; Naik, Rajesh R.
2009-03-01
A coarse-grained description is used to study the structure and dynamics of peptide chains (CR3-1, S2) in presence of a clay surface on a cubic lattice. A peptide chain is represented by the specific sequence of amino acids. Specificity of residues is captured via an interaction matrix based on the insight gained from the atomistic simulation, i.e., each residue interacts with surrounding residues, solvent, and the clay surface with a unique interaction potential. We use a standard LJ potential with its coefficient controlled by the interaction matrix. Simulations are performed with a number of peptide chains. Along with the global energy and dynamics of peptides, we keep track of mobility, energy (total and adsorption), and correlation with the local structure from the density profiles of each residue. Based on the analysis of local and global quantities, we are able to assess the probability of adsorption of peptides to clay surface in agreement with experiment. The probability of adsorption of S2 is found to be much higher than that of CR3-1 in which S2 is anchored by Lysine. The procedure is complementary to biopanning experiments since it allows screening a large number of peptides (more than 10E+5) on the surface to estimate their binding potential.
Coarse graining flow of spin foam intertwiners
Dittrich, Bianca; Seth, Cameron J; Steinhaus, Sebastian
2016-01-01
Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behaviour on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group $\\text{SU}(2)_k \\times \\text{SU}(2)_k$, which implement the simplicity constraints analogous to 4D Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a 2D topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different ...
Entropy production in coarse grained Vlasov equations
The Vlasov equation is analyzed for coarse grained distributions. This coarse graining resembles a finite width of test-particles as used in numerical implementations. It is shown that this coarse grained distribution obeys a kinetic equation similar to the Vlasov equation, but with additional terms. These terms give rise to entropy production indicating dissipative features. The reason is a nonlinear mode coupling due to the finite width of the test-particles. The interchange of coarse graining and dynamical evolution is discussed with the help of an exactly solvable model and practical consequences are worked out. By calculating analytically the stationary solution we can show that a sum of modified Boltzmann-like distributions is approached dependent on the initial distribution. This behavior is independent of degeneracy and only controlled by the width of test-particles. The condition for approaching a stationary solution is derived in that the coarse graining energy given by momentum coarse graining should be smaller than a quarter of the kinetic energy. Observable consequences of this coarse graining are: (i) In the thermodynamics the coarse graining leads to spatial correlations in observables. (ii) Too large radii of nucleus in self-consistent treatments are observed and an explicit correction term appears in the Thomas Fermi equation. (iii) The momentum coarse graining translates into a structure term in the response function and resembles to a certain extent vertex correction correlations or internal structure effects. (iv) The coarse graining which is numerically unavoidable leads to a modified centroid energy and higher damping width of collective modes. The numerical codes should be revised in that a refolding is proposed. (author)
Fluctuation preserving coarse graining for biochemical systems
Altaner, Bernhard
2011-01-01
Finite stochastic Markov models play a major role for modelling biochemical pathways. Such models are a coarse-grained description of the underlying microscopic dynamics and can be considered mesoscopic. The level of coarse-graining is to a certain extend arbitrary since it depends on the resolution of accomodating measurements. Here, we present a way to simplify such stochastic descriptions, which preserves both the meso-micro and the meso-macro connection. The former is achieved by demanding locality, the latter by considering cycles on the network of states. Using single- and multicycle examples we demonstrate how our new method preserves fluctuations of observables much better than na\\"ive approaches.
Coarse-grained Modeling of DNA Curvature
Freeman, Gordon S; Lequieu, Joshua P; Whitmer, Jonathan K; de Pablo, Juan J
2014-01-01
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient exploration of binding configurations. It is known that the local structure of DNA can significantly affect its protein-binding properties (i.e. intrinsic curvature in DNA-histone complexes). In a step towards comprehensive DNA-protein modeling, we expand the 3SPN.2 coarse-grained model to include intrinsic shape, and validate the refined model against experimental data including melting temperature, local flexibility, persistence length, and minor groove width profile.
Measuring Crack Length in Coarse Grain Ceramics
Salem, Jonathan A.; Ghosn, Louis J.
2010-01-01
Due to a coarse grain structure, crack lengths in precracked spinel specimens could not be measured optically, so the crack lengths and fracture toughness were estimated by strain gage measurements. An expression was developed via finite element analysis to correlate the measured strain with crack length in four-point flexure. The fracture toughness estimated by the strain gaged samples and another standardized method were in agreement.
Coarse-graining polymers as soft colloids
Louis, A. A.; Bolhuis, P. G.; Finken, R.; Krakoviack, V.; Meijer, E. J.; Hansen, J. P.
2001-01-01
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.
Coarse grained description of the protein folding
Cieplak, Marek; Hoang, Trinh Xuan
1998-01-01
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that al...
Coarse-grained modelling of supercoiled RNA
Matek, Christian; Šulc, Petr; Randisi, Ferdinando; Doye, Jonathan P. K.; Louis, Ard A.
2015-12-01
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
Coarse-Grain Modeling of Energetic Materials
Brennan, John
2015-06-01
Mechanical and thermal loading of energetic materials can incite responses over a wide range of spatial and temporal scales due to inherent nano- and microscale features. Many energy transfer processes within these materials are atomistically governed, yet the material response is manifested at the micro- and mesoscale. The existing state-of-the-art computational methods include continuum level approaches that rely on idealized field-based formulations that are empirically based. Our goal is to bridge the spatial and temporal modeling regimes while ensuring multiscale consistency. However, significant technical challenges exist, including that the multiscale methods linking the atomistic and microscales for molecular crystals are immature or nonexistent. To begin addressing these challenges, we have implemented a bottom-up approach for deriving microscale coarse-grain models directly from quantum mechanics-derived atomistic models. In this talk, a suite of computational tools is described for particle-based microscale simulations of the nonequilibrium response of energetic solids. Our approach builds upon recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics that includes chemical reactions.
Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
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.
Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.
2008-01-01
The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sam...
Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena
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...
Buchert coarse-graining and the classical energy conditions
Visser, Matt
2015-01-01
So-called "Buchert averaging" is actually a coarse-graining procedure, where fine detail is "smeared out" due to limited spatio-temporal resolution. For technical reasons, (to be explained herein), "averaging" is not really an appropriate term, and I shall consistently describe the process as a "coarse-graining". Because Einstein gravity is nonlinear the coarse-grained Einstein tensor is typically not equal to the Einstein tensor of the coarse-grained spacetime geometry. The discrepancy can be viewed as an "effective" stress-energy, and this "effective" stress-energy often violates the classical energy conditions. To keep otherwise messy technical issues firmly under control, I shall work with conformal-FLRW (CFLRW) cosmologies. These CFLRW-based models are particularly tractable, and are also particularly attractive observationally: the CMB is not distorted. In this CFLRW context one can prove some rigorous theorems regarding the interplay between Buchert coarse-graining, tracelessness of the effective stres...
Coarse-grained Simulations of Viral Assembly
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
Perez Sirkin, Yamila A; Factorovich, Matías H; Molinero, Valeria; Scherlis, Damian A
2016-06-14
The vapor pressure of water is a key property in a large class of applications from the design of membranes for fuel cells and separations to the prediction of the mixing state of atmospheric aerosols. Molecular simulations have been used to compute vapor pressures, and a few studies on liquid mixtures and solutions have been reported on the basis of the Gibbs Ensemble Monte Carlo method in combination with atomistic force fields. These simulations are costly, making them impractical for the prediction of the vapor pressure of complex materials. The goal of the present work is twofold: (1) to demonstrate the use of the grand canonical screening approach ( Factorovich , M. H. J. Chem. Phys. 2014 , 140 , 064111 ) to compute the vapor pressure of solutions and to extend the methodology for the treatment of systems without a liquid-vapor interface and (2) to investigate the ability of computationally efficient high-resolution coarse-grained models based on the mW monatomic water potential and ions described exclusively with short-range interactions to reproduce the relative vapor pressure of aqueous solutions. We find that coarse-grained models of LiCl and NaCl solutions faithfully reproduce the experimental relative pressures up to high salt concentrations, despite the inability of these models to predict cohesive energies of the solutions or the salts. A thermodynamic analysis reveals that the coarse-grained models achieve the experimental activity coefficients of water in solution through a compensation of severely underestimated hydration and vaporization free energies of the salts. Our results suggest that coarse-grained models developed to replicate the hydration structure and the effective ion-ion attraction in solution may lead to this compensation. Moreover, they suggest an avenue for the design of coarse-grained models that accurately reproduce the activity coefficients of solutions. PMID:27196963
Coarse-Grained Simulations of Membranes under Tension
Neder, Jörg; Nielaba, Peter; Schmid, Friederike
2010-01-01
We investigate the properties of membranes under tension by Monte-Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area per lipid, the monolayer overlap, the nematic order, and pressure profiles. Both the low-temperature regime, where the membranes are in a gel phase, and the high-temperature regime, where they are in the fluid phase, are considered. In the gel state, the membrane is hardly influenced by tension. In the fluid state, high tensions lead to structural changes in the membrane, which result in different compressibility regimes. The ripple state, which is found at tension zero in the transition regime between the fluid and the gel phase, disappears under tension and gives way to an interdigitated phase. We also study the membrane fluctuations in the fluid phase. In the low tension regime the data can be fitted nicely to a suitably extended elastic theory. At higher tensions the elas...
Conveying of Coarse-Grained Particles in Pipes
Vlasák, P.; Chára, Z.; Konfršt, J. (Jiří); Sobota , J.; Kysela, B. (Bohuš)
2013-01-01
The effect of slurry velocity and concentration on the coarse-grained particle–water mixtures flow behavior and pressure drops was studied in horizontal and inclined pipes of inner diameter 100 mm. The study revealed that the coarse-grained particle-water mixtures were significantly stratified, the particles moved principally in a layer close to the pipe invert, for higher flow velocities particle saltation becomes dominant mode of conveying. Frictional pressure drops in vertical pipe ...
Energy-conserving coarse-graining of complex molecules.
Español, Pep; Serrano, Mar; Pagonabarraga, Ignacio; Zúñiga, Ignacio
2016-05-25
Coarse-graining (CG) of complex molecules is a method to reach time scales that would be impossible to access through brute force molecular simulations. In this paper, we formulate a coarse-grained model for complex molecules using first principles caculations that ensures energy conservation. Each molecule is described in a coarse way by a thermal blob characterized by the position and momentum of the center of mass of the molecule, together with its internal energy as an additional degree of freedom. This level of description gives rise to an entropy-based framework instead of the usual one based on the configurational free energy (i.e. potential of mean force). The resulting dynamic equations, which account for an appropriate description of heat transfer at the coarse-grained level, have the structure of the dissipative particle dynamics with energy conservation (DPDE) model but with a clear microscopic underpinning. Under suitable approximations, we provide explicit microscopic expressions for each component (entropy, mean force, friction and conductivity coefficients) appearing in the coarse-grained model. These quantities can be computed directly using MD simulations. The proposed non-isothermal coarse-grained model is thermodynamically consistent and opens up a first principles CG strategy for the study of energy transport issues that are not accessible using current isothermal models. PMID:27127809
Bayesian parametrization of coarse-grain dissipative dynamics models
Dequidt, Alain; Solano Canchaya, Jose G.
2015-08-01
We introduce a new bottom-up method for the optimization of dissipative coarse-grain models. The method is based on Bayesian optimization of the likelihood to reproduce a coarse-grained reference trajectory obtained from analysis of a higher resolution molecular dynamics trajectory. This new method is related to force matching techniques, but using the total force on each grain averaged on a coarse time step instead of instantaneous forces. It has the advantage of not being limited to pairwise short-range interactions in the coarse-grain model and also yields an estimation of the friction parameter controlling the dynamics. The theory supporting the method is exposed in a practical perspective, with an analytical solution for the optimal set of parameters. The method was first validated by using it on a system with a known optimum. The new method was then tested on a simple system: n-pentane. The local molecular structure of the optimized model is in excellent agreement with the reference system. An extension of the method allows to get also an excellent agreement for the equilibrium density. As for the dynamic properties, they are also very satisfactory, but more sensitive to the choice of the coarse-grain representation. The quality of the final force field depends on the definition of the coarse grain degrees of freedom and interactions. We consider this method as a serious alternative to other methods like iterative Boltzmann inversion, force matching, and Green-Kubo formulae.
Coarse-graining two-dimensional turbulence via dynamical optimization
Turkington, Bruce; Thalabard, Simon
2015-01-01
A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosit...
Coarse-graining the Lin-Maldacena geometries
The Lin-Maldacena geometries are nonsingular gravity duals to degenerate vacuum states of a family of field theories with SU(2|4) supersymmetry. In this note, we show that at large N, where the number of vacuum states is large, there is a natural 'macroscopic' description of typical states, giving rise to a set of coarse-grained geometries. For a given coarse-grained state, we can associate an entropy related to the number of underlying microstates. We find a simple formula for this entropy in terms of the data that specify the geometry. We see that this entropy function is zero for the original microstate geometries and maximized for a certain 'typical state' geometry, which we argue is the gravity dual to the zero-temperature limit of the thermal state of the corresponding field theory. Finally, we note that the coarse-grained geometries are singular if and only if the entropy function is non-zero
Vesicles and vesicle fusion: coarse-grained simulations
Shillcock, Julian C.
2010-01-01
compounds inside vesicles delays their clearance from the blood stream. In this chapter, we survey the biological role and physico-chemical properties of phospholipids, and describe progress in coarse-grained simulations of vesicles and vesicle fusion. Because coarse-grained simulations retain only those...... molecular details that are thought to influence the large-scale processes of interest, they act as a model embodying our current understanding. Comparing the predictions of these models with experiments reveals the importance of the retained microscopic details and also the deficiencies that can suggest...
Systematic coarse-graining in nucleation theory
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
Systematic coarse-graining in nucleation theory
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.
Generalized coarse-grained Becker-Doering equations
We present and apply a generalized coarse-graining method of reducing the Becker-Doering model; originally formulated to describe the stepwise aggregation and fragmentation of clusters during nucleation. Previous formulations of the coarse-graining procedure have allowed a temporal rescaling of the coarse-grained reaction rates; this is generalized to allow the rescaling to depend on cluster size. The form of this factor is derived for general reaction rates and general mesh function so that the steady-state solution is preserved; in the case of an even mesh function the kinetics can also be accurately reproduced. With a size-dependent mesh function the equilibrium solution and the form of convergence to this state are matched for a specific example. Finally we consider reaction rates relevant to the classical nucleation theory of spherical cluster growth, and numerically compare solutions of the full system to the generalized coarse-grained system in both constant monomer and constant mass formulations, demonstrating the accuracy of the method
Free-energy coarse-grained potential for C60
We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C60. Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures
Coarse graining and scaling in dissipative particle dynamics
Füchslin, Rudolf M; Fellermann, Harold; Eriksson, Anders;
2009-01-01
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic...
Coarse-graining and scaling in dissipative particle dynamics
Fuechslin, Rudolf; Fellermann, Harold; Eriksson, Anders;
2009-01-01
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic...
Deformation operators of spin networks and coarse-graining
In the context of loop quantum gravity, quantum states of geometry are mathematically defined as spin networks living on graphs embedded in the canonical space-like hypersurface. In the effort to study the renormalization flow of loop gravity, a necessary step is to understand the coarse-graining of these states in order to describe their relevant structure at various scales. Using the spinor network formalism to describe the phase space of loop gravity on a given graph, we focus on a bounded (connected) region of the graph and coarse-grain it to a single vertex using a gauge-fixing procedure. We discuss the ambiguities in the gauge-fixing procedure and its consequences for coarse-graining spin(or) networks. This allows to define the boundary deformations of that region in a gauge-invariant fashion and to identify the area preserving deformations as U(N) transformations similarly to the already well-studied case of a single intertwiner. The novelty is that the closure constraint is now relaxed and the closure defect interpreted as a local measure of the curvature inside the coarse-grained region. It is nevertheless possible to cancel the closure defect by a Lorentz boost. We further identify a Lorentz-invariant observable related to the area and closure defect, which we name ‘rest area’. Its physical meaning remains an open issue. (paper)
Notes on coarse grainings and functions of observables
Dvurecenskij, A; Pulmannova, S; Ylinen, K
2004-01-01
Using the Naimark dilation theory we investigate the question under what conditions an observable which is a coarse graining of another observable is a function of it. To this end, conditions for the separability and for the Boolean structure of an observable are given.
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. PMID:26930454
Determination of the scale of coarse graining in earthquake network
Abe, Sumiyoshi
2009-01-01
In a recent paper [S. Abe and N. Suzuki, Europhys. Lett., 65 (2004) 581], the concept of earthquake network has been introduced in order to describe complexity of seismicity. There, the cell size, which is the scale of coarse graining needed for constructing an earthquake network, has remained as a free parameter. Here, a method is presented for determining it based on the scaling behavior of the network. Quite remarkably, both the exponent of the power-law connectivity distribution and the clustering coefficient are found to approach the respective universal values and remain invariant as the cell size becomes larger than a certain value, $l_*$, which depends on the number of events contained in the analysis, in general. This $l_*$ fixes the scale of coarse graining. Universality of the result is demonstrated for all of the networks constructed from the data independently taken from California, Japan and Iran.
A nucleotide-level coarse-grained model of RNA
Šulc, Petr; Ouldridge, Thomas E; Doye, Jonathan P K; Louis, Ard A
2014-01-01
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture
Wu, Kehuai; Kanstein, Andreas; Madsen, Jan;
2007-01-01
The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl’s law, this paper proposes to extend ADRES to MT-ADRES (Multi-Threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned in multiple...
Experimental investigation of coarse-grained particles in pipes
Vlasák, P.; Chára, Z.; Konfršt, J. (Jiří); Kysela, B. (Bohuš)
2013-01-01
The effect of solid concentration and mixture velocity on the flow behaviour and pressure drops of coarse-grained particle-water mixtures in the turbulent flow was experimentally investigated. Concentration distribution in the pipe cross-section was also studied. Graded basalt pebbles as a model of solid particles were studied on an experimental pipe loop with horizontal, vertical, and inclined sections of smooth stainless steel pipes of inner diameter D = 100 mm. The study revealed that the ...
Experimental investigation of coarse-grained particles in pipes
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Kysela, Bohuš
Rostock: University of Rostock, 2013 - (Sobota, J.; Eckstädt, H.), s. 265-273 ISBN 978-83-927084-9-0. ISSN 1232-3071. [16th International conference transport and sedimentation of solid particles. Rostock (DE), 18.09.2013-20.09.2013] R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : hydraulic conveying * coarse-grained slurry * pressure drops * concentration distribution * pipe inclination Subject RIV: BK - Fluid Dynamics
PRIMO: A Transferable Coarse-grained Force Field for Proteins
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael
2013-01-01
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born mode...
Experimental investigation of coarse-grained particles in pipes
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Kysela, Bohuš
Rostock : University of Rostock, 2013 - (Sobota, J.; Eckstädt, H.), s. 265-273 ISBN 978-83-927084-9-0. ISSN 1232-3071. [16th International conference transport and sedimentation of solid particles. Rostock (DE), 18.09.2013-20.09.2013] R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : hydraulic conveying * coarse-grained slurry * pressure drops * concentration distribution * pipe inclination Subject RIV: BK - Fluid Dynamics
Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations
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.
Moving Beyond Watson-Crick Models of Coarse Grained DNA
Dorfman, Kevin; Linak, Margaret; Tourdot, Richard
2012-02-01
DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.
High capacitance of coarse-grained carbide derived carbon electrodes
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury
2016-02-01
We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.
It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model
Nguyen, Hung; Van, Thanh Dac; Le, Ly
2015-10-01
The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.
Adaptive Multilevel Monte Carlo Simulation
Hoel, H
2011-08-23
This work generalizes a multilevel forward Euler Monte Carlo method introduced in Michael B. Giles. (Michael Giles. Oper. Res. 56(3):607–617, 2008.) for the approximation of expected values depending on the solution to an Itô stochastic differential equation. The work (Michael Giles. Oper. Res. 56(3):607– 617, 2008.) proposed and analyzed a forward Euler multilevelMonte Carlo method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a standard, single level, Forward Euler Monte Carlo method. This work introduces an adaptive hierarchy of non uniform time discretizations, generated by an adaptive algorithmintroduced in (AnnaDzougoutov et al. Raùl Tempone. Adaptive Monte Carlo algorithms for stopped diffusion. In Multiscale methods in science and engineering, volume 44 of Lect. Notes Comput. Sci. Eng., pages 59–88. Springer, Berlin, 2005; Kyoung-Sook Moon et al. Stoch. Anal. Appl. 23(3):511–558, 2005; Kyoung-Sook Moon et al. An adaptive algorithm for ordinary, stochastic and partial differential equations. In Recent advances in adaptive computation, volume 383 of Contemp. Math., pages 325–343. Amer. Math. Soc., Providence, RI, 2005.). This form of the adaptive algorithm generates stochastic, path dependent, time steps and is based on a posteriori error expansions first developed in (Anders Szepessy et al. Comm. Pure Appl. Math. 54(10):1169– 1214, 2001). Our numerical results for a stopped diffusion problem, exhibit savings in the computational cost to achieve an accuracy of ϑ(TOL),from(TOL−3), from using a single level version of the adaptive algorithm to ϑ(((TOL−1)log(TOL))2).
Coarse Grained Transport Model for Neutrals in Turbulent SOL Plasmas
Full text: Edge plasmas of magnetic fusion devices exhibit strong intermittent turbulence, which governs perpendicular transport of particles and heat. Turbulent fluxes result from the coarse graining procedure used to derive the transport equation, which entails time averaging of the underlying equations governing the turbulent evolution of the electron and ion fluids. In previous works, we have pointed out that this averaging is not carried out on the Boltzmann equation that describes the transport of neutral particles (atoms, molecules) in current edge code suites (such as SOLPS). Since fluctuations in the far SOL are of order unity, calculating the transport of neutral particles, hence the source terms in plasma fluid equations, in the average plasma background might lead to misleading results. In particular, retaining the effects of fluctuations could affect the estimation of the importance of main chamber recycling, hence first wall sputtering by charge exchange atoms, as well as main chamber impurity contamination and transport. In this contribution, we obtain an exact coarse-grained equation for the average neutral density, assuming that density fluctuations are described by multivariate Gamma statistics. This equation is a scattering free Boltzmann equation, where the ionization rate has been renormalized to account for fluctuations. The coarse grained transport model for neutrals has been implemented in the EIRENE code, and applications in 2D geometry with ITER relevant plasma parameters are presented. Our results open the way for the implementation of the effects of turbulent fluctuations on the transport of neutral particles in coupled plasma/neutral edge codes like B2-EIRENE. (author)
A Coarse-Grained Protein Model in a Water-like Solvent
Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene
2013-05-01
Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.
Flow behavior of coarse-grained slurries in pipes
Vlasák, P.; Chára, Z.; Kysela, B. (Bohuš); Sobota , J.
2011-01-01
The paper describes the experimental investigation of model coarse-grained slurry on a recirculation pipe loop with smooth stainless steel pipes. Graded pebble gravel and glass balls were used as a model for poly-metallic nodules, and very fine glass beads as a model for fine-grained sand. The investigation was focused on evaluating the effect of slurry velocity and particle concentration on pressure drops and the slurry flow behavior in the turbulent regime. Also the effect of fine-grained p...
Conveying of Coarse-Grained Particles in Pipes
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Sobota, J.; Kysela, Bohuš
Vol. 10. Sczecin: The International Society of Offshore and Polar Engineers, 2013, s. 215-220. ISBN 978-1-880653-92-0. ISSN 1946-0066. [The Tenth (2013) ISOPE Ocean Mining & Gas Hydrates Symposium. Szczecin (PL), 22.09.2013-26.09.2013] R&D Projects: GA ČR GAP105/10/1574 Grant ostatní: InterOceanMetal(CZ) 501-4.1.2/1-11 Institutional support: RVO:67985874 Keywords : hydraulic conveying * coarse-grained slurry * concentration distribution * pressure drops * pipe inclination Subject RIV: BK - Fluid Dynamics
Conveying of Coarse-Grained Particles in Pipes
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Sobota, J.; Kysela, Bohuš
Vol. 10. Sczecin : The International Society of Offshore and Polar Engineers, 2013, s. 215-220. ISBN 978-1-880653-92-0. ISSN 1946-0066. [The Tenth (2013) ISOPE Ocean Mining & Gas Hydrates Symposium. Szczecin (PL), 22.09.2013-26.09.2013] R&D Projects: GA ČR GAP105/10/1574 Grant ostatní: InterOceanMetal(CZ) 501-4.1.2/1-11 Institutional support: RVO:67985874 Keywords : hydraulic conveying * coarse-grained slurry * concentration distribution * pressure drops * pipe inclination Subject RIV: BK - Fluid Dynamics
Realistic coarse-grained cosmic structure from Szekeres models
Sussman, Roberto A
2015-01-01
A systematic self-consistent procedure is provided to describe by means of the Szekeres dust models the evolution of multiple self-gravitating cold dark matter structures (over-densities and density voids), whose spatial location can be prescribed beforehand for all times by suitable initial conditions that define the free parameters of the models. Following this procedure makes it possible to obtain a fully relativistic non-perturbative coarse grained description of actually existing cosmic structure at various scales. We discuss possible astrophysical and cosmological applications.
Folding and design in coarse-grained protein models
Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders are discussed. Similar patterns for non-randomness are found for real proteins. Dynamical parameter MC methods, such as the tempering and multisequence algorithms, are essential in order to obtain these results. Also, a new MC method for design, the inverse of folding, is presented. Here, one maximizes conditional probabilities rather than minimizing energies. By construction, this method ensures that the designed sequences represent good folders thermodynamically
Coarse-grained parallelism for full-core transport calculations
In this paper we analyze the synergy between the Domain Decomposition Method and the Coarse-Mesh Finite Difference technique. In contrast to massively parallel computations, we construct a coarse-grained parallelism for daily run calculations on standard SIMD workstations based on shared memory architecture. We evaluate the effectiveness of the algorithm for several high-fidelity calculations spanning different types of color-sets up to the full-core. We show that CPU times for a best-estimate 2D calculation of the EPR can be reduced from several days to few hours using a standard workstation. (author)
Symmetry-based coarse-graining of evolved dynamical networks
Karalus, Steffen
2015-01-01
Networks with prescribed subdiffusive dynamical behavior can be generated by evolutionary optimization applied to the spectrum of the graph Laplacian. When the evolution algorithm is constrained to preserve degree-regularity, the evolved networks display an abundance of certain motifs arranged into loops and long linear segments. We use algebraic graph theory to construct the quotient networks induced by the symmetries underlying the motifs. The resulting coarse-grained networks display improved pectral properties and provide an intuitive view of how the anomalous diffusive properties are realized in the evolved structures.
MICROTHREAD BASED (MTB) COARSE GRAINED FAULT TOLERANCE SUPERSCALAR PROCESSOR ARCHITECTURE
无
2006-01-01
Fault tolerance in microprocessor systems has become a popular topic of architecture research.Much work has been done at different levels to accomplish reliability against soft errors, and some fault tolerance architectures have been proposed. But little attention is paid to the thread level superscalar fault tolerance.This letter introduces microthread concept into superscalar processor fault tolerance domain, and puts forward a novel fault tolerance architecture, namely, MicroThread Based (MTB) coarse grained transient fault tolerance superscalar processor architecture, then discusses some detailed implementations.
Entropy production and coarse graining in Markov processes
We study the large time fluctuations of entropy production in Markov processes. In particular, we consider the effect of a coarse-graining procedure which decimates fast states with respect to a given time threshold. Our results provide strong evidence that entropy production is not directly affected by this decimation, provided that it does not entirely remove loops carrying a net probability current. After the study of some examples of random walks on simple graphs, we apply our analysis to a network model for the kinesin cycle, which is an important biomolecular motor. A tentative general theory of these facts, based on Schnakenberg's network theory, is proposed
A system for coarse-grained location-based synchronisation
Coelho, André; Silva, Mário; José, Rui
2010-01-01
This paper describes a system for supporting coarse-grained location-based synchronisation. This type of synchronisation may occur when people need only some awareness about the location of others within the specific context of an on-going activity. We have identified a number of reference scenarios for this type of synchronisation and we have implemented and deployed a prototype to evaluate the type of support provided. The results of the evaluation suggest a good acceptance of the overall concept, indicating that this might be a valuable approach for many of the indicated scenarios, possibly replacing or complementing existing synchronisation practices.
Neural Adaptive Sequential Monte Carlo
Gu, Shixiang; Ghahramani, Zoubin; Turner, Richard E
2015-01-01
Sequential Monte Carlo (SMC), or particle filtering, is a popular class of methods for sampling from an intractable target distribution using a sequence of simpler intermediate distributions. Like other importance sampling-based methods, performance is critically dependent on the proposal distribution: a bad proposal can lead to arbitrarily inaccurate estimates of the target distribution. This paper presents a new method for automatically adapting the proposal using an approximation of the Ku...
An exactly solvable coarse-grained model for species diversity
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)
An exactly solvable coarse-grained model for species diversity
Suweis, Samir; Rinaldo, Andrea; Maritan, Amos
2012-07-01
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.
Million atom DFT calculations using coarse graining and petascale computing
Nicholson, Don; Odbadrakh, Kh.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X. G.; Stocks, G. M.
2014-03-01
Researchers performing classical Molecular Dynamics (MD) on defect structures often find it necessary to use millions of atoms in their models. It would be useful to perform density functional calculations on these large configurations in order to observe electron-based properties such as local charge and spin and the Helmann-Feynman forces on the atoms. The great number of atoms usually requires that a subset be ``carved'' from the configuration and terminated in a less that satisfactory manner, e.g. free space or inappropriate periodic boundary conditions. Coarse graining based on the Locally Self-consistent Multiple Scattering method (LSMS) and petascale computing can circumvent this problem by treating the whole system but dividing the atoms into two groups. In Coarse Grained LSMS (CG-LSMS) one group of atoms has its charge and scattering determined prescriptively based on neighboring atoms while the remaining group of atoms have their charge and scattering determined according to DFT as implemented in the LSMS. The method will be demonstrated for a one-million-atom model of a displacement cascade in Fe for which 24,130 atoms are treated with full DFT and the remaining atoms are treated prescriptively. Work supported as part of Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, Basic Energy Sciences, used Oak Ridge Leadership Computing Facility, Oak Ridge National Lab, of DOE Office of Science.
A coarse-grained model of microtubule self-assembly
Regmi, Chola; Cheng, Shengfeng
Microtubules play critical roles in cell structures and functions. They also serve as a model system to stimulate the next-generation smart, dynamic materials. A deep understanding of their self-assembly process and biomechanical properties will not only help elucidate how microtubules perform biological functions, but also lead to exciting insight on how microtubule dynamics can be altered or even controlled for specific purposes such as suppressing the division of cancer cells. Combining all-atom molecular dynamics (MD) simulations and the essential dynamics coarse-graining method, we construct a coarse-grained (CG) model of the tubulin protein, which is the building block of microtubules. In the CG model a tubulin dimer is represented as an elastic network of CG sites, the locations of which are determined by examining the protein dynamics of the tubulin and identifying the essential dynamic domains. Atomistic MD modeling is employed to directly compute the tubulin bond energies in the surface lattice of a microtubule, which are used to parameterize the interactions between CG building blocks. The CG model is then used to study the self-assembly pathways, kinetics, dynamics, and nanomechanics of microtubules.
Coarse-grained molecular dynamics simulation of small ferrogel objects
The microstructure of ferrogels (FG) is investigated with the aid of coarse-grained molecular dynamics. Small FGs samples are considered: about 100 magnetic nanoparticles placed in the nodes of a piece of a quasi-regular polymer mesh. The changes of internal configuration under variations of the intensity of interparticle dipolar interaction, concentration and temperature are monitored. The obtained results evidence that the radial distribution function is a sensitive indicator of self-organization of the magnetic nanoparticles in FGs, thus yielding a robust basis for interpretation of spectroscopic measurements. - Highlights: • Ferrogel (objects containing a countable number of magnetic nanoparticles) are considered with the aid of coarse-grained molecular dynamics. • ESPResSo software, being a versatile computer code, is a convenient tool to do that. • The simulations deliver a detailed information on the relevant structure features of microferrogels; in particular, the chain-like equilibrium structures due to the interparticle dipolar fields are clearly revealed in terms of radial distribution function
Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers
West, Beate; Schmid, Friederike
2008-01-01
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: Direct interactions, lipid-induced depletion interactions, lipid bridging, lipid packing, and a smooth long-range contribution. The mechan...
A hybrid multiscale coarse-grained method for dynamics on complex networks
Shen, Chuansheng; Hou, Zhonghuai; Kurths, Jürgen
2016-01-01
Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only interested in the property of local part and not in the whole network. Here, we propose a hybrid multiscale coarse-grained(HMCG) method which combines a fine Monte Carlo(MC) simulation on the part of nodes of interest with a more coarse Langevin dynamics on the rest part. We demonstrate the validity of our method by analyzing the equilibrium Ising model and the nonequilibrium susceptible-infected-susceptible model. It is found that HMCG not only works very well in reproducing the phase transitions and critical phenomena of the microscopic models, but also accelerates the evaluation of dynamics with significant computational savings compared to microscopic MC simulations directly for the whole networks. The proposed method is general and can be applied to a wide variety of network...
Coarse-grain parallelism using remote method invocation
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)
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity
Frigori, Rafael B; Alves, Nelson A
2012-01-01
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid $\\beta$-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method (REM) is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid $\\beta$ isoforms and Src SH3 domain indicated that th...
Coarse-grained cellular automaton for traffic systems
Krawczyk, Malgorzata J
2012-01-01
A coarse-grained cellular automaton is proposed to simulate traffic systems. There, cells represent road sections. A cell can be in two states: jammed or passable. Numerical calculations are performed for a piece of square lattice with open boundary conditions, for the same piece with some cells removed and for a map of a small city. The results indicate the presence of a phase transition in the parameter space, between two macroscopic phases: passable and jammed. The results are supplemented by exact calculations of the stationary probabilities of states for the related Kripke structure constructed for the traffic system. There, the symmetry-based reduction of the state space allows to partially reduce the computational limitations of the numerical method.
Coarse grained NN potential with Chiral Two Pion Exchange
Perez, R Navarro; Arriola, E Ruiz
2013-01-01
We determine the chiral constants of the Nucleon-Nucleon Two Pion Exchange potential deduced from Chiral Perturbation Theory. By using a coarse grained representation of the short distance interactions with 30 parameters, the Partial Wave Analysis fit gives chi^2/dof = 1.1 to a mutually consistent set of 6713 data previously built from all published proton-proton and neutron proton scattering data from 1950 till 2013 with LAB energy below 350 MeV. We obtain (c1, c3, c4)=(-0.41+- 1.08,-4.66+- 0.60, 4.31+- 0.17)/GeV with an almost 100% anti-correlation between c1 and c3. We also provide the errors in the short distance parameters and propagate them to the deuteron properties and low partial waves phase shifts.
A Coarse-Grained Model for Simulating Chitosan Hydrogels
Xu, Hongcheng; Matysiak, Silvina
Hydrogels are biologically-derived materials composed of water-filled cross-linking polymer chains. It has widely been used as biodegradable material and has many applications in medical devices. The chitosan hydrogel is stimuli-responsive for undergoing pH-sensitive self-assembly process, allowing programmable tuning of the chitosan deposition through electric pulse. To explore the self-assembly mechanism of chitosan hydroge, we have developed an explicit-solvent coarse-grained chitosan model that has roots in the MARTINI force field, and the pH change is modeled by protonating chitosan chains using the Henderson-Hasselbalch equation. The mechanism of hydrogel network formation will be presented. The self-assembled polymer network qualitatively reproduce many experimental observables such as the pH-dependent strain-stress curve, bulk moduli, and structure factor. Our model is also capable of simulating other similar polyelectrolyte polymer systems.
Effective thermostat induced by coarse-graining of SPC water
Eriksson, Anders; Nyström, Johan; Tunstrøm, Kolbjørn
2008-01-01
We investigate how the transport properties of a united atoms fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the thermostat strongly affects the hydrodynamics, especially diffusion, viscosity, and local escape times. As model system we use SPC water, from which projected trajectories are used to determine the effective interactions in the united atoms model. The simulation results support our argument that the thermostat should be viewed as an integral part of the coarse-grained dynamics, rather than a tool for approaching thermal equilibrium. As our main result we show that the united atoms model with the adjusted effective interactions approximately reproduce the diffusion constant and the viscosity of the underlying detailed SPC water model.
Coarse-Grained Molecular Simulations of Allosteric Cooperativity
Nandigrami, Prithviraj
2015-01-01
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two calcium ions to each domain of calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein's conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding is treated implicitly at the mean field level. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energy to the open and closed ensembles accurately describe...
Coarse-graining RNA nanostructures for molecular dynamics simulations
A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes
MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture
Wu, Kehuai; Kanstein, Andreas; Madsen, Jan; Berekovic, Mladen
The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl’s law, this paper proposes to extend ADRES to MT-ADRES (Multi-Threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned in multiple...... smaller arrays that can execute threads in parallel. Because the partition can be changed dynamically, this extension provides more flexibility than a multi-core approach. This article presents details of the enhanced architecture and results obtained from an MPEG-2 decoder implementation that exploits a...
Coarse-grain parallelism using remote method invocation
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)
Polysaccharide-Protein Complexes in a Coarse-Grained Model.
Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek
2015-09-10
We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4-α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al. PMID:26291477
Anisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials
Shen, Hujun; LI Yan; Ren, Pengyu; Zhang, Dinglin; Li, Guohui
2014-01-01
Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental ...
Robotic action acquisition with cognitive biases in coarse-grained state space.
Uragami, Daisuke; Kohno, Yu; Takahashi, Tatsuji
2016-07-01
Some of the authors have previously proposed a cognitively inspired reinforcement learning architecture (LS-Q) that mimics cognitive biases in humans. LS-Q adaptively learns under uniform, coarse-grained state division and performs well without parameter tuning in a giant-swing robot task. However, these results were shown only in simulations. In this study, we test the validity of the LS-Q implemented in a robot in a real environment. In addition, we analyze the learning process to elucidate the mechanism by which the LS-Q adaptively learns under the partially observable environment. We argue that the LS-Q may be a versatile reinforcement learning architecture, which is, despite its simplicity, easily applicable and does not require well-prepared settings. PMID:27195484
Relative entropy and optimization-driven coarse-graining methods in VOTCA
We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations.We have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process
Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water
Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore;
2010-01-01
We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations 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....
Influence of fines content on the anti-frost properties of coarse-grained soil
TianLiang Wang; ZuRun Yue; TieCheng Sun; JinChuang Hua
2015-01-01
This paper aims to determine the optimal fines content of coarse-grained soil required to simultaneously achieve weaker frost susceptibility and better bearing capacity. We studied the frost susceptibility and strength properties of coarse-grained soil by means of frost heaving tests and static triaxial tests, and the results are as follows: (1) the freezing temperature of coarse-grained soil decreased gradually and then leveled off with incremental increases in the percent content of fines; (2) the fines content proved to be an important factor influencing the frost heave susceptibility and strength properties of coarse-grained soil. With incremental increases in the percent content of fines, the frost heave ratio increased gradually and the cohesion function of fines effectively enhanced the shear strength of coarse-grained soil before freeze-thaw, but the frost susceptibility of fines weakened the shear strength of coarse-grained soil after freeze-thaw; (3) with increasing numbers of freeze-thaw cycles, the shear strength of coarse-grained soil decreased and then stabilized after the ninth freeze-thaw cycle, and therefore the mechanical indexes of the ninth freeze-thaw cycle are recommended for the engi-neering design values; and (4) considering frost susceptibility and strength properties as a whole, the optimal fines content of 5% is recommended for railway subgrade coarse-grained soil fillings in frozen regions.
Entrainment of coarse grains using a discrete particle model
Conventional bedload transport models and incipient motion theories relying on a time-averaged boundary shear stress are incapable of accounting for the effects of fluctuating near-bed velocity in turbulent flow and are therefore prone to significant errors. Impulse, the product of an instantaneous force magnitude and its duration, has been recently proposed as an appropriate criterion for quantifying the effects of flow turbulence in removing coarse grains from the bed surface. Here, a discrete particle model (DPM) is used to examine the effects of impulse, representing a single idealized turbulent event, on particle entrainment. The results are classified according to the degree of grain movement into the following categories: motion prior to entrainment, initial dislodgement, and energetic displacement. The results indicate that in all three cases the degree of particle motion depends on both the force magnitude and the duration of its application and suggest that the effects of turbulence must be adequately accounted for in order to develop a more accurate method of determining incipient motion. DPM is capable of simulating the dynamics of grain entrainment and is an appropriate tool for further study of the fundamental mechanisms of sediment transport
Coarse-grained DNA model capable of simulating ribose flexibility
Kovaleva, Natalya A; Mazo, Mikhail A; Zubova, Elena A
2014-01-01
We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA forms. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the sugar CG DNA model are: (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one non-harmonic potential and one three-particle potential, (2) explicit representation of sodium counterions and (3) implicit solvent approach. Effects of solvation and of partial charge screening at small distances are taken into account through the shape of potentials of interactions between charged particles. We obtain parameters of the sugar CG DNA model from the all-atom AMBER model. The suggested model allows adequate simulation of the transitions between A- and B-DNA forms, as well as of large deformations of long DNA molecules, for example, in binding with proteins. Small modifications of the model can provide th...
Cellulose microfibril formation within a coarse grained molecular dynamics
Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration
2014-03-01
Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.
Improving the treatment of coarse-grain electrostatics: CVCEL
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.
Generic Coarse-Grained Model for Protein Folding and Aggregation
Bereau, Tristan; Deserno, Markus
2009-03-01
The complexity involved in protein structure is not only due to the rich variety of amino acids, but also the inherent weak interactions, comparable to thermal energy, and important cooperative phenomena. This presents a challenge in atomistic simulations, as it is associated with high-dimensionality and ruggedness of the energy landscape as well as long equilibration times. We have recently developed a coarse-grained (CG) implicit solvent peptide model which has been designed to reproduce key consequences of the abovementioned weak interactions. Its intermediate level of resolution, four beads per amino acid, allows for accurate sampling of local conformations by designing a force field that relies on simple interactions. A realistic ratio of α-helix to β-sheet content is achieved by mimicking a nearest-neighbor dipole interaction. We tune the model in order to fold helical proteins while systematically comparing the structure with NMR data. Very good agreement is achieved for proteins that have simple tertiary structures. We further probe the effects of cooperativity between amino acids by looking at peptide aggregation, where hydrophobic peptide fragments cooperatively form large-scale β-sheet structures. The model is able to reproduce features from atomistic simulations on a qualitative basis.
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G.
2013-09-01
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
Coarse-Grained Model for Water Involving a Virtual Site.
Deng, Mingsen; Shen, Hujun
2016-02-01
In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones. PMID:26747089
Efficient Topology-aware Coarse Graining for Synchronization in Directed Networks
Zeng, An
2010-01-01
Coarse graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve the same statistical properties as well as the dynamic behaviors as the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse graining in directed networks lacks of consideration. In this paper, we proposed a Topology-aware Coarse Graining (TCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree-like networks and variants of Barab\\'{a}si-Albert networks, Watts-Strogatz networks and Erd\\"{o}s-R\\'{e}nyi networks, we find our method can effectively preserve the network synchronizability.
Application of phased array techniques to coarse grain components inspection
Ultrasonic inspection of cast stainless steel components from primary and auxiliary cooling circuits of 'French Nuclear Power Plant has to face with major difficulties due to the coarse grained structure of these materials. Attenuation losses and structural noise are encountered, which limits the performances of defect detection ability, mostly in terms of degraded signal-to-noise ratio and poor sensitivity. To overcome such problems, theoretical and experimental studies have been achieved at the French Atomic Energy Commission, with support from the French Institute for Radiological Protection and Nuclear Safety. Experimental studies have been performed over stainless steel specimen of known coarse structure (equi-axial grains and/or elongated grains), containing artificial reflectors (cylindrical holes and electro-eroded surface breaking notches). Those mock-ups have been inspected using contact probes of different array designs (linear or matrix splitting), and using pulse echo or dual-element techniques. Such arrays allow to control the ultrasonic beam so as to investigate different inspection angles and focusing depths. Experiments were carried out using oblique longitudinal waves, using delay laws computed by a specific model, taking account of acoustical and geometrical properties of the probes and the inspected component. In addition, specific reconstruction techniques have been investigated to enhance the signal-to-noise ratio as well as spatial resolution. These techniques are based on beam-forming summation and multi-angle inspections. Experimental results show that such techniques allow to reduce the speckle noise and to optimise the beam resolution. Those increased performances allow to detect and to size small planar defects located at the inner wall of a thick specimen, using corner and tip diffraction echoes. (authors)
STOCK: Structure mapper and online coarse-graining kit for molecular simulations
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DLCGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si
Biological and synthetic membranes: What can be learned from a coarse-grained description?
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special attention to model development and computational techniques. Applications of coarse-grained models to changes of the membrane topology are illustrated with studies of membrane fusion utilizing simulations and self-consistent field theory
Coarse graining the distribution function of cold dark matter - II
Henriksen, R. N.
2004-12-01
We study analytically the coarse- and fine-grained distribution function (DF) established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase-space sheet substructure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best-fitting analytic density function is likely to be provided by a high-order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. As we find that the central flattening is progressive in time, dynamically young systems such as galaxy clusters may well possess a Navarro, Frenk and White type density profile, while primordial dwarf galaxies, for example, are expected to have cores. This progressive flattening is expected to end either in the non-singular isothermal sphere, or in the non-singular metastable polytropic cores; as the DFs associated with each of these arise naturally in the bulk halo during the infall. We suggest, based on previous studies of the evolution of de-stabilized polytropes, that a collisionless system may pass through a family of polytropes of increasing order, finally approaching the limit of the non-singular isothermal sphere, if the `violent' collective relaxation is frequently re-excited by `merger' events. Thus central dominant (cD) galaxies, and indeed all bright galaxies that have grown in this fashion, should be in polytropic states. Our results suggest that no physics beyond that of wave-particle scattering is necessary to explain the nature of dark matter density profiles. However, this may be assisted by the scattering of particles from the centre of the
Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion
Moore, Timothy C; McCabe, Clare
2015-01-01
A coarse-grained water model is developed using multistate iterative Boltzmann inversion. Following previous work, the k-means algorithm is used to dynamically map multiple water molecules to a single coarse-grained bead, allowing the use of structure-based coarse-graining methods. The model is derived to match the bulk and interfacial properties of liquid water and improves upon previous work that used single state iterative Boltzmann inversion. The model accurately reproduces the density and structural correlations of water at 305 K and 1.0 atm, stability of a liquid droplet at 305 K, and shows little tendency to crystallize at physiological conditions. This work also illustrates several advantages of using multistate iterative Boltzmann inversion for deriving generally applicable coarse-grained forcefields.
Atomistic description of binary lanthanoid salt solutions: A coarse-graining approach
The experimental difficulties inherent to the solution chemistry of actinoids and lanthanoids have led to the use of a wide variety of models, from the microscopic to the macroscopic scale, in an attempt to represent their solution properties. Molecular dynamics (MD) simulations, with explicit solvents, have been successfully used to describe the structural characteristics, but the limits on the accessible length and time scales do not allow for an equivalent description of the macroscopic properties. In this study, we propose a multi-scale approach, based on MD simulation results, to study the thermodynamic and structural properties of a series of lanthanoid-chloride aqueous solutions. An inversion procedure, based on the approximate hypernetted chain (HNC) closure and the Stillinger-Lovett sum rules for ionic liquids, is used to obtain the effective ion-ion potentials from MD-generated radial distribution functions (RDF). Implicit solvent Monte Carlo (MC) simulations are then performed to compute the osmotic coefficients of the salt solutions. This coarse-grained strategy provides accurate effective pair potentials for the lanthanoid salts, derived from an atomic model. The method presented here is an attempt to bridge the gap between MD and the thermodynamic properties of solutions that are experimentally measured. (authors)
Effect of concentration and velocity on conveying of coarse grained mixtures in pipe
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Krupička, Jan
Vol. 24. Busan: BEXCO, 2014, s. 66-71. ISBN 978-1-880653-91-3. ISSN 1098-6189. [The 24th international ocean and polar engineering conference. Busan (KR), 15.06.2014-20.06.2014] R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : mixture velocity * particle-water mixtures * coarse-grained mixtures * hydraulic conveying * coarse-grained slurry * pressure drops * pipe inclination * concentration distribution Subject RIV: BK - Fluid Dynamics
Biological and synthetic membranes: What can be learned from a coarse-grained description?
Mueller, Marcus; Katsov, Kirill; Schick, Michael
2006-01-01
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special att...
Effect of concentration and velocity on conveying of coarse grained mixtures in pipe
Vlasák, Pavel; Chára, Zdeněk; Konfršt, Jiří; Krupička, Jan
Vol. 24. Busan : BEXCO, 2014, s. 66-71. ISBN 978-1-880653-91-3. ISSN 1098-6189. [The 24th international ocean and polar engineering conference. Busan (KR), 15.06.2014-20.06.2014] R&D Projects: GA ČR GAP105/10/1574 Institutional support: RVO:67985874 Keywords : mixture velocity * particle-water mixtures * coarse-grained mixtures * hydraulic conveying * coarse-grained slurry * pressure drops * pipe inclination * concentration distribution Subject RIV: BK - Fluid Dynamics
Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.
Li, Min; Zhang, John Zenghui; Xia, Fei
2016-04-12
Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10 000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems. PMID:26930392
Systematic and Simulation-Free Coarse-Graining of Polymer Melts using Soft Potentials
Yang, Delian; Wang, Qiang
2014-03-01
Full atomistic simulations of multi-chain systems are not feasible at present due to their formidable computational requirements. Molecular simulations with coarse-grained models have to be used instead, where each segment represents, for example, the center-of-mass of a group of atoms or real monomers. While atoms interact with hard excluded-volume interactions (e.g., the Lennard-Jones potential) and cannot overlap, the coarse-grained segments can certainly overlap and should therefore interact with soft potentials that allow complete particle overlapping. Coarse-grained models, however, reduce the chain conformational entropy, which plays an essential role in the behavior of polymeric systems. In this work, we use integral-equation theories, instead of molecular simulations, to perform both the structure-based and relative-entropy-based coarse-graining of homopolymer melts, and systematically examine how the coarse-grained soft potential varies with N (the number of segments on each chain) and how well the coarse-grained models reproduce both the structural and thermodynamic properties of the original system. This provides us with a quantitative basis for choosing small N-values that can still capture the chain conformational entropy, a characteristics of polymers.
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.
Tan, Robert K Z; Petrov, Anton S; Harvey, Stephen C
2006-05-01
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily. PMID:22844233
Coarse-graining using the relative entropy and simplex-based optimization methods in VOTCA
Rühle, Victor; Jochum, Mara; Koschke, Konstantin; Aluru, N. R.; Kremer, Kurt; Mashayak, S. Y.; Junghans, Christoph
2014-03-01
Coarse-grained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarse-graining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides a uniform platform for coarse-graining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarse-graining. The methods are illustrated by coarse-graining SPC/E bulk water and a water-methanol mixture. Both CG models reproduce the pair distributions accurately. SYM is supported by AFOSR under grant 11157642 and by NSF under grant 1264282. CJ was supported in part by the NSF PHY11-25915 at KITP. K. Koschke acknowledges funding by the Nestle Research Center.
Stanzione, Francesca; Jayaraman, Arthi
2016-05-01
In-silico design of polymeric biomaterials requires molecular dynamics (MD) simulations that retain essential atomistic/molecular details (e.g., explicit water around the biofunctional macromolecule) while simultaneously achieving large length and time scales pertinent to macroscale function. Such large-scale atomistically detailed macromolecular MD simulations with explicit solvent representation are computationally expensive. One way to overcome this limitation is to use an adaptive resolution scheme (AdResS) in which the explicit solvent molecules dynamically adopt either atomistic or coarse-grained resolution depending on their location (e.g., near or far from the macromolecule) in the system. In this study we present the feasibility and the limitations of AdResS methodology for studying polyethylene glycol (PEG) in adaptive resolution water, for varying PEG length and architecture. We first validate the AdResS methodology for such systems, by comparing PEG and solvent structure with that from all-atom simulations. We elucidate the role of the atomistic zone size and the need for calculating thermodynamic force correction within this AdResS approach to correctly reproduce the structure of PEG and water. Lastly, by varying the PEG length and architecture, we study the hydration of PEG, and the effect of PEG architectures on the structural properties of water. Changing the architecture of PEG from linear to multiarm star, we observe reduction in the solvent accessible surface area of the PEG, and an increase in the order of water molecules in the hydration shells. PMID:27108869
Shi, Ya-Zhou; Wu, Yuan-Yan; Tan, Zhi-Jie
2014-01-01
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (less than or equal to 45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 {\\AA} and an overall minimum RMSD of 1.9 {\\AA} from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ~ 1.0 degrees Celsius of melting temperatures, as compared wi...
On adaptive Markov chain Monte Carlo algorithms
Atchadé, Yves F.; Rosenthal, Jeffrey S.
2005-01-01
We look at adaptive Markov chain Monte Carlo algorithms that generate stochastic processes based on sequences of transition kernels, where each transition kernel is allowed to depend on the history of the process. We show under certain conditions that the stochastic process generated is ergodic, with appropriate stationary distribution. We use this result to analyse an adaptive version of the random walk Metropolis algorithm where the scale parameter σ is sequentially adapted using a Robbins-...
Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles
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.
Computational Study of Uniaxial Deformations in Silica Aerogel Using a Coarse-Grained Model.
Ferreiro-Rangel, Carlos A; Gelb, Lev D
2015-07-01
Simulations of a flexible coarse-grained model are used to study silica aerogels. This model, introduced in a previous study (J. Phys. Chem. C 2007, 111, 15792), consists of spherical particles which interact through weak nonbonded forces and strong interparticle bonds that may form and break during the simulations. Small-deformation simulations are used to determine the elastic moduli of a wide range of material models, and large-deformation simulations are used to probe structural evolution and plastic deformation. Uniaxial deformation at constant transverse pressure is simulated using two methods: a hybrid Monte Carlo approach combining molecular dynamics for the motion of individual particles and stochastic moves for transverse stress equilibration, and isothermal molecular dynamics simulations at fixed Poisson ratio. Reasonable agreement on elastic moduli is obtained except at very low densities. The model aerogels exhibit Poisson ratios between 0.17 and 0.24, with higher-density gels clustered around 0.20, and Young's moduli that vary with aerogel density according to a power-law dependence with an exponent near 3.0. These results are in agreement with reported experimental values. The models are shown to satisfy the expected homogeneous isotropic linear-elastic relationship between bulk and Young's moduli at higher densities, but there are systematic deviations at the lowest densities. Simulations of large compressive and tensile strains indicate that these materials display a ductile-to-brittle transition as the density is increased, and that the tensile strength varies with density according to a power law, with an exponent in reasonable agreement with experiment. Auxetic behavior is observed at large tensile strains in some models. Finally, at maximum tensile stress very few broken bonds are found in the materials, in accord with the theory that only a small fraction of the material structure is actually load-bearing. PMID:26039801
Coarse-graining the dynamics of network evolution: the rise and fall of a networked society
We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse-grained models can be developed. We illustrate our approach through a particular social network model: the ‘rise and fall’ of a networked society (Marsili M et al 2004 Proc. Natl Acad. Sci. USA 101 1439). We implement our low-dimensional description computationally using the equation-free approach and show how it can be used to (i) accelerate simulations and (ii) extract system-level stability/bifurcation information from the detailed dynamic model. We discuss other system-level tasks that can be enabled through such a computer-assisted coarse-graining approach. (paper)
The geometry of generalized force matching in coarse-graining and related information metrics
Kalligiannaki, Evangelia; Katsoulakis, Markos A; Plechac, 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 on 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 in order 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 syst...
A unified data representation theory for network visualization, ordering and coarse-graining
Kovács, István A; Csermely, Peter
2014-01-01
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of huge data sets in science, by reve...
Iig, Patrick
2011-01-01
Complex fluids, such as polymers, colloids, liquid-crystals etc., show intriguing viscoelastic properties, due to the complicated interplay between flow-induced structure formation and dynamical behavior. Starting from microscopic models of complex fluids, a systematic coarse-graining method is presented that allows us to derive closed-form and thermodynamically consistent constitutive equations for such fluids. Essential ingredients of the proposed approach are thermodynamically guided simulations within a consistent coarse-graining scheme. In addition to this new type of multiscale simulations, we reconstruct the building blocks that constitute the thermodynamically consistent coarse-grained model. We illustrate the method for low-molecular polymer melts, which are subject to different imposed flow fields like planar shear and different elongational flows. The constitutive equation for general flow conditions we obtain shows rheological behavior including shear thinning, normal stress differences, and elongational viscosities in good agreement with reference results. PMID:21678766
Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study
Yang, Delian; Wang, Qiang
2015-02-01
We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of Nm 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 < Nm.
Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study
We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of Nm 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 < Nm
Effect of coarse-grain contents on strength and fracture toughness of fine-grained graphite
Takahashi, Tsuneo; Ishihara, Masahiro; Baba, Shinichi; Hayashi, Kimio [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment; Arai, Taketoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Konishi, Takashi [Toyo Tanso Co. Ltd., Osaka (Japan)
2001-03-01
To investigate the effect of the coarse-grain content on strength and fracture toughness of fine-grained graphite, bending and fracture toughness tests were conducted for specimens with different contents of coarse-grains. In the study the standard specimen was made of fine-grained isotropic graphite (IG-11) with a mean grain size of 20 {mu}m, and two kinds of different grain size specimens were prepared by 20 and 40% mixing of coarse-grains with a mean grain size of 125 {mu}m. The bending test revealed a strength increase for the 40% specimen with a small deviation compared with that for the standard specimen. As for the fracture toughness, two kinds of fracture toughnesses were investigated on the basis of the crack initiation load and the maximum applied load. The initiation load based fracture toughness for the 20% and 40% specimens was higher than that for the standard one; however, the difference for the 20% and 40% specimens was not observed clearly. These results suggest that the fracture toughness tends to saturate at a relatively low coarse-grain content, which is below 20% in the present study. On the other hand, the maximum load based fracture toughness increased with increasing coarse-grain content; thus the difference with different coarse-grain contents was observed. Moreover, the present authors applied a probabilistic strength model to the bending test results, using the pore size distributions obtained by image analysis of microstructures observed by optical microscopy. The model had been proposed by Burchell under uniaxial stress conditions, in consideration of pore size distributions. The prediction by the present model indicated a good correlation with the experimental results. (author)
Effect of coarse-grain contents on strength and fracture toughness of fine-grained graphite
To investigate the effect of the coarse-grain content on strength and fracture toughness of fine-grained graphite, bending and fracture toughness tests were conducted for specimens with different contents of coarse-grains. In the study the standard specimen was made of fine-grained isotropic graphite (IG-11) with a mean grain size of 20 μm, and two kinds of different grain size specimens were prepared by 20 and 40% mixing of coarse-grains with a mean grain size of 125 μm. The bending test revealed a strength increase for the 40% specimen with a small deviation compared with that for the standard specimen. As for the fracture toughness, two kinds of fracture toughnesses were investigated on the basis of the crack initiation load and the maximum applied load. The initiation load based fracture toughness for the 20% and 40% specimens was higher than that for the standard one; however, the difference for the 20% and 40% specimens was not observed clearly. These results suggest that the fracture toughness tends to saturate at a relatively low coarse-grain content, which is below 20% in the present study. On the other hand, the maximum load based fracture toughness increased with increasing coarse-grain content; thus the difference with different coarse-grain contents was observed. Moreover, the present authors applied a probabilistic strength model to the bending test results, using the pore size distributions obtained by image analysis of microstructures observed by optical microscopy. The model had been proposed by Burchell under uniaxial stress conditions, in consideration of pore size distributions. The prediction by the present model indicated a good correlation with the experimental results. (author)
Coevolution Based Adaptive Monte Carlo Localization (CEAMCL)
Luo Ronghua; Hong Bingrong
2004-01-01
An adaptive Monte Carlo localization algorithm based on coevolution mechanism of ecological species is proposed. Samples are clustered into species, each of which represents a hypothesis of the robot's pose. Since the coevolution between the species ensures that the multiple distinct hypotheses can be tracked stably, the problem of premature convergence when using MCL in highly symmetric environments can be solved. And the sample size can be adjusted adaptively over time according to the unce...
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
Jonikas, Magdalena A; RADMER, RANDALL J.; Altman, Russ B
2009-01-01
Motivation: 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. Results: 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 ...
A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation
Xicheng Wang; Honglin Li; Fang Bai; Junfeng Gu
2012-01-01
Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal int...
Competition of Two Types of Correlations in Coarse-Grained Natural Written Texts
Melnyk, S S; Yampolskii, V A; Golick, V A
2004-01-01
A theory of additive Markov chains with long-range memory is used for a description of correlation properties of literary texts. The coarse-grained naturally written texts are shown to be strongly correlated sequences that possess antipersistent properties at small distances (in the region of grammatical rules action, $L 300$). For some concrete examples of literary texts, a memory function is constructed and its power-law behavior is revealed at long distances. This behavior is shown to be a cause for self-similarity of coarse-grained texts with respect to the decimation procedure.
Glade, R.; Jerolmack, D. J.; Pelletier, J. D.
2014-12-01
Coarse-grained ripples, also known as "megaripples," are large sand ripples found in both aeolian and aquatic environments on Earth, and are common on Mars. The formation and morphology of coarse-grained ripples are not as well understood as more common splash ripples. Current understanding suggests that formative wind speeds are above the saltation threshold for the fine grains, but below this threshold for coarse grains found on the crests, such that they creep. Based on this idea, we hypothesize that wind speeds above this coarse-grain saltation threshold will destroy the ripples. We further hypothesize that these ripples do not have an equilibrium size; rather, their size is related to the persistence of formative winds in a given direction. To test this model, we studied windblown coarse-grained ripples in White Sands, New Mexico. Terrestrial LiDAR was used to obtain high resolution ripple morphology and migration over a three month period. Wind velocity profiles and concurrent saltating grain size data were collected during a wind storm to directly relate modes of transport to particle size and wind stress. These local data were used to calibrate wind records from a nearby meteorological station to estimate local fluid stress using a long-term record. LiDAR data indicate that these ripples were destroyed and reoriented between March and June 2013, while the wind record shows that the coarse-grain saltation threshold was indeed exceeded during this time. Morphological analysis indicates that the lee slope of these ripples is set by saltation impact - similar to splash ripples - but that height, wavelength and stoss slope are not related to instantaneous transport conditions. The historical wind record also shows that the range of wind directions decreases rapidly with increasing speed, restricting strong winds to a narrow range of direction. From these results we explore the idea that coarse-grained ripples are typically larger and less frequently destroyed
Coevolution Based Adaptive Monte Carlo Localization (CEAMCL
Luo Ronghua
2008-11-01
Full Text Available An adaptive Monte Carlo localization algorithm based on coevolution mechanism of ecological species is proposed. Samples are clustered into species, each of which represents a hypothesis of the robot's pose. Since the coevolution between the species ensures that the multiple distinct hypotheses can be tracked stably, the problem of premature convergence when using MCL in highly symmetric environments can be solved. And the sample size can be adjusted adaptively over time according to the uncertainty of the robot's pose by using the population growth model. In addition, by using the crossover and mutation operators in evolutionary computation, intra-species evolution can drive the samples move towards the regions where the desired posterior density is large. So a small size of samples can represent the desired density well enough to make precise localization. The new algorithm is termed coevolution based adaptive Monte Carlo localization (CEAMCL. Experiments have been carried out to prove the efficiency of the new localization algorithm.
Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case
Rossi, G.; Monticelli, L.; Puisto, S. R.;
2011-01-01
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...
DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model
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...
Diffusion-Based Coarse Graining in Hybrid Continuum--Discrete Solvers: Applications in CFD--DEM
Sun, Rui
2014-01-01
In this work, a coarse graining method previously proposed by the authors based on solving diffusion equations is applied to CFD--DEM simulations, where coarse graining is used to obtain solid volume fraction, particle phase velocity, and fluid--particle interaction forces. By examining the conservation requirements, the variables to solve diffusion equations for in CFD--DEM simulations are identified. The algorithm is then implemented to a CFD--DEM solver based on OpenFOAM and LAMMPS, the former being a general-purpose, three-dimensional CFD solver based on unstructured meshes. Numerical simulations are performed for a fluidized bed by using the CFD--DEM solver with the diffusion-based coarse graining algorithm. Converged results are obtained on successively refined meshes, even for meshes with cell sizes comparable to or smaller than the particle diameter. This is a critical advantage of the proposed method over many existing coarse graining methods, and would be particularly valuable when small cells are r...
Free-energy coarse-grained potential for C{sub 60}
Edmunds, D. M., E-mail: david.edmunds09@imperial.ac.uk; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C. [Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom)
2015-10-28
We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C{sub 60}. Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures.
Path-space variational inference for non-equilibrium coarse-grained systems
Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr
2016-06-01
In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.
Molecular Dynamics Simulation of Coarse-Grain Model of Silicon Functionalized Graphene
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.
Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks
Cieplak, Marek; Thompson, Damien
2008-06-01
A coarse-grained molecular dynamics (MD) model is developed to study the multivalent, or multisite, binding of small functionalized dendrimer molecules to β-cyclodextrin-terminated self-assembled monolayers, the so-called ``molecular printboards'' used to print ``ink'' molecules on surfaces with a high degree of positional control and specificity. Some current and future bionanotechnology applications are in the creation of nanoparticle assemblies, directed protein assembly, platforms for biosensing, and cell:surface attachment. The coarse-grained model allows us to probe up to microsecond timescales and model ink diffusion, crucial for the application of the printboard in, for example, medical diagnostics. Recent all-atom MD simulations identified and quantified the molecular strain limiting the stability of nanopatterns created with small dendrimer inks, and explained the different patterns obtained experimentally with different dendrimer inks. In the present work, the all-atom simulations are ``scaled up'' to longer timescales via coarse graining, without incurring significant additional computational expense, and, crucially, without significant loss in atom-scale detail, the coarse-grained MD simulations yielding properties similar to those obtained from the all-atom simulations. The anchoring of the ink molecules to the monolayer is of multivalent nature and the degree of multivalency shows a sharp dependence on temperature, control of temperature thus providing a further operational ``switch'' for directed molecular assembly. The computational protocol developed can, in principle, be extended to model any multivalent assembly, for example, virus-cell complexation.
Chemically transferable coarse-grained potentials from conditional reversible work calculations.
Brini, E; van der Vegt, N F A
2012-10-21
The representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of n-alkanes, the coarse-grained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a free-energy-based coarse-graining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRW-CG potentials may be readily obtained from a single simulation of the liquid state using the free energy perturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules. PMID:23083154
Coarse-grain model for internal energy excitation and dissociation of molecular nitrogen
Graphical abstract: A rovibrational collisional coarse-grain model allows to reduce a detailed mechanism for the internal energy excitation and dissociation processes behind a strong shockwave in nitrogen. Highlights: ► A rovibrational coarse-grain model is developed for nitrogen. ► In this model, energy levels of an ab initio database are lumped into bins. ► Rate coefficients are averaged assuming a uniform distribution within each bin. ► The coarse-grain model is used to study a 1D strong shockwave. ► Relaxation and dissociation processes are accurately described using a few equations. - Abstract: A rovibrational collisional coarse-grain model has been developed to reduce a detailed mechanism for the internal energy excitation and dissociation processes behind a strong shockwave in a nitrogen flow. The rovibrational energy levels of the electronic ground state of the nitrogen molecule were lumped into a smaller number of bins. The reaction rate coefficients of an ab initio database developed at NASA Ames Research Center were averaged for each bin based on a uniform distribution of the energy levels within the bin. The results were obtained by coupling the Master equation for the reduced mechanism with a one-dimensional flow solver for conditions expected for reentry into Earth’s atmosphere at 10 km/s. The coarse-grain collisional model developed allow us to describe accurately the internal energy relaxation and dissociation processes based on a smaller number of equations, as opposed to existing reduced models assuming thermal equilibrium between the rotational and translational energy modes.
Leonard, T.; Lander, B.; Seifert, U. [II. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Speck, T. [Institut für Theoretische Physik II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany)
2013-11-28
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for the work still hold albeit for a different, apparent, change of free energy.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations
Microstructure and Property of Coarse Grain HAZ X80 Pipeline Steel
ZHOU Yun; XUE Xiao-huai; QIAN Bai-nian; LI Jing-li; SHAN Yi-Yin; LOU Song-nian
2005-01-01
The coarse grain HAZ microstructure and property of X80 pipeline steel with different carbon content was investigated. The weld thermal simulation test was carried out on Gleeble 1500 thermal mechanical test machine. The Charpy tests were completed at -20 ℃ for evaluating the toughness of coarse grain heat affected zone (CGHAZ). The microstructure was examined by optical microscope (OM) and transmission electron microscopy (TEM), and the austenite constituent was quantified by X-ray diffraction. The results showed that the ultra-low carbon can improve the toughness of CGHAZ by suppressing the formation of carbide, decreasing the martensite austenite (M-A) constituent and increasing the residual austenite in the M-A.
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers
Deformation nanotwins in coarse-grained aluminum alloy at ambient temperature and low strain rate
In order to reveal the possible occurrence of deformation twins in coarse-grained aluminum/aluminum alloy at normal experimental conditions, a 5A02-O aluminum alloy with coarse grains was compressed quasi-statically to various plastic strains at ambient temperature, followed by high-resolution transmission electron analysis. The results revealed some long streaks produced by the thin plate-like structure with 2 atomic planes thick in the specimen undergoing a large strain, while under a relatively small plastic strain, the striped characteristics disappeared. The fast Fourier transform and theoretical analysis have shown that these long streaks are nanotwins, derived from the overlapping of stacking fault ribbons formed by Shockley partial dislocation on adjacent slip planes, which are triggered by the large plastic strain
Deformation nanotwins in coarse-grained aluminum alloy at ambient temperature and low strain rate
Xu, Zhu; Li, Ning, E-mail: hslining@mail.hust.edu.cn; Jiang, Huawen; Liu, Lin
2015-01-05
In order to reveal the possible occurrence of deformation twins in coarse-grained aluminum/aluminum alloy at normal experimental conditions, a 5A02-O aluminum alloy with coarse grains was compressed quasi-statically to various plastic strains at ambient temperature, followed by high-resolution transmission electron analysis. The results revealed some long streaks produced by the thin plate-like structure with 2 atomic planes thick in the specimen undergoing a large strain, while under a relatively small plastic strain, the striped characteristics disappeared. The fast Fourier transform and theoretical analysis have shown that these long streaks are nanotwins, derived from the overlapping of stacking fault ribbons formed by Shockley partial dislocation on adjacent slip planes, which are triggered by the large plastic strain.
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. PMID:24718295
Haxton, Thomas K; Zuckermann, Ronald N; Whitelam, Stephen
2014-01-01
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale dynamic processes in biology and materials science, understanding the details of this supramolecular assembly process requires a modeling approach that captures behavior on a wide range of length and time scales, from those on which individual sidechains fluctuate to those on which assemblies of polymers evolve. Here we demonstrate that a new coarse-grained modeling approach is accurate and computationally efficient enough to do so. Our approach uses only a minimal number of coarse-grained sites, but retains independently fluctuating orientational degrees of freedom for each site. These orientational degrees of freedom allow us to accurately parameterize both bonded and nonbonded interactions, and to generate all-atom configurations with sufficient accuracy to perform atomic sca...
Annealing behavior of coarse-grained titanium deformed by cold rolling
This work describes the annealing behavior of coarse-grained titanium deformed by cold rolling. A longitudinal section of a high-purity coarse-grained titanium ingot obtained by double electron beam melting (EBM) was cold rolled to thickness reductions varying from 10 to 70%. Vacuum annealing was performed at 500, 700 and 800 deg. C for 1 h (α-phase field). Microstructural characterization was performed in both cold rolled and annealed specimens using light optical microscopy (LOM), scanning electron microscopy (SEM), electron backscattered diffraction (EBSD) and Vickers microhardness testing. Orientation effects associated with the coarse initial grain structure of oligocrystalline titanium were observed during annealing. In certain regions the microstructure of annealed titanium consists of alternating bands of recrystallized grains with local variations in grain size and texture and a few elongated areas marking the presence of individual grains softened by recovery
Self assembly of peptides near or within membranes using coarse grained MD simulations
Coarse grain modeling has recently emerged as an alternative to classical atomistic simulations in the study of spontaneous self assembly and structural organization of complex molecular systems. For surfactant and lipid systems, it was shown to allow, under appropriate conditions, in-silico self assembly of a variety of architectures. Recently, this approach has been extended to peptides for which force fields allowing self assembly of mixed peptides-lipid systems were proposed. Here we introduce elements of a coarse grained force field that accurately describe self assembly of hydrophobic cyclic peptides [Trp-Leu]4 and their reorganization within lipid membranes to form transmembrane channels in agreement with experiments. Extension to hydrophobic helical transmembrane, and amphipatic helical antimicrobial peptides show that the model is robust enough to constitute a building block for more complete and appropriate force field describing peptide interactions with membranes.
Moving beyond Watson-Crick models of coarse grained DNA dynamics
Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.
2011-11-01
DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.
Turbulent channel flow simulations using a coarse-grained extension of the Lattice Boltzmann method
Amati, G; Benzi, R; Amati, Giorgio; Succi, Sauro; Benzi, Roberto
1996-01-01
A coarse-grained version of the Lattice Boltzmann (LB) method is developed with the intent of enhancing its geometrical flexibility so as to be able to tackle a wider class of flows of engineering interest. To this purpose, the original uniform LB technique is combined with standard finite-volume techniques based upon a blend of piecewise constant and piecewise linear interpolation schemes. A series of validation tests for the three dimensional channel flow with one-dimensional (cross-channel) statistical behaviour are presented. The main conclusion is that, although the method does indeed mark a significant stride forward with respect to the original uniform LB scheme, better interpolation schemes should be developed before the coarse-grain LB can become fully competitive with modern CFD schemes.
Ito, Hiroaki; Shimokawa, Naofumi
2016-01-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the p...
MT-ADRES: multi-threading on coarse-grained reconfigurable architecture
Wu, Kehuai; Kanstein, Andreas; Madsen, Jan;
2008-01-01
The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high......-ILP architectures achieve only low parallelism when executing partially sequential code segments, which is also known as Amdahl's law, this article proposes to extend ADRES to MT-ADRES (multi-threaded ADRES) to also exploit thread-level parallelism. On MT-ADRES architectures, the array can be partitioned...
Coarse-Grained Molecular Dynamics Simulation of a Red Blood Cell
Jiang, Li-Guo; Wu, Heng-An; Zhou, Xiao-Zhou; Wang, Xiu-Xi
2010-02-01
A worm-like chain model based on a spectrin network is employed to study the biomechanics of red blood cells. Coarse-grained molecular dynamics simulations are performed to obtain a stable configuration free of external loadings. We also discuss the influence of two parameters: the average bending modulus and the persistence length. The change in shape of a malaria-infected red blood cell can contribute to the change in its molecular-based structure. As the persistence length of the membrane network in the infected red blood cell decreases, the deformability decreases and the biconcave shape is destroyed. The numerical results are comparable with previously reported experimental results. The coarse-grained model can be used to study the relationship between macro-mechanical properties and molecular-scale structures of cells.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
Najafi, Saeed; Potestio, Raffaello, E-mail: potestio@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)
2015-12-28
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Wei, Zonghui [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Luijten, Erik, E-mail: luijten@northwestern.edu [Graduate Program in Applied Physics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208 (United States); Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208 (United States); Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208 (United States)
2015-12-28
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
Premelting, fluctuations, and coarse-graining of water-ice interfaces
Limmer, David T., E-mail: dlimmer@princeton.edu [Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey 08540 (United States); Chandler, David [Department of Chemistry, University of California, Berkeley, California 94609 (United States)
2014-11-14
Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
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
Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
2015-01-01
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop accurate coarse-grained simulation models that can reach these time scales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0 and 40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudobond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the “angle-corrected model”) slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other
Nguyen, O. T.; Ortiz, M.
2001-01-01
We present two approaches for coarse-graining interplanar potentials and determining the corresponding macroscopic cohesive laws based on energy relaxation and the renormalization group. We analyze the cohesive behavior of a large---but finite---number of interatomic planes and find that the macroscopic cohesive law adopts a universal asymptotic form. The universal form of the macroscopic cohesive law is an attractive fixed point of a suitably-defined renormalization-group transformation.
Dalgıçdir, Cahit; Şensoy, Özge; Sayar, Mehmet; Peter, Christine
2013-01-01
A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition Cahit Dalgicdir, Ozge Sensoy, Christine Peter, and Mehmet Sayar Citation: The Journal of Chemical Physics 139, 234115 (2013); doi: 10.1063/1.4848675 View online: http://dx.doi.org/10.1063/1.4848675 View Table of Contents: http://scitation.aip.org/content/aip/journal/jcp/139/23?ver=pdfcov Published by the AIP Publishing Articles you may be interested in...
Schnabel, Stefan; Bachmann, Michael; Janke, Wolfhard
2007-01-01
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well ...
Theoretical coarse-graining approach to bridge length scales in diblock copolymer liquids
Sambriski, E. J.; Guenza, M. G.
2007-01-01
A microscopic theory for coarse graining diblock copolymers into dumbbells of interacting soft colloidal particles has been developed, based on the solution of liquid-state integral equations. The Ornstein-Zernike equation is solved to provide a mesoscopic description of the diblock copolymer system at the level of block centers of mass, and at the level of polymer centers of mass. Analytical forms of the total correlation functions for block-block, block-monomer, and center-of-mass pairs are...
Coarse-graining complex dynamics: Continuous Time Random Walks vs. Record Dynamics
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 distribution of the waiting time between consecutive jumps. We first argue that CTRW are inadequate to describe macroscopic relaxation processes for three reasons: macroscopic variables are not self-averaging...
Coarse-graining complex dynamics:Continuous Time Random Walks vs. Record Dynamics
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 distribution of the waiting time between consecutive jumps. We first argue that CTRW are inadequate to describe macroscopic relaxation processes for three reasons: macroscopic variables are not self-averaging...
Flow behaviour and structure of coarse-grained slurries in pipe
Vlasák, Pavel; Kysela, Bohuš; Chára, Zdeněk
Madrid: International Freight Pipeline Society, 2011, s. 144-153. ISBN 978-84-96398-51-1. [ International Freight Pipeline Society Symposium /14./. Madrid (ES), 28.06.2011-01.07.2011] R&D Projects: GA ČR(CZ) GAP105/10/1574 Institutional research plan: CEZ:AV0Z20600510 Keywords : coarse-grained slurry * pressure drop * turbulent flow * flow structure Subject RIV: BK - Fluid Dynamics
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Andrzej Koliński; Maksim Kouza; Dominik Gront; Sebastian Kmiecik; Jacek Wabik
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combi...
Predicting RNA 3D structure using a coarse-grain helix-centered model
Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L
2015-01-01
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sampl...
Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation
Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.
2013-01-01
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as t...
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
2014-01-01
In this work, we investigate aspects of the electron, muon and tau gyromagnetic ratios (g-factor) in a fractional coarse-grained scenario, by adopting a Modified Riemann-Liouville (MRL) fractional calculus. We point out the possibility of mapping the experimental values of the specie's g-factors into a theoretical parameter which accounts for fractionality, without computing higher-order QED calculations. We wish to understand whether the value of (g-2) may be traced back to a fractionality o...
Stretching and twisting of the DNA duplexes in coarse grained dynamical models
Niewieczerzał, Szymon; Cieplak, Marek
2008-01-01
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behavior and, in particular, lead to a torque-force phase diagrams qualitatively consistent with experiments and all-atom simulations.
Choon-Peng Chng; Lee-Wei Yang
2008-01-01
Abstract: In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the ...
Flow structure of coarse-grained slurry in a horizontal pipe
Vlasák, Pavel; Kysela, Bohuš; Chára, Zdeněk
2012-01-01
Roč. 60, č. 2 (2012), s. 115-124. ISSN 0042-790X R&D Projects: GA ČR GAP105/10/1574 Institutional research plan: CEZ:AV0Z20600510 Keywords : coarse-grained slurry * turbulent flow * pressure drop * velocity distribution * flow structure * concentration effect Subject RIV: BK - Fluid Dynamics Impact factor: 0.653, year: 2012
Coarse-grained simulation of a real-time process control network under peak load
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
Sandim, H.; Raabe, D.
2004-01-01
Orientation effects concerning grain subdivision and further annealing behavior of three neighboring grains were observed in 80% cold-rolled coarse-grained niobium. The present study which was conducted as a cooperation on the basis of DAAD and CAPES funding attempts to clarify the microstructural evolution of deformed niobium and the differences in terms of stored energy (boundary distribution) using high-resolution electron backscattering diffraction (FE-EBSD).
Procedures for Residual Stress Analysis in Textured and in Coarse Grained Materials
Reimers, W.; Dupke, R.
1995-01-01
For the investigation of residual stresses by means of X-ray diffraction, special procedures for the registration and evaluation of the experimental strain data are necessary for textured and coarse grained materials. In both cases inhomogeneous diffraction intensity patterns are present which lead to the formation of intensity poles or even to Bragg reflections. Such experimental findings indicate also that the material properties within the investigated gauge volume are anisotropic so that ...
Trément, Sébastien; Schnell, Benoît; Petitjean, Laurent; Couty, Marc; Rousseau, Bernard
2014-04-01
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems. PMID:24712786
Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)
2014-04-07
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems
Model reduction for agent-based social simulation: Coarse-graining a civil violence model
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).
Lyubimov, I. Y.; Guenza, M. G.
2013-03-01
The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-polybutadiene melts where each chain is described as a soft interacting colloidal particle. The rescaling formalism accounts for the corrections in the dynamics due to the change in entropy and the change in friction that are a consequence of the coarse-graining procedure. By including these two corrections the dynamics is rescaled to reproduce the realistic dynamics of the system described at the atomistic level. The rescaled diffusion coefficient obtained from mesoscale simulations of coarse-grained cis-1,4-polybutadiene melts shows good agreement with data from united atom simulations performed by Tsolou et al. [Macromolecules 38, 1478 (2005)], 10.1021/ma0491210. The derived monomer friction coefficient is used as an input to the theory for cooperative dynamics that describes the internal dynamics of a polymer moving in a transient regions of slow cooperative motion in a liquid of macromolecules. Theoretically predicted time correlation functions show good agreement with simulations in the whole range of length and time scales in which data are available.
Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid
Daehyeon Kim
2014-02-01
Full Text Available In order to design civil structures that are supported by soils, the shear strength parameters of soils are required. Due to the large particle size of coarse-grained soils, large direct shear tests should be performed. In this study, large direct shear tests on three types of coarse grained soils (4.5 mm, 7.9 mm, and 15.9 mm were performed to evaluate the effects of particle size on the shear behavior of coarse grained soils with/without geogrid reinforcements. Based on the direct shear test results, it was found that, in the case of no-reinforcement, the larger the maximum particle size became, the larger the friction angle was. Compared with the no-reinforcement case, the cases reinforced with either soft geogrid or stiff geogrid have smaller friction angles. The cohesion of the soil reinforced with stiff geogrid was larger than that of the soil reinforced with soft geogrid. The difference in the shear strength occurs because the case with a stiff geogrid has more soil to geogrid contact area, leading to the reduction in interlocking between soil particles.
Coarse-grained molecular dynamics studies of cluster-bombarded benzene crystals
As high-energy cluster projectile beams become standard analysis probes for SIMS, simulating larger crystals is now a requirement for the modeling community due to the large sputtering yields. As crystals get larger, computer resources become a limitation. Even though computer technology has evolved to include large memory systems and fast processors, there are still issues with having sufficient resources to run a calculation. This manuscript reports a method of studying a full crystal of benzene after impact with a 500 eV C60 projectile using a coarse-grained model. The potentials developed for this model incorporate the C-H bond of benzene into a single coarse-grained bead. This coarse-grained method has several advantages over atomistic models-the amount of time to perform these calculations has been drastically reduced and the potentials for this sample are pair-wise additive potentials. A discussion is made as to how these results compare to those obtained with fully atomistic calculations using the AIREBO potential
Multiscale simulation of thin-film lubrication: Free-energy-corrected coarse graining
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), 10.1063/1.1806811]. 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.
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.
Quantitative comparison of alternative methods for coarse-graining biological networks
Bowman, Gregory R.; Meng, Luming; Huang, Xuhui
2013-09-01
Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results.
Choon-Peng Chng
2008-01-01
Full Text Available Abstract: In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CGMD approach, to be introduced in the second paper of this two-part series.
Yang, Lee-Wei; Chng, Choon-Peng
2008-01-01
In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764
Strom, Alexander M.; Fehling, Samuel C.; Bhattacharyya, Sudeep; Hati, Sanchita
2014-01-01
Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthet...
Xu, Peijun; Shen, Hujun; Yang, Lu; Ding, Yang; Li, Beibei; Shao, Ying; Mao, Yingchen; Li, Guohui
2013-02-01
Coarse-grained studies of CH(3)SH, CH(3)CHO and CHCl(3) liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen. PMID:22961621
Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.
Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.
2010-09-01
This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and
Vögele, Martin [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany); Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M. (Germany); Holm, Christian; Smiatek, Jens, E-mail: smiatek@icp.uni-stuttgart.de [Institute for Computational Physics, University of Stuttgart, Stuttgart (Germany)
2015-12-28
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
Vögele, Martin; Holm, Christian; Smiatek, Jens
2015-12-01
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
Spiriti, Justin; Zuckerman, Daniel M.
2015-12-01
Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As an alternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for small rigid molecules or molecular fragments [S. Lettieri and D. M. Zuckerman, J. Comput. Chem. 33, 268-275 (2012); J. Spiriti and D. M. Zuckerman, J. Chem. Theory Comput. 10, 5161-5177 (2014)]. We treat proteins as rigid and construct distance and orientation-dependent tables of the interaction energy between them. Arbitrarily detailed interactions may be incorporated into the tables, but as a proof-of-principle, we tabulate a simple α-carbon Gō-like model for interactions between dimeric subunits of the hepatitis B viral capsid. This model is significantly more structurally realistic than previous models used in capsid assembly studies. We are able to increase the speed of Monte Carlo simulations by a factor of up to 6700 compared to simulations without tables, with only minimal further loss in accuracy. To obtain further enhancement of sampling, we combine tabulation with the weighted ensemble (WE) method, in which multiple parallel simulations are occasionally replicated or pruned in order to sample targeted regions of a reaction coordinate space. In the initial study reported here, WE is able to yield pathways of the final ˜25% of the assembly process.
Coarse-grained treatment of the self-assembly of colloids suspended in a nematic host phase.
Püschel-Schlotthauer, Sergej; Stieger, Tillmann; Melle, Michael; Mazza, Marco G; Schoen, Martin
2016-01-14
The complex interplay of molecular scale effects, nonlinearities in the orientational field and long-range elastic forces makes liquid-crystal physics very challenging. A consistent way to extract information from the microscopic, molecular scale up to the meso- and macroscopic scale is still missing. Here, we develop a hybrid procedure that bridges this gap by combining extensive Monte Carlo (MC) simulations, a local Landau-de Gennes theory, classical density functional theory, and finite-size scaling theory. As a test case to demonstrate the power and validity of our novel approach we study the effective interaction among colloids with Boojum defect topology immersed in a nematic liquid crystal. In particular, at sufficiently small separations colloids attract each other if the angle between their center-of-mass distance vector and the far-field nematic director is about 30°. Using the effective potential in coarse-grained two-dimensional MC simulations we show that self-assembled structures formed by the colloids are in excellent agreement with experimental data. PMID:26477506
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.
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). PMID:27566318
Padding, J. T.; Louis, A. A.
2006-09-01
We describe in detail how to implement a coarse-grained hybrid molecular dynamics and stochastic rotation dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The importance of carefully tuning the simulation parameters to correctly resolve the multiple time and length scales of this problem is emphasized. We systematically analyze how our coarse-graining scheme resolves dimensionless hydrodynamic numbers such as the Reynolds number Re, which indicates the importance of inertial effects, the Schmidt number Sc, which indicates whether momentum transport is liquidlike or gaslike, the Mach number, which measures compressibility effects, the Knudsen number, which describes the importance of noncontinuum molecular effects, and the Peclet number, which describes the relative effects of convective and diffusive transport. With these dimensionless numbers in the correct regime the many Brownian and hydrodynamic time scales can be telescoped together to maximize computational efficiency while still correctly resolving the physically relevant processes. We also show how to control a number of numerical artifacts, such as finite-size effects and solvent-induced attractive depletion interactions. When all these considerations are properly taken into account, the measured colloidal velocity autocorrelation functions and related self-diffusion and friction coefficients compare quantitatively with theoretical calculations. By contrast, these calculations demonstrate that, notwithstanding its seductive simplicity, the basic Langevin equation does a remarkably poor job of capturing the decay rate of the velocity autocorrelation function in the colloidal regime, strongly underestimating it at short times and strongly overestimating it at long times. Finally, we discuss in detail how to map the parameters of our method onto physical systems and from this extract more general lessons—keeping in mind that there
A. V. Milovanov
2000-01-01
Full Text Available The concept of the generalized entropy is analyzed, with the particular attention to the definition postulated by Tsallis [J. Stat. Phys. 52, 479 (1988]. We show that the Tsallis entropy can be rigorously obtained as the solution of a nonlinear functional equation; this equation represents the entropy of a complex system via the partial entropies of the subsystems involved, and includes two principal parts. The first part is linear (additive and leads to the conventional, Boltzmann, definition of entropy as the logarithm of the statistical weight of the system. The second part is multiplicative and contains all sorts of multilinear products of the partial entropies; inclusion of the multiplicative terms is shown to reproduce the generalized entropy exactly in the Tsallis sense. We speculate that the physical background for considering the multiplicative terms is the role of the long-range correlations supporting the "macroscopic" ordering phenomena (e.g., formation of the "coarse-grained" correlated patterns. We prove that the canonical distribution corresponding to the Tsallis definition of entropy, coincides with the so-called "kappa" redistribution which appears in many physical realizations. This has led us to associate the origin of the "kappa" distributions with the "macroscopic" ordering ("coarse-graining" of the system. Our results indicate that an application of the formalism based on the Tsallis notion of entropy might actually have sense only for the systems whose statistical weights, Ω, are relatively small. (For the "coarse-grained" systems, the weight omega could be interpreted as the number of the "grains". For large Ω (i.e., Ω -> ∞, the standard statistical mechanical formalism is advocated, which implies the conventional, Boltzmann definition of entropy as ln Ω.
Ramanan, B; Holmes, W M; Sloan, W T; Phoenix, V R
2012-01-01
Quantifying nanoparticle (NP) transport inside saturated porous geological media is imperative for understanding their fate in a range of natural and engineered water systems. While most studies focus upon finer grained systems representative of soils and aquifers, very few examine coarse-grained systems representative of riverbeds and gravel based sustainable urban drainage systems. In this study, we investigated the potential of magnetic resonance imaging (MRI) to image transport behaviors of nanoparticles (NPs) through a saturated coarse-grained system. MRI successfully imaged the transport of superparamagnetic NPs, inside a porous column composed of quartz gravel using T(2)-weighted images. A calibration protocol was then used to convert T(2)-weighted images into spatially resolved quantitative concentration maps of NPs at different time intervals. Averaged concentration profiles of NPs clearly illustrates that transport of a positively charged amine-functionalized NP within the column was slower compared to that of a negatively charged carboxyl-functionalized NP, due to electrostatic attraction between positively charged NP and negatively charged quartz grains. Concentration profiles of NPs were then compared with those of a convection-dispersion model to estimate coefficients of dispersivity and retardation. For the amine functionalized NPs (which exhibited inhibited transport), a better model fit was obtained when permanent attachment (deposition) was incorporated into the model as opposed to nonpermanent attachment (retardation). This technology can be used to further explore transport processes of NPs inside coarse-grained porous media, either by using the wide range of commercially available (super)paramagnetically tagged NPs or by using custom-made tagged NPs. PMID:22091923
Moritsugu, Kei; Smith, Jeremy C
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. PMID:18469078
CG-OoO: Energy-Efficient Coarse-Grain Out-of-Order Execution
Mohammadi, Milad; Aamodt, Tor M.; Dally, William J.
2016-01-01
We introduce the Coarse-Grain Out-of-Order (CG- OoO) general purpose processor designed to achieve close to In-Order processor energy while maintaining Out-of-Order (OoO) performance. CG-OoO is an energy-performance proportional general purpose architecture that scales according to the program load. Block-level code processing is at the heart of the this architecture; CG-OoO speculates, fetches, schedules, and commits code at block-level granularity. It eliminates unnecessary accesses to ener...
On the Zitterbewegung Transient Regime in a Coarse-Grained Space-Time
Weberszpil, José
2014-01-01
In the present contribution, by studying a fractional version of Dirac's equation for the electron, we show that the phenomenon of Zitterbewegung in a coarse-grained medium exhibits a transient oscillatory behavior, rather than a purely oscillatory regime, as it occurs in the integer case, $\\alpha=1$. Our result suggests that, in such systems, the Zitterbewegung-type term related to a trembling motion of a quasiparticle is tamed by its complex interactions with other particles and the medium. This can justify the difficulties in the observation of this interesting phenomenon. The possibility that the Zitterbewegung be accompanied by a damping factor supports the viewpoint of particle substructures in Quantum Mechanics.
Deformation twinning with zero macroscopic strain in a coarse-grained Ni–Co-based superalloy
Macroscopically zero-strained twin lamellae are observed in a coarse-grained Ni–Co-based superalloy after plastic deformation. The twin lamellae presented as three layers of overlapping stacking faults with zero overall Burgers vector. The atomic stacking sequence in the twin lamellae is consistent with pairs of parallel stacking faults at neighboring or next-neighboring glide planes. The twinning is facilitated by the low stacking fault energy of the superalloy and the lengthening of stacking faults by shear stress from nearby stacking faults
V.PURUSHOTHAM REDDY
2011-02-01
Full Text Available In computer networks the routing is based on shortest path routing algorithms. Based on its advantages, an alternative method is used known as Genetic Algorithm based routing algorithm, which is highly scalable and insensitive to variations in network topology. Here we propose a coarse-grained parallel genetic algorithm to solve the shortest path routing problem with the primary goal of computation time reduction along with the use of migration scheme. This algorithm is developed and implemented on an MPI cluster. The effects of migration and its performance is studied in this paper.
MARTINI Coarse-Grained Model of Triton TX-100 in Pure DPPC Monolayer and Bilayer Interfaces.
Pizzirusso, Antonio; De Nicola, Antonio; Milano, Giuseppe
2016-04-28
The coarse-grained MARTINI model of Triton TX-100 has been validated by direct comparison of the experimental and calculated area increase in pure DPPC lipid bilayers and monolayers at water/air interfaces in the presence of surfactant and by comparison of electron density profiles calculated with more detailed atomistic models based on the CHARMM force field. Bilayer simulations have been performed and compared with monolayers and with atomistic models. The validated CG model has been employed to study the phase separation of TX-100 molecules in lipid bilayers and the effect of the lipid bilayer curvature. PMID:27042862
Water hammer in coarse-grained solid-liquid flows in hydraulic hoisting for ocean mining
韩文亮; 王光谦; 吴保生; 刘少军; 邹伟生
2002-01-01
The particles of polymetallic nodules in hydraulic hoisting flows that are used for mining in deep sea are rather coarse, therefore their flow velocity is smaller than that of the surrounding water. The characteristics of solid-liquid flows such as their density, concentration, elastic modulus and resistance were discussed. The wave propagation speed and the continuity and momentum equations of water hammer in coarse-grained solid-liquid flows were theoretically derived, and a water hammer model for such flows was developed.
Towards a unified framework for coarse-graining particle-based simulations.
Junghans, Christoph [Los Alamos National Laboratory
2012-06-28
Different coarse-graining techniques for soft matter systems have been developed in recent years, however it is often very demanding to find the method most suitable for the problem studied. For this reason we began to develop the VOTCA toolkit to allow for easy comparison of different methods. We have incorporated 6 different techniques into the package and implemented a powerful and parallel analysis framework plus multiple simulation back-ends. We will discuss the specifics of the package by means of various studies, which have been performed with the toolkit and highlight problems we encountered along the way.
Deformation bands in ⟨120⟩ grains in coarse-grained aluminium
Bilde-Sørensen, Jørgen
1986-01-01
Coarse-grained aluminium, deformed in tension to a strain of 0.05, was examined in a scanning electron microscope by channelling contrast. Pronounced bands with a width typically of the order of 200 μm were found in some grains with an orientation close to [120]. When observed on surfaces close 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)[011](111) and...
Coarse-grained modelling of pressure-related effects in staphylococcal nuclease and ubiquitin
Wojciechowski, Michal; Cieplak, Marek [Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw (Poland)
2007-07-18
Folding and unfolding kinetics of proteins are affected by the application of high hydrostatic pressure. In order to study the pressure-related effects within geometry-based coarse-grained models, we propose adding a pressure-controlled hump to the contact potentials. This approach qualitatively reproduces the experimental findings on conformational changes in staphylococcal nuclease and predicts a non-monotonic dependence of the unfolding time with pressure. The pressure-induced unfolding is shown to be distinct from unfolding induced by a high temperature.
Functional RG flow equation: regularization and coarse-graining in phase space
Vacca, G P
2011-01-01
Starting from the basic path integral in phase space we reconsider the functional approach to the RG flow of the one particle irreducible effective average action. On employing a balanced coarse-graining procedure for the canonical variables we obtain a functional integral with a non trivial measure which leads to a modified flow equation. We first address quantum mechanics for boson and fermion degrees of freedom and we then extend the construction to quantum field theories. For this modified flow equation we discuss the reconstruction of the bare action and the implications on the computation of the vacuum energy density.
Lee, Hwankyu; de Vries, Alex H.; Marrink, Siewert-Jan; Pastor, Richard W.
2009-01-01
A coarse-grained (CG) model for polyethylene oxide (PEO) and polyethylene glycol (PEG) developed within the framework of the MARTINI CG force field (FF) using the distributions of bonds, angles, and dihedrals from the CHARMM all-atom FF is presented. Densities of neat low molecular weight PEO agree with experiment, and the radius of gyration R-g = 19.1 angstrom +/- 0.7 for 76-mers of PEO (M-w approximate to 3400), in excellent agreement with neutron scattering results for an equal sized PEG. ...
Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that
Davtyan, Aram; Dama, James F.; Voth, Gregory A. [Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Andersen, Hans C., E-mail: hca@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)
2015-04-21
Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that
Lee-Wei Yang
2008-01-01
Full Text Available Molecular dynamics (MD simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.
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
Español, Pep; Donev, Aleksandar
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 simulations as input
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
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model
Coarse-grained simulation of lipid vesicles with ``n-atic'' orientational order
Geng, Jun; Selinger, Jonathan; Selinger, Robin
2012-02-01
We perform coarse-grained simulation studies of fluid lipid vesicles with in-plane ``n-atic'' orientational order associated with the shape of lipid head group, to test the theoretical predictions of Park, Lubensky and MacKintosh [1] for resulting vesicle shape and defect structures. Our simulation model uses a single layer coarse-grained implicit-solvent approach proposed by Yuan et al [2], with addition of an extra vector degree of freedom representing in-plane orientational order. We carry out simulation studies for n=1 to 6, examining in each case the spatial distribution of defects and resulting deformation of the vesicle. An initially spherical vesicle (genus zero) with n-atic order has a ground state with 2n vortices of strength 1/n, as expected, but the observed equilibrium shapes are sometimes quite different from those predicted theoretically. For the n=1 case, we find that the vesicle may become trapped in a disordered, long-lived metastable state with extra +/- defects whose pair-annihilation is inhibited by local changes in membrane curvature, and thus may never reach its predicted ground state. [4pt] [1] J. Park, T. C. Lubensky, and F. C. MacKintosh, Europhys. Lett. 20, 279 (1992)[0pt] [2] H. Yuan, C. Huang, Ju Li, G. Lykotrafitis, and S. Zhang, Phys. Rev. E 82, 011905 (2010)
Deviation of permeable coarse-grained boundary resistance from Nikuradse's observations
Cheng, Nian-Sheng; Liu, Xingnian; Chen, Xingwei; Qiao, Changkai
2016-02-01
Nikuradse's (1933) rough pipe study is enormously influential in the understanding of flow resistance over a sediment bed. However, the rough boundary employed in Nikuradse's study differs from permeable sediment beds in rivers. This implies that the results derived from the rough pipe experiments may not be applicable for flows over a permeable coarse-grained bed. The present study aimed to explore to what extent the flow resistance of a permeable coarse-grained boundary deviates from the Nikuradse's observations. Experiments were conducted with rough pipes, which were prepared by overlaying the inner wall with one to four layers of spherical beads. The single layer roughness resembles the experimental setup reported in Nikuradse's study, while the multilayer of grains allows significant flow to pass through the porous roughness layer. In addition, the ratio of grain diameter, k, to pipe diameter, d, was chosen to be one to two orders greater than the range (0.001 open channel resistance in the presence of large-scale roughness. The measurements also suggest the existence of a laminar flow regime, in which the friction factor is inversely proportional to the Reynolds number. The observed variations in the flow resistance are attributed to both wall permeability and large-scale roughness.
Conformational Properties of Comb-Like Polyelectrolytes: A Coarse-Grained MD Study.
Ghelichi, Mahdi; Eikerling, Michael H
2016-03-17
This article presents a coarse-grained molecular dynamics study of single comb-like polyelectrolyte or ionomer chains in aqueous solution. The model polymer is comprised of a hydrophobic backbone chain with grafted side chains that terminate in anionic headgroups. The comb-polymer is modeled at a coarse-grained level with implicit treatment of the solvent. The computational study rationalizes conformational properties of the backbone chain and localization of counterions as functions of side chain length, grafting density of side chains, backbone stiffness, and counterion valence. The main interplay that determines the ionomer properties unfolds between electrostatic interactions among charged groups, hydrophobic backbone interactions, and steric effects induced by the pendant side chains. Depending on the density of branching sites, we have found two opposing effects of side chain length on the backbone gyration radius and local persistence length. Variation in comb-polyelectrolyte architecture is shown to have nontrivial effects on the localization of mobile counterions. Changes in Bjerrum length and counterion valence are also shown to alter the strength of Coulomb interactions and emphasize the role of excluded-volume effects on controlling the backbone conformational behavior. The results of simulations are in qualitative agreement with existing experimental and theoretical studies. The comprehensive conformational picture provides a framework for future studies of comb-polyelectrolyte systems. PMID:26910617
Macro-micromechanical approaches for non-coaxiality of coarse grained soils
无
2011-01-01
For coarse grained soils,their principal stress directions may change when the water level of embankment dam varies instantaneously.In this loading case,the principal directions of stress and strain rate will become non-coaxial.In an effort to model non-coaxial behavior,a modified three-dimensional non-coaxial model is developed in the context of vertex yield(tangent plasticity) theory.Discrete Element Method(PFC) incorporating user-defined interparticle contact models is also employed to gain an insight into microscopic mechanism of non-coaxiality.The analysis focuses on non-coaxial behaviors under simple shear condition.It has been shown that the proposed non-coaxial model gives good predictions for non-coaxiality with reference to microscopic observations while the classical coaxial model fails to simulate the non-coaxial behaviors.In general,non-coaxiality as a result of the rotation of principal stress,is large at a small shear strain,and inclined to become negligible with increasing shear strain.For coarse grained soils,their non-coaxiality tends to largely depend on the initial normal pressure,where a larger degree of non-coaxiality can be observed at a higher pressure.
Coarse-grained quantum transport simulation for analyzing leakage-mobility antagonism in GNRFET
Ito, Masakatsu; Sato, Shintaro; Yokoyama, Naoki; Joachim, Christian; Green Nanoelectronics Center Team; CEMES-CNRS and Mana Satellite Collaboration
2013-03-01
Since it became clear that graphene transistors based on the classical MOSFET principle suffer from serious performance problems, researchers have explored new graphene device design using quantum transport simulations. A first-principle quantum transport simulation, however, still takes unaffordable computational cost to deal with a realistic size of graphene transistor (>104 atoms). This motivated us to import ESQC (elastic scattering quantum chemistry) technique from the research field of molecular electronics and to develop its coarse-grained version. To eliminate the atomic scale details, we reformulated ESQC technique using the continuum limit description of graphene charge carriers, which is given by the massless Dirac equation. Since the potential function in this Dirac equation is electrostatic potential distribution, it can be obtained from Poisson equation with the boundary conditions of gate voltages in a self-consistent manner. We are now applying this coarse-grained quantum transport simulation to GNRFETs (graphene nanoribbon field effect transistors) for resolving the mobility-leakage antagonism, where opening a bandgap in a graphene channel improves its switching ability but at the same time deteriorates the electron channel mobility.
Optimal matched filter design for ultrasonic NDE of coarse grain materials
Li, Minghui; Hayward, Gordon
2016-02-01
Coarse grain materials are widely used in a variety of key industrial sectors like energy, oil and gas, and aerospace due to their attractive properties. However, when these materials are inspected using ultrasound, the flaw echoes are usually contaminated by high-level, correlated grain noise originating from the material microstructures, which is time-invariant and demonstrates similar spectral characteristics as flaw signals. As a result, the reliable inspection of such materials is highly challenging. In this paper, we present a method for reliable ultrasonic non-destructive evaluation (NDE) of coarse grain materials using matched filters, where the filter is designed to approximate and match the unknown defect echoes, and a particle swarm optimization (PSO) paradigm is employed to search for the optimal parameters in the filter response with an objective to maximise the output signal-to-noise ratio (SNR). Experiments with a 128-element 5MHz transducer array on mild steel and INCONEL Alloy 617 samples are conducted, and the results confirm that the SNR of the images is improved by about 10-20 dB if the optimized matched filter is applied to all the A-scan waveforms prior to image formation. Furthermore, the matched filter can be implemented in real-time with low extra computational cost.
Coarse-grained analysis of a lattice Boltzmann model for planar streamer fronts
Vanroose, W; Van Leemput, P; Vanroose, Wim; Samaey, Giovanni; Leemput, Pieter Van
2007-01-01
We study the traveling wave solutions of a lattice Boltzmann model for the planar streamer fronts that appear in the transport of electrons through a gas in a strong electrical field. To mimic the physical properties of the impact ionization reaction, we introduce a reaction matrix containing reaction rates that depend on the electron velocities. Via a Chapman--Enskog expansion, one is able to find only a rough approximation for a macroscopic evolution law that describes the traveling wave solution. We propose to compute these solutions with the help of a coarse-grained time-stepper, which is an effective evolution law for the macroscopic fields that only uses appropriately initialized simulations of the lattice Boltzmann model over short time intervals. The traveling wave solution is found as a fixed point of the sequential application of the coarse-grained time-stepper and a shift-back operator. The fixed point is then computed with a Newton-Krylov Solver. We compare the resulting solutions with those of th...
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912 (United States); Li, Xiantao [Department of Mathematics, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-01
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu
2011-10-01
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene
Differences between real and particle-in-cell plasmas: effects of coarse-graining
Melzani, Mickaël; Folini, Doris; Winisdoerffer, Christophe
2013-01-01
The PIC model relies on two building blocks. The first stems from the capability of computers to handle only up to $\\sim10^{10}$ particles, while real plasmas contain from $10^4$ to $10^{20}$ particles per Debye sphere: a coarse-graining step must be used, whereby of the order of $p\\sim10^{10}$ real particles are represented by a single computer superparticle. The second is field storage on a grid with its subsequent finite superparticle size. We introduce the notion of coarse-graining dependent quantities, i.e. physical quantities depending on the number $p$. They all derive from the plasma parameter $\\Lambda$, which we show to be proportional to $1/p$. We explore three examples: the rapid collision- and fluctuation-induced thermalization of plasmas with different temperatures, that scale with the number of superparticles per grid cell and are a factor $p\\sim10^{10}$ faster than in real plasmas; the high level of electrostatic fluctuations in a thermal plasma, with corrections due to the finite superparticle...
A coarse-grained model to study calcium activation of the cardiac thin filament
Zhang, Jing; Schwartz, Steven
2015-03-01
Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.
Path statistics, memory, and coarse-graining of continuous-time random walks on networks
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.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.
2015-11-01
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany)
2015-11-07
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
An Impulse-C Hardware Accelerator for Packet Classification Based on Fine/Coarse Grain Optimization
O. Ahmed
2013-01-01
Full Text Available Current software-based packet classification algorithms exhibit relatively poor performance, prompting many researchers to concentrate on novel frameworks and architectures that employ both hardware and software components. The Packet Classification with Incremental Update (PCIU algorithm, Ahmed et al. (2010, is a novel and efficient packet classification algorithm with a unique incremental update capability that demonstrated excellent results and was shown to be scalable for many different tasks and clients. While a pure software implementation can generate powerful results on a server machine, an embedded solution may be more desirable for some applications and clients. Embedded, specialized hardware accelerator based solutions are typically much more efficient in speed, cost, and size than solutions that are implemented on general-purpose processor systems. This paper seeks to explore the design space of translating the PCIU algorithm into hardware by utilizing several optimization techniques, ranging from fine grain to coarse grain and parallel coarse grain approaches. The paper presents a detailed implementation of a hardware accelerator of the PCIU based on an Electronic System Level (ESL approach. Results obtained indicate that the hardware accelerator achieves on average 27x speedup over a state-of-the-art Xeon processor.
Parameters influencing the preparation of coarse grained Al{sub 2}O{sub 3} ceramics
Kosmos, A. [Institut za Elektroniko in Vakuumsko Tehniko, Ljubljana (Slovenia); Susnik, D.; Kolar, D. [Institut za Elektroniko in Vakuumsko Tehniko, Ljubljana (Slovenia)]|[Jozef Stefan Inst., Jamova, Ljubljana (Slovenia)
1997-12-31
Metal-ceramic seals are widely used in high vacuum technology. High alumina ceramic is one of the ceramics used in these seals. Coarse grained ceramics with average grain diameter from 15 to 20 {mu}m and densities over 3.70 g/cm{sup 3} are required. In the present work 98% Al{sub 2}O{sub 3} ceramics with additives from the CaO-SiO{sub 2} and CaO-MgO-SiO{sub 2} systems were investigated. The influence of sintering conditions, additive composition and starting alumina powder on densification and microstructure development was studied. The most suitable microstructures with average grain diameters of 14 and 20 {mu}m were achieved with a coarse grained starting alumina powder and an additive composition of 35% CaO, 5% MgO, 60% SiO{sub 2} or 40% CaO and 60% SiO{sub 2}, with prolonged sintering at 1700 C. The microstructures have a wide grain size distribution. (orig.) 11 refs.
Coarse-Grained Modeling of Genetic Circuits as a Function of the Inherent Time Scales
Labavic, Darka; Hildegard, Wolfhard Janke; Meyer-Ortmanns,
2012-01-01
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory behavior. Here we consider a specific realization of this motif as a genetic circuit, in which genes are described as directly producing proteins, leaving out the intermediate step of mRNA production. We focus on the effect that inherent time scales on the underlying fine-grained scale can have on the bifurcation patterns on a coarser scale in time. Time scales are set by the binding and unbinding rates of the transcription factors to the promoter regions of the genes. Depending on the ratio of these rates to the decay times of the proteins, the appropriate averaging procedure for obtaining a coarse-grained description changes and leads to sets of deterministic equations, which differ in their bifurcation structure. In particular the desired intermediate range of regular limit cyc...
Simulation of ballistic performance of coarse-grained metals strengthened by nanotwinned regions
Yang, G.; Guo, X.; Weng, G. J.; Zhu, L. L.; Ji, R.
2015-12-01
Coarse-grained (CG) metals strengthened by nanotwinned (NT) regions have both ultrahigh strength and good ductility. The presence of the NT regions contributes to their ultrahigh strength, while their good ductility is attributed to the recrystallized coarse grains. These characteristics make them a potential candidate for bullet-proof material. In this paper, numerical simulations based on the mechanism-based strain gradient plasticity and the Johnson-Cook failure criterion are carried out to investigate the effects of twin spacing and microstructural attributes on the ballistic performance of CG copper strengthened by NT regions. We investigate the performance of fourteen idealized microstructures, and find that smaller twin spacing and regular distribution of NT regions are more conducive to the promotion of the ballistic performance. We also uncover that the role of the shape of NT regions is significantly affected by twin spacing. Furthermore, we make a comparison with its CG counterpart without NTs, and find that microstructures with array arrangement of NT regions have higher limit velocities and smaller relative displacements than the single phase CG structure. This makes them a strong candidate for helmets and other personal protective equipments. It is believed that the simulated results could provide useful insights into the development of this advanced class of metals for ballistic protection.
The ELBA force field for coarse-grain modeling of lipid membranes.
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.
Adaptive Hamiltonian and Riemann Manifold Monte Carlo Samplers
Wang, Ziyu; MOHAMED, SHAKIR; De Freitas, Nando
2013-01-01
In this paper we address the widely-experienced difficulty in tuning Hamiltonian-based Monte Carlo samplers. We develop an algorithm that allows for the adaptation of Hamiltonian and Riemann manifold Hamiltonian Monte Carlo samplers using Bayesian optimization that allows for infinite adaptation of the parameters of these samplers. We show that the resulting sampling algorithms are ergodic, and that the use of our adaptive algorithms makes it easy to obtain more efficient samplers, in some ca...
Baertschiger, T; Joyce, M; Gabrielli, A; Sylos Labini, F
2007-07-01
We study the evolution under their self-gravity of particles evolving from infinite "shuffled lattice" initial conditions. We focus here specifically on the comparison between the evolution of such a system and that of "daughter" coarse-grained particle distributions. These are sparser (i.e., lower density) particle distributions, defined by a simple coarse-graining procedure, which share the same large-scale mass fluctuations. We consider both the case that such coarse-grainings are performed (i) on the initial conditions, and (ii) at a finite time with a specific additional prescription. In numerical simulations we observe that, to a first approximation, these coarse-grainings represent well the evolution of the two-point correlation properties over a significant range of scales. We note, in particular, that the form of the two-point correlation function in the original system, when it is evolving in the asymptotic "self-similar" regime, may be reproduced well in a daughter coarse-grained system in which the dynamics are still dominated by two-body (nearest neighbor) interactions. This provides a simple physical description of the origin of the form of part of the asymptotic nonlinear correlation function. Using analytical results on the early time evolution of these systems, however, we show that small observed differences between the evolved system and its coarse-grainings at the initial time will in fact diverge as the ratio of the coarse-graining scale to the original interparticle distance increases. The second coarse-graining studied, performed at a finite time in a specified manner, circumvents this problem. It also makes it more physically transparent why gravitational dynamics from these initial conditions tends toward a self-similar evolution. We finally discuss the precise definition of a limit in which a continuum (specifically Vlasov-type) description of the observed linear and nonlinear evolution should be applicable. This requires the introduction
Choo, H.; Kim, J.; Lee, W.; Lee, C.
2016-04-01
This theoretical and experimental study investigates the variations of both the hydraulic conductivity and the electrical conductivity of coarse-grained soils as a function of pore water conductivity, porosity, and median particle size, with the ultimate goal of developing the relationship between the hydraulic conductivity (K) and the formation factor (F) in coarse-grained soils as a function of particle size. To monitor the variations of both the hydraulic conductivity and electrical conductivity (formation factor) of six sands with varying particle sizes, a series of hydraulic conductivity tests were conducted using a modified constant head permeameter equipped with a four electrode resistivity probe. It is demonstrated that K of the tested coarse-grained soils is mainly determined by the porosity and particle size. In contrast, the effect of particle size on the measured electrical conductivity (or F) is negligible, and the variation of F of the tested soils is mainly determined by porosity. Because the porosity may act as a connecting characteristic between K and F, the relation between them in coarse-grained soils can be expressed as a function of particle size. Finally, simple charts are developed for estimating the hydraulic conductivity of coarse-grained soils from the measured particle sizes and formations factors.
Shen, Hujun; Li, Yan; Ren, Pengyu; Zhang, Dinglin; Li, Guohui
2014-02-10
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927
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.
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
Static Recrystallized Grain Size of Coarse-Grained Austenite in an API-X70 Pipeline Steel
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.
Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr
2015-08-01
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.
Abbott, Lauren J.; Stevens, Mark J.
2015-12-01
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.
Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model
Sayar, Mehmet; Kabakcioglu, Alkan
2009-01-01
Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially depe...
A coarse-grained simulation for the folding of molybdenum disulphide
We investigate the folding of molybdenum disulphide (MoS2) using coarse-grained (CG) simulations, in which all the parameters are determined analytically from the Stillinger–Weber atomic potential. Owing to its simplicity, the CG model can be used to derive analytic predictions for the relaxed configuration of the folded MoS2 and the resonant frequency for the breathing-like oscillation. We disclose two interesting phenomena for the breathing-like oscillation in the folded MoS2. First, the breathing-like oscillation is self-actuated, since this oscillation can be actuated by intrinsic thermal vibrations without any external actuation force. Second, the resonant frequency of the breathing-like oscillation is insensitive to the adsorption effect. These two features enable practical applications of the folded MoS2 based nanoresonators, where stable resonant oscillations are desirable. (paper)
Pandey, Harsh; Underhill, Patrick T
2015-11-01
The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large. PMID:26651689
Coarse-grained entropy and causal holographic information in AdS/CFT
We propose bulk duals for certain coarse-grained entropies of boundary regions. The ‘one-point entropy’ is defined in the conformal field theory by maximizing the entropy in a domain of dependence while fixing the one-point functions. We conjecture that this is dual to the area of the edge of the region causally accessible to the domain of dependence (i.e. the ‘causal holographic information’ of Hubeny and Rangamani). The ‘future one-point entropy’ is defined by generalizing this conjecture to future domains of dependence and their corresponding bulk regions. We show that the future one-point entropy obeys a nontrivial second law. If our conjecture is true, this answers the question “What is the field theory dual of Hawking’s area theorem?”
Structural investigation of MscL gating using experimental data and coarse grained MD simulations.
Evelyne Deplazes
Full Text Available The mechanosensitive channel of large conductance (MscL has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the gating mechanism remain unknown. In this study we combine coarse grained simulations with restraints from EPR and FRET experiments to study the structural changes involved in gating with much greater level of conformational sampling than has previously been possible. We generated a set of plausible open pore structures that agree well with existing open pore structures and gating models. Most interestingly, we found that membrane thinning induces a kink in the upper part of TM1 that causes an outward motion of the periplasmic loop away from the pore centre. This previously unobserved structural change might present a new mechanism of tension sensing and might be related to a functional role in osmoregulation.
A coarse-grain force field for RDX: Density dependent and energy conserving
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Tunable-slip boundaries for coarse-grained simulations of fluid flow
Smiatek, Jens; Schmid, Friederike
2007-01-01
On the micro- and nanoscale, classical hydrodynamic boundary conditions such as the no-slip condition no longer apply. Instead, the flow profiles exhibit ``slip`` at the surface, which is characterized by a finite slip length (partial slip). We present a new, systematic way of implementing partial-slip boundary conditions with arbitrary slip length in coarse-grained computer simulations. The main idea is to represent the complex microscopic interface structure by a spatially varying effective viscous force. An analytical equation for the resulting slip length can be derived for planar and for curved surfaces. The comparison with computer simulations of a DPD (dissipative particle dynamics) fluid shows that this expression is valid from full-slip to no-slip.
Development of DPD coarse-grained models: From bulk to interfacial properties
Solano Canchaya, José G.; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice
2016-08-01
A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.
A polarizable coarse-grained protein model for dissipative particle dynamics.
Peter, Emanuel K; Lykov, Kirill; Pivkin, Igor V
2015-10-01
We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece. PMID:26339692
Bridging the Coarse-grained to Microscopic information gap: A numerical optimization method
Mansour, Andrew Abi
2013-01-01
Atom-resolved states must be constructed as part of a multiscale algorithm that coevolves the system at the atomic and coarse-grained (CG) scales. The CG description does not capture the constraints on distances and angles imposed by stiff bonded interactions. Thus, in isothermal simulations, using only CG information to construct the initial conditions yields microstates of negligible Boltzmann weight. In this paper, we present a reversible CG to all-atom mapping algorithm that overcomes this difficulty. The result is a scalable algorithm for simulating mesoscopic systems with atomic precision, over long periods of time, and with great efficiency over conventional MD. The mapping algorithm is implemented in parallel for distributed memory systems as part of the Deductive Multiscale Simulator software. It is demonstrated for Lactoferrin, an assembly of Nudaurelia Capensis Omega proteins, and Cowpea Chlorotic Mottle virus capsid.
Transferable coarse-grained potential for $\\textit{de novo}$ protein folding and design
Coluzza, Ivan
2014-01-01
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and folding is introduced. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences are not yet fully realistic and require further experimental testing. For an independent set of proteins, notoriously difficult to fold, the correct folding of both the designed and the natural sequences is also demonstrated. The folding properties are characterized by free energy calculations. which not only are consistent among natural and designed proteins, but we also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, this novel coarse-grained protein model ...
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Andrzej Koliński
2013-05-01
Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
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.
Tian, Pu
2015-01-01
Free energy is arguably the most important thermodynamic property for physical systems. Despite the fact that free energy is a state function, presently available rigorous methodologies, such as those based on thermodynamic integration (TI) or non-equilibrium work (NEW) analysis, involve energetic calculations on path(s) connecting the starting and the end macrostates. Meanwhile, presently widely utilized approximate end-point free energy methods lack rigorous treatment of conformational variation within end macrostates, and are consequently not sufficiently reliable. Here we present an alternative and rigorous end point free energy calculation formulation based on microscopic configurational space coarse graining, where the configurational space of a high dimensional system is divided into a large number of sufficiently fine and uniform elements, which were termed conformers. It was found that change of free energy is essentially decided by change of the number of conformers, with an error term that accounts...
Simulations of room temperature ionic liquids: From polarizable to coarse-grained force fields
Salanne, Mathieu
2015-01-01
Room temperature ionic liquids (RTILs) are solvent with unusual properties, which are difficult to characterize experimentally because of their intrinsic complexity (large number of atoms, strong Coulomb interactions). Molecular simulations have therefore been essential in our understanding of these systems. Depending on the target property and on the necessity to account for fine details of the molecular structure of the ions, a large range of simulation techniques are available. Here I focus on classical molecular dynamics, in which the level of complexity of the simulation, and therefore the computational cost, mostly depends on the force field. Depending on the representation of the ions, these are either classified as all-atom or coarse-grained. In addition, all-atom force fields may account for polarization effects if necessary. The most widely used methods for RTILs are described together with their main achievements and limitations.
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
We here propose to extend the concept of helicity to include it in a fractional scenario and we write down the left- and the right-handed Weyl equations from first principles in this extended framework. Next, by coupling the different fractional Weyl sectors by means of a mass parameter, we arrive at the fractional version of Dirac's equation which, whenever coupled to an external electromagnetic field and reduced to the nonrelativistic regime, yields a fractional Pauli-type equation. From the latter, we are able to present an explicit expression for the gyromagnetic ratio of charged fermions in terms of the fractionality parameter. We then focus our efforts to relate the coarse-grained property of space-time to fractionality and to the (g-2) anomalies of the different leptonic species
Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark; Voth, Gregory A.
2016-05-01
The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.
Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
Šulc, Petr; Romano, Flavio; Doye, Jonathan P K; Louis, Ard A
2012-01-01
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators.
A Dynamically Reconfigurable Video Compression Scheme Using FPGAs with Coarse-grain Parallelism
S. Ramachandran
2002-01-01
Full Text Available A dynamically reconfigurable scheme for video encoder to switch among many different applications is presented. The scheme is suitable for FPGA implementation and conforms to JPEG, MPEG-1, MPEG-2, and H.263 standards. The scheme has emerged as an efficient and cost-effective solution for video compression as a result of innovative design using well-partitioned algorithms, highly pipelined architecture and coarse-grain parallelism. The reconfiguration time of the video encoder is less than 320 μs while switching from one standard to another. Although the dynamic reconfiguration scheme is presented for a video encoder, the same design methodology may be applied effectively for any other application.
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej
2013-01-01
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
Lipid Bilayer Vesicle extrusion through nanopores: a coarse grained molecular dynamics study
Bertrand, Martin; Joos, Bela
2011-03-01
We conducted Coarse-Grained Molecular Dynamics simulations of the pressure extrusion of vesicles in nanopores that confirm and help explain prior experimental observations (Patty, P. and Frisken, B., Biophys. J., 85, 2003). We demonstrate that, to a first approximation, the final size of extruded vesicles can be obtained by considering an invariable inner vesicle volume enclosed by a finitely extensible lipid bilayer. Using our data, we also describe in details the mechanics of vesicle rupture in a nanopore when pushed by various pressure gradients. This is made possible by tracking local variations of the stress in the lipid membrane via changes in surface area using a triangulation algorithm. The simulations are executed using state of the art GPU accelerated software. Our findings could potentially be useful in the design of liposome based drug delivery systems and in getting a better understanding of how the cell nucleus and the cell as a whole react in similar conditions. Work supported by NSERC and FQRNT.
Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
Grime, John M. A.; Dama, James F.; Ganser-Pornillos, Barbie K.; Woodward, Cora L.; Jensen, Grant J.; Yeager, Mark; Voth, Gregory A.
2016-01-01
The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies. PMID:27174390
Proteins at air-water interfaces: a coarse-grained model.
Cieplak, Marek; Allan, Daniel B; Leheny, Robert L; Reich, Daniel H
2014-11-01
We present a coarse-grained model to describe the adsorption and deformation of proteins at an air-water interface. The interface is introduced empirically in the form of a localized field that couples to a hydropathy scale of amino acids. We consider three kinds of proteins: protein G, egg-white lysozyme, and hydrophobin. We characterize the nature of the deformation and the orientation of the proteins induced by their proximity to and association with the interface. We also study protein diffusion in the layer formed at the interface and show that the diffusion slows with increasing concentration in a manner similar to that for a colloidal suspension approaching the glass transition. PMID:25310625
Coarse-grained Dynamic Taint Analysis for Defeating Control and Non-control Data Attacks
Kohli, Pankaj
2009-01-01
Memory corruption attacks remain the primary threat for computer security. Information flow tracking or taint analysis has been proven to be effective against most memory corruption attacks. However, there are two shortcomings with current taint analysis based techniques. First, these techniques cause application slowdown by about 76% thereby limiting their practicality. Second, these techniques cannot handle non-control data attacks i.e., attacks that do not overwrite control data such as return address, but instead overwrite critical application configuration data or user identity data. In this work, to address these problems, we describe a coarse-grained taint analysis technique that uses information flow tracking at the level of application data objects. We propagate a one-bit taint over each application object that is modified by untrusted data thereby reducing the taint management overhead considerably. We performed extensive experimental evaluation of our approach and show that it can detect all critic...
In this study, 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
Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study
Telenius, J.; Koivuniemi, A.; Kulovesi, P.;
2012-01-01
Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse......-grained simulations of a lipid layer comprising phospholipids, free fatty acids, cholesteryl esters, and triglycerides at the air-water interface to shed light on the properties of TFLL. We consider structural as well as dynamical properties of the lipid layer as a function of surface pressure. Simulations revealed...... monolayer system, we found drastic differences in both structural and dynamical properties that explain the prominent role of neutral lipids as stabilizers of the TFLL. Based on our results, we suggest that neutral lipids are able to increase the stability of the TFLL by modulating its dynamical and...
Generalization of the DLA process with different immiscible components by time-scale coarse graining
Postnikov, E B [Kursk State University, Theoretical Physics Department, Radishcheva st, 33, 305000, Kursk (Russian Federation); Ryabov, A B [MV Lomonosov Moscow State University, Physics Faculty, 119992 Moscow (Russian Federation); Loskutov, A [MV Lomonosov Moscow State University, Physics Faculty, 119992 Moscow (Russian Federation)
2007-10-05
In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.
Generalization of the DLA process with different immiscible components by time-scale coarse graining
Postnikov, E. B.; Ryabov, A. B.; Loskutov, A.
2007-10-01
In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.
Rudzinski, Joseph F
2016-01-01
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent, dynamics. In this work, we rely on Markov state models to simultaneously characterize the static and kinetic properties of two CG peptide force fields---one top-down and one bottom-up. Instead of a rigorous evolution of CG dynamics (e.g., using a generalized Langevin equation), we attempt to improve the description of kinetics by simply altering the existing CG models, which employ standard Langevin dynamics. By varying masses and relevant force-field parameters, we can improve the timescale separation of the slow kinetic processes, achieve a more consistent ratio of mean-first-passage times between metastable states, and refine the relative free-energies between these states. Importantly, we show that the incorporation of kinetic information into a structure-based parametriz...
Virtual ultrasound sources for inspecting nuclear components of coarse-grained structure
This work describes an ultrasonic inspection procedure designed for verifying coarse-grained structure materials, which are commonly used on nuclear reactors. In this case, conventional phased array techniques cannot be used due to attenuating characteristics and backscattered noise from microstructures inside the material. Thus, synthetic aperture ultrasonic imaging (SAFT) is used for this approach in contact conditions. In order to increase energy transferred to the medium, synthetic transmit aperture is formed by several elements which generate a diverging wavefront equivalent to a virtual ultrasound source behind the transducer. On the other hand, the phase coherence technique has been applied to reduce more structural noise and improve the image quality. The beamforming process has been implemented over a GPU platform to reduce computing time
Macroscopic and large scale phenomena coarse graining, mean field limits and ergodicity
Rademacher, Jens; Zagaris, Antonios
2016-01-01
This book is the offspring of a summer school school “Macroscopic and large scale phenomena: coarse graining, mean field limits and ergodicity”, which was held in 2012 at the University of Twente, the Netherlands. The focus lies on mathematically rigorous methods for multiscale problems of physical origins. Each of the four book chapters is based on a set of lectures delivered at the school, yet all authors have expanded and refined their contributions. Francois Golse delivers a chapter on the dynamics of large particle systems in the mean field limit and surveys the most significant tools and methods to establish such limits with mathematical rigor. Golse discusses in depth a variety of examples, including Vlasov--Poisson and Vlasov--Maxwell systems. Lucia Scardia focuses on the rigorous derivation of macroscopic models using $\\Gamma$-convergence, a more recent variational method, which has proved very powerful for problems in material science. Scardia illustrates this by various basic examples and a mor...
Power-Aware Rationale for Using Coarse-Grained Transponders in IP-Over-WDM Networks
Saldaña Cercos, Silvia; Resendo, Leandro C.; Ribeiro, Moises R. N.;
2015-01-01
practical constraints which were neglected by previous works, so that there is correspondence between interface modules and transponders instead of assuming a single type of interface module per line card, and we use accurate power consumption values instead of using approximations per port. We also present......Power consumption is becoming one of the most significant limitations while seeking new solutions to cope with the traffic demand increase. 100 Gbps optical transmission technology has the potential to accommodate upcoming traffic demands with improved figures for W/Gbps compared to previous...... 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...
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.
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
Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.
2015-12-01
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.
Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.
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.
PRAM C:a new programming environment for fine-grain and coarse-grain parallelism.
Brown, Jonathan Leighton; Wen, Zhaofang.
2004-11-01
In the search for ''good'' parallel programming environments for Sandia's current and future parallel architectures, they revisit a long-standing open question. Can the PRAM parallel algorithms designed by theoretical computer scientists over the last two decades be implemented efficiently? This open question has co-existed with ongoing efforts in the HPC community to develop practical parallel programming models that can simultaneously provide ease of use, expressiveness, performance, and scalability. Unfortunately, no single model has met all these competing requirements. Here they propose a parallel programming environment, PRAM C, to bridge the gap between theory and practice. This is an attempt to provide an affirmative answer to the PRAM question, and to satisfy these competing practical requirements. This environment consists of a new thin runtime layer and an ANSI C extension. The C extension has two control constructs and one additional data type concept, ''shared''. This C extension should enable easy translation from PRAM algorithms to real parallel programs, much like the translation from sequential algorithms to C programs. The thin runtime layer bundles fine-grained communication requests into coarse-grained communication to be served by message-passing. Although the PRAM represents SIMD-style fine-grained parallelism, a stand-alone PRAM C environment can support both fine-grained and coarse-grained parallel programming in either a MIMD or SPMD style, interoperate with existing MPI libraries, and use existing hardware. The PRAM C model can also be integrated easily with existing models. Unlike related efforts proposing innovative hardware with the goal to realize the PRAM, ours can be a pure software solution with the purpose to provide a practical programming environment for existing parallel machines; it also has the potential to perform well on future parallel architectures.
Shendruk, Tyler N., E-mail: tyler.shendruk@physics.ox.ac.uk [The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Bertrand, Martin; Harden, James L.; Slater, Gary W. [Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5 (Canada); Haan, Hendrick W. de [Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St. North, Oshawa, Ontario L1H 7K4 (Canada)
2014-12-28
Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.
Coarse-graining to the meso and continuum scales with molecular-dynamics-like models
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.
Grünberger, Alexander; Lai, Pin-Kuang; Blanco, Marco A; Roberts, Christopher J
2013-01-24
A series of coarse-grained models, with different levels of structural resolution, were tested to calculate the steric contributions to protein osmotic second virial coefficients (B(22,S)) for proteins ranging from small single-domain molecules to large multidomain molecules, using the recently developed Mayer sampling method. B(22,S) was compared for different levels of coarse-graining: four-beads-per-amino-acid (4bAA), one-bead-per-amino-acid (1bAA), one-sphere-per-domain (1sD), and one-sphere-per-protein (1sP). Values for the 1bAA and 4bAA models were quantitatively indistinguishable for both spherical and nonspherical proteins, and the agreement with values from all-atom models improved with increasing protein size, making the CG approach attractive for large proteins of biotechnological interest. Interestingly, in the absence of detailed structural information, the hydrodynamic radius (R(h)) along with a simple 1sP approximation provided reasonably accurate values for B(22,S) for both globular and highly asymmetric protein structures, while other 1sP approximations gave poorer agreement; this helps to justify the currently empirical practice of estimating B(22,S) from R(h) for large proteins such as antibodies. The results also indicate that either 1bAA or 4bAA CG models may be good starting points for incorporating short-range attractions. Comparison of gD-crystallin B(22) values including both sterics and short-range attractions shows that 1bAA and 4bAA models give equivalent results when properly scaled to account for differences in the number of surface beads in the two CG descriptions. This provides a basis for future work that will also incorporate long-ranged electrostatic attractions and repulsions. PMID:23245189
A coarse-grained model for synergistic action of multiple enzymes on cellulose
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
Hydrogen accumulation in nanostructured as compared to the coarse-grained tungsten
Highlights: • Study of the hydrogen behaviour in nanostructured as compare to coarse grained tungsten samples. • Comparison between single (H), sequentially (C plus H) and simultaneously (C and H) implanted samples. • Study of the stability of the nanostructures after implantation at different temperatures. • Implantation energies for H and C above the displacement damage threshold. • Study of the hydrogen behaviour as a function of the implantation temperature. - Abstract: We report on the influence of sample microstructure and of irradiation conditions on the H behaviour in Tungsten (W). For this purpose, commercial coarse grained (CGW) and nanostructured W (NW) samples were implanted with (i) H at room temperature (RT), (ii) sequentially with C and H at RT, and (iii) simultaneously (co-implanted) with C and H at RT. To study the possible effect of implantation temperature on H behaviour, a CGW sample and a NW sample were sequentially implanted with C at RT and with H at 673 K. The H and C implantation fluence was 5 × 1020 m−2 and the implantation energies were 160 keV for H and 650 keV for C which are above the displacement damage threshold. Scanning electron microscopy images show that nanostructured samples consist of columns with an average diameter of about 100 nm. These nanocolumns are stable under the studied implantations conditions. Moreover, surface modification is absent in all studied samples. X-ray diffraction data illustrate that all samples are mono-phase (α-W phase) and that none of the implantations led to the appearance of secondary phases. Resonant nuclear reaction analysis data show that the H retention in NW samples is larger than in CGW and that synergistic effect has a significant influence on the H retention in CGW samples but not in NW samples
Polarizable water model for the coarse-grained MARTINI force field.
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.
On the second law of thermodynamics: The significance of coarse-graining and the role of decoherence
We take up the question why the initial entropy in the universe was small, in the context of evolution of the entropy of a classical system. We note that coarse-graining is an important aspect of entropy evaluation which can reverse the direction of the increase in entropy, i.e., the direction of thermodynamic arrow of time. Then we investigate the role of decoherence in the selection of coarse-graining and explain how to compute entropy for a decohered classical system. Finally, we argue that the requirement of low initial entropy imposes constraints on the decoherence process
Terzi, Sofiane; Couturier, Raphael; Guétaz, Laure; Viguier, Bernard
2008-01-01
The study of creep deformation in a coarse-grained Udimet 720 superalloy obtained by powder-metallurgy reveals a good resistance associated to a dislocational deformation mechanism. A model is proposed for simulating creep and tensile curves. This model is used to understand the effect of microstructural changes on the deformation mechanisms.
Multi-scale coarse-graining of non-conservative interactions in molecular liquids
Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)
2014-03-14
A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger
Couillard: Parallel Programming via Coarse-Grained Data-Flow Compilation
Marzulo, Leandro A J; França, Felipe M G; Costa, Vítor Santos
2011-01-01
Data-flow is a natural approach to parallelism. However, describing dependencies and control between fine-grained data-flow tasks can be complex and present unwanted overheads. TALM (TALM is an Architecture and Language for Multi-threading) introduces a user-defined coarse-grained parallel data-flow model, where programmers identify code blocks, called super-instructions, to be run in parallel and connect them in a data-flow graph. TALM has been implemented as a hybrid Von Neumann/data-flow execution system: the \\emph{Trebuchet}. We have observed that TALM's usefulness largely depends on how programmers specify and connect super-instructions. Thus, we present \\emph{Couillard}, a full compiler that creates, based on an annotated C-program, a data-flow graph and C-code corresponding to each super-instruction. We show that our toolchain allows one to benefit from data-flow execution and explore sophisticated parallel programming techniques, with small effort. To evaluate our system we have executed a set of real...
Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.
2016-01-01
State-of-the-art block copolymer (BCP)-directed self-assembly (DSA) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication despite free-energy calculations that suggest equilibrium defect densities are much lower than is necessary for economic fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that bulk simulations yield an exponential drop in defect heal rate above χN˜30. Thin films show no change in rate associated with the energy barrier below χN˜50, significantly higher than the χN values found previously for self-consistent field theory studies that neglect fluctuations. Above χN˜50, the simulations show an increase in energy barrier scaling with 1/2 to 1/3 of the bulk systems. This is because thin films always begin healing at the free interface or the BCP-underlayer interface, where the increased A-B contact area associated with the transition state is minimized, while the infinitely thick films cannot begin healing at an interface.
Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion
In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems
Application-specific coarse-grained reconfigurable array: architecture and design methodology
Zhou, Li; Liu, Dongpei; Zhang, Jianfeng; Liu, Hengzhu
2015-06-01
Coarse-grained reconfigurable arrays (CGRAs) have shown potential for application in embedded systems in recent years. Numerous reconfigurable processing elements (PEs) in CGRAs provide flexibility while maintaining high performance by exploring different levels of parallelism. However, a difference remains between the CGRA and the application-specific integrated circuit (ASIC). Some application domains, such as software-defined radios (SDRs), require flexibility with performance demand increases. More effective CGRA architectures are expected to be developed. Customisation of a CGRA according to its application can improve performance and efficiency. This study proposes an application-specific CGRA architecture template composed of generic PEs (GPEs) and special PEs (SPEs). The hardware of the SPE can be customised to accelerate specific computational patterns. An automatic design methodology that includes pattern identification and application-specific function unit generation is also presented. A mapping algorithm based on ant colony optimisation is provided. Experimental results on the SDR target domain show that compared with other ordinary and application-specific reconfigurable architectures, the CGRA generated by the proposed method performs more efficiently for given applications.
Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.
2016-02-01
Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.
Spreading of a Unilamellar Liposome on Charged Substrates: A Coarse-Grained Molecular Simulation.
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. PMID:27019394
Effect of forming conditions on the softening behavior in coarse grained structures
Rehrl, C., E-mail: christian.rehrl@oeaw.ac.at [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstr. 12, 8700 Leoben (Austria); Kleber, S. [Boehler Edelstahl GmbH, Kapfenberg, Mariazeller Str. 25, 8605 Kapfenberg (Austria); Renk, O.; Pippan, R. [Erich Schmid Institute of Materials Science, Austrian Academy of Sciences, Jahnstr. 12, 8700 Leoben (Austria)
2011-07-25
Highlights: {yields} Unexpected warm forming behavior of coarse grained pure Ni. {yields} Coarsening in starting microstructure leads to a higher flow stress and higher hardening rate. {yields} Grain boundary movement is strongly dependent on the initial grain size. {yields} Discontinuous dynamic recrystallization (DDRX) is retarded by coarsening of initial grain size. {yields} DDRX generates a metastable grain size finer than the steady state grain size. - Abstract: Polycrystalline nickel with a purity of 99.99 wt% and different starting grain sizes of 240 {mu}m and 770 {mu}m has been investigated. The effects of the initial grain size on the hot deformation behavior were studied by compression tests at various forming conditions. The microstructure was captured after deformation, using electron back scatter diffraction technique (EBSD). A variation of the initial grain size has unexpected effects on the acting softening mechanisms. A coarsening in the starting microstructure leads to a higher flow stress and a remarkable higher hardening at elevated temperatures. Furthermore, the nucleation of dynamic recrystallized grains is enormously retarded due to the less pronounced grain boundary bulging in a coarser grained microstructure compared to a finer one. As a consequence, discontinuous dynamic recrystallization generates a metastable grain size, that is finer than the steady state grain size.
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2013-05-15
A multiscale coarse-grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long-range solute/solvent electrostatic microscopic interactions, up to the 1-μm scale, by considering a reduced amount of computational resources. All the required parameters are assigned to reproduce available data concerning the solvation of single ions. Such a strategy makes it possible to reproduce with good accuracy the solvation properties concerning simple ion pairs in solution (in particular, the asymptotic behavior of the ion pair potentials of mean force). This new method represents an extension of the polarizable pseudoparticle solvent model, which has been recently improved to account for the main features of hydrophobic effects in liquid water (Masella et al., J. Comput. Chem. 2011, 32, 2664). This multiscale approach is well suited to be used for computing the impact of charge changes in free energy computations, in terms of both accuracy and efficiency. PMID:23382002
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
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.
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments
Protein secondary-structure description with a coarse-grained model.
Kneller, Gerald R; Hinsen, Konrad
2015-07-01
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913
Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.
Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma
2015-11-01
Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time. PMID:26386454
A Ciampalini; M Firpo
2015-12-01
This study aims to develop a better understanding of the stratigraphy of the southern side of the Maritime Alps and of the Ligurian Sea during the Plio-Pleistocene. Five stratigraphic sections were measured and studied in the Segno River valley (Liguria, Italy). These sections are composed of Lower to Middle Pleistocene marine and continental deposits. Based on detailed mapping and sedimentological analysis, 12 marine and deltaic facies were identified. These facies were grouped into facies associations. Two allostratigraphic units were recognized, namely U1 and U2 from oldest to youngest. The lower unit (U1) represents the evolution of a coarse-grained delta developed in a valley or embayment. Within the deltaic sequence, transgressive and highstand systems tracts were recognized. The coarsening/shallowing upward trend observed within the sections suggests that the delta prograded rapidly in the landward portion of the canyon adjacent to the paleo-river outlet. The upper boundary of U1 is represented by a subaerial unconformity overlain by U2, which is composed of sediments deposited by several alluvial fan systems.
Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation.
Villa, Alessandra; Peter, Christine; van der Vegt, Nico F A
2009-03-28
We discuss the development of a coarse-grained (CG) model for molecular dynamics (MD) simulation of a hydrophobic dipeptide, diphenylalanine, in aqueous solution. The peptide backbone is described with two CG beads per amino acid, the side groups and charged end groups are each described with one CG bead. In the derivation of interaction functions between CG beads we follow a bottom-up strategy where we devise potentials such that the resulting CG simulation reproduces the conformational sampling and the intermolecular interactions observed in an atomistic simulation of the same peptide. In the CG model, conformational flexibility of the peptide is accounted for through a set of intra-molecular (bonded) potentials. The approach followed to obtain the bonded potentials is discussed in detail. The CG potentials for nonbonded interactions are based on potentials of mean force obtained by atomistic simulations in aqueous solution. Following this approach, solvent mediation effects are included in the effective bead-bead nonbonded interactions and computationally very efficient (solvent-free) simulations of self-assembly processes can be performed. We show that the conformational properties of the all-atom dipeptide in explicit solvent can be accurately reproduced with the CG model. Moreover, preliminary simulations of peptide self-assembly performed with the CG model illustrate good agreement with results obtained from all-atom, explicit solvent simulations. PMID:19280018
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V.
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V., E-mail: aneimark@rutgers.edu [Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, New Jersey 08854-8058 (United States)
2016-01-07
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments. PMID:26747818
Coarse-graining complex dynamics: Continuous Time Random Walks vs. Record Dynamics
Sibani, Paolo
2013-02-01
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 distribution of the waiting time between consecutive jumps. We first argue that CTRW are inadequate to describe macroscopic relaxation processes for three reasons: macroscopic variables are not self-averaging, memory effects require an all-knowing observer, and different mechanisms whereby the jumps affect 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-law and logarithmic relaxation behaviors ubiquitous in complex dynamics, together with the sub-diffusive time dependence of the Mean Square Displacement characteristic of single particles moving in a complex environment.
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
Weberszpil, J
2013-01-01
In this work, we investigate aspects of the electron, muon and tau gyromagnetic ratios (g-factor) in a fractional coarse-grained scenario, by adopting a Modified Riemann-Liouville (MRL) fractional calculus. We point out the possibility of mapping the experimental values of the specie's g-factors into a theoretical parameter which accounts for fractionality, without computing higher-order QED calculations. We wish to understand whether the value of (g-2) may be traced back to a fractionality of space-time.The justification for the difference between the experimental and the theoretical value g=2 stemming from the Dirac equation is given in the terms of the complexity of the interactions of the charged leptons, considered as pseudo-particles and "dressed" by the interactions and the medium. Stepwise, we build up a fractional Dirac equation from the fractional Weyl equation that, on the other hand, was formulated exclusively in terms of the helicity operator. From the fractional angular momentum algebra, in a co...
A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals
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
A coarse-grained generalized second law for holographic conformal field theories
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.
pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study
Enciso, Marta; Site, Luigi Delle
2013-01-01
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This protein structure presents a remarkable chain stiffness andis formed by two or more long helical peptides that are interacting like the strands of a rope. Chain length and rigidity are the key aspects needed to extend previous peptide interaction potentials to this particular case; however the original model is naturally recovered when the length or the ridigity of the simulated chain are reduced. We apply the model and discuss results for two cases: (a) the folding/unfolding transition of a generic coiled coil as a function of pH; (b) behavior of a specific sequence as a function of the acidity conditions. In this latter case results are compared with experimental data from the literature in order to comment about the consistency of our approach.
Coarse-graining the distribution function of cold dark matter II
Henriksen, R N
2004-01-01
We study analytically the coarse and fine-grained distribution function established by the self-similar infall of collisionless matter. We find this function explicitly for isotropic and spherically symmetric systems in terms of cosmological initial conditions. The coarse-grained function is structureless and steady but the familiar phase space sheet sub-structure is recovered in the fine-grained limit. By breaking the self-similarity of the halo infall we are able to argue for a central density flattening. In addition there will be an edge steepening. The best fitting analytic density function is likely to be provided by a high order polytrope fit smoothly to an outer power law of index -3 for isolated systems. There may be a transition to a -4 power law in the outer regions of tidally truncated systems. We find a progressive central flattening that is expected to end either in the non-singular isothermal sphere, or in non-singular metastable polytropic cores. Therefore a collisionless system may pass throug...
Coarse-Grain QoS-Aware Dynamic Instance Provisioning for Interactive Workload in the Cloud
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.
Stretching and twisting of the DNA duplexes in coarse-grained dynamical models
Niewieczerzał, Szymon; Cieplak, Marek
2009-11-01
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching—unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.
Stretching and twisting of the DNA duplexes in coarse-grained dynamical models
Niewieczerzal, Szymon; Cieplak, Marek [Institute of Physics, Polish Academy of Science, Aleja Lotnikow 32/48, 02-668 Warsaw (Poland)
2009-11-25
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching-unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.
Thermal Dileptons from Coarse-Grained Transport as Fireball Probes at SIS Energies
Galatyuk, Tetyana; Rapp, Ralf; Seck, Florian; Stroth, Joachim
2015-01-01
Utilizing a coarse-graining method to convert hadronic transport simulations of Au+Au collisions at SIS energies into local temperature, baryon and pion densities, we compute the pertinent radiation of thermal dileptons based on an in-medium $\\rho$ spectral function that describes available spectra at ultrarelativistic collision energies. In particular, we analyze in how far the resulting yields and slopes of the invariant-mass spectra can probe the lifetime and temperatures of the fireball. We find that dilepton radiation sets in after the initial overlap phase of the colliding nuclei of about 7 fm/c, and lasts for about 13 fm/c. This duration closely coincides with the development of the transverse collectivity of the baryons, thus establishing a direct correlation between hadronic collective effects and thermal EM radiation, and supporting a near local equilibration of the system. This fireball "lifetime" is substantially smaller than the typical 20-30 fm/c that naive considerations of the density evolutio...
Cosmic spherical void via coarse-graining and averaging non-spherical structures
Inhomogeneous cosmological models are able to fit cosmological observations without dark energy under the assumption that we live close to the 'center' of a very large-scale under-dense region. Most studies fitting observations by means of inhomogeneities also assume spherical symmetry, and thus being at (or very near) the center may imply being located at a very special and unlikely observation point. We argue that such spherical voids should be treated only as a gross first approximation to configurations that follow from a suitable smoothing out of the non-spherical part of the inhomogeneities on angular scales. In this Letter we present a toy construction that supports the above statement. The construction uses parts of the Szekeres model, which is inhomogeneous and anisotropic thus it also addresses the limitations of spherical inhomogeneities. By using the thin-shell approximation (which means that the Israel-Darmois continuity conditions are not fulfilled between the shells) we construct a model of evolving cosmic structures, containing several elongated supercluster-like structures with underdense regions between them, which altogether provides a reasonable coarse-grained description of cosmic structures. While this configuration is not spherically symmetric, its proper volume average yields a spherical void profile of 250 Mpc that roughly agrees with observations. Also, by considering a non-spherical inhomogeneity, the definition of a 'center' location becomes more nuanced, and thus the constraints placed by fitting observations on our position with respect to this location become less restrictive.
Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei
2016-02-01
In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.
2015-06-01
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.
Coarse-grained molecular simulations of the melting kinetics of small unilamellar vesicles.
Patel, Lara A; Kindt, James T
2016-02-14
Simulations of small unilamellar lipid bilayer vesicles have been performed to model their response to an instantaneous rise in temperature, starting from an initial low-temperature structure, to temperatures near or above the main chain transition temperature. The MARTINI coarse-grained force-field was used to construct slabs of gel-phase DPPC bilayers, which were assembled into truncated icosahedral structures containing 13 165 or 31 021 lipids. Equilibration at 280 K produced structures with several (5-8) domains, characterized by facets of lipids packed in the gel phase connected by disordered ridges. Instantaneous heating to final temperatures ranging from 290 K to 310 K led to partial or total melting over 500 ns trajectories, accompanied by changes in vesicle shape and the sizes and arrangements of remaining gel-phase domains. At temperatures that produced partial melting, the gel-phase lipid content of the vesicles followed an exponential decay, similar in form and timescale to the sub-microsecond phase of melting kinetics observed in recent ultrafast IR temperature-jump experiments. The changing rate of melting appears to be the outcome of a number of competing contributions, but changes in curvature stress arising from the expansion of the bilayer area upon melting are a major factor. The simulations give a more detailed picture of the changes that occur in frozen vesicles following a temperature jump, which will be of use for the interpretation of temperature-jump experiments on vesicles. PMID:26701014
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
A coarse-grained generalized second law for holographic conformal field theories
Bunting, William; Marolf, Donald
2015-01-01
We consider the universal sector of a $d$-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 $S_{CFT} + \\frac{A(H_{B, \\text{perturbed}})}{4G_{d}}$ is non-decreasing, where $A(H_{B, \\text{perturbed}})$ 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 $A_{ren}(H_{\\rm bulk})$ 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. Anothe...
Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations
Nandigrami, Prithviraj
2015-01-01
Calmodulin (CaM) is a ubiquitous calcium binding protein consisting of two structurally similar domains with distinct stabilities, binding affinities, and flexibilities. We present coarse grained simulations that suggest the mechanism for the domain's allosteric transitions between the open and closed conformations depend on subtle differences in the folded state topology of the two domains. Throughout a wide temperature range, the simulated transition mechanism of the N-terminal domain (nCaM) follows a two-state transition mechanism while domain opening in the C-terminal domain (cCaM) involves unfolding and refolding of the tertiary structure. The appearance of the unfolded intermediate occurs at a higher temperature in nCaM than it does in cCaM. That is, we find that cCaM unfolds more readily along the transition route than nCaM. Furthermore, unfolding and refolding of the domain significantly slows the domain opening and closing rates of cCaM, a distinct scenario which can potentially influence the mechani...
Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)
2013-12-21
One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.
Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet
2013-12-01
One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.
Synthetic Aperture Focusing Technique in Ultrasonic Inspection of Coarse Grained Materials
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
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.
One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties
Computer simulation of strength and ductility of nanotwin-strengthened coarse-grained metals
Guo, X.; Ji, R.; Weng, G. J.; Zhu, L. L.; Lu, J.
2014-10-01
The superior strength-ductility combination in nanotwin (NT)-strengthened metals has provided a new potential for optimizing the mechanical properties of coarse-grained (CG) metals. In this paper computer simulations based on the mechanism-based strain gradient plasticity and the Johnson-Cook failure criterion have been carried out to uncover the critical factors that serve to provide this dual function. Our results indicate that both the distribution characteristics of the NT regions and the constitutive relations of the NT phase can have a significant impact on the strength and ductility of the CG Cu strengthened by the NT regions. In particular, twin spacing, distribution characteristics such as arrangement, shape and orientation, together with volume fraction of the NT regions, can all have significant effects. Along the way, we also discovered that microcrack initiation, coalescence and deflection constituted the entire failure process. Significant insights into the morphology of NT regions that could deliver superior strength and ductility combination for CG metals have been established.
Equation of state for a coarse-grained DPPC monolayer at the air/water interface
Adhangale, Parag S.; Gaver, Donald P., III
Pulmonary surfactant, a complex mixture of phospholipids and proteins, secreted by the type II epithelial cells in the lungs, is crucial to reducing the effort required for breathing. A lack of adequate amounts of pulmonary surfactant in underdeveloped lungs of premature infants results in infant respiratory distress syndrome (RDS). Surfactant replacement therapy (SRT) is the approved method of mitigating the effects of RDS. The development of new SRT regimens requires a fundamental understanding of the links between surfactant biochemistry and functionality. We use a coarse-grained (CG) model to predict the surface pressure-surface concentration relationship (equation of state) for pure DPPC, which is a major component of endogenous and synthetic pulmonary surfactant mixtures. We show that the model can be efficiently used to predict the equation of state in excellent agreement with experimental results. We also study the structure of the monolayer as a function of the surface tension of the system. We show that a decrease in the applied surface tension results in an increase in order in the head group region and a decrease in order in the tail region of DPPC. This technique may be useful in the prediction of equations of state for surfactant replacements.
Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization
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
Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling.
Zheng, Wenjun
2016-08-01
Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc. PMID:27090373
Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array
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
Global- and local-scale characterisation of bed surface structure in coarse-grained alluvial rivers
Powell, Mark; Ockelford, Annie; Nguyen, Thao; Wood, Jo; Rice, Steve; Reid, Ian; Tate, Nick
2013-04-01
It is widely recognised that adjustments in bed surface grain size (texture) and grain arrangement (structure) exert significant controls on the stability of coarse-grained alluvial rivers. Modifications to bed surface texture and structure occur during active sediment transport and are mediated by the process of mobile armouring which concentrates coarser-than-average particles on the surface and organises them into a variety of grain- and bedform-scale configurations. Textural aspects of surface armouring are well understood to the extent that sediment transport models can be used to predict the size distribution of armours that develop under different sediment supply regimes and shear stresses. Research has also found that the adjustment of bed surface grain size is often patchy and that the development of finer-grained and coarser-grained areas of the bed has important implications for both the rate and grain size of transported sediment. The structural aspects of stream-bed armouring, however, are less well understood, largely because of the difficulty of recognising and characterising bedforms and bed-structures that have dimensions similar to their constituent particles. Moreover, bed structure is generally parameterised using global scale descriptors of the bed surface such that information on the spatial heterogeneity of the structure is lost. The aim of this poster is to characterise the structural characteristics of water-worked river gravels, paying particular attention to quantifying the spatial heterogeneity of those characteristics using local scale descriptors. Results reported from a number of flume experiments designed to simulate the spatio-temporal evolution of bed configurations (surface texture and structure) as the system adjusts to a condition of equilibrium transport are used to evaluate the spatial variability of bed surface structure and explore its significance for modelling sediment transport rates in gravel-bed rivers. Keywords: bed
The impact of resolution upon entropy and information in coarse-grained models
Foley, Thomas T. [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Shell, M. Scott, E-mail: shell@engineering.ucsb.edu [Department of Chemical Engineering, University of California, Santa Barbara, California 93106 (United States); Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2015-12-28
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, S{sub W}, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into S{sub W}. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, −TS{sub W} is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.
Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array
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
Flechsig, Holger
2016-02-01
ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter
Hu, Hongda; Shu, Hong
2015-05-01
Heavy computation limits the use of Kriging interpolation methods in many real-time applications, especially with the ever-increasing problem size. Many researchers have realized that parallel processing techniques are critical to fully exploit computational resources and feasibly solve computation-intensive problems like Kriging. Much research has addressed the parallelization of traditional approach to Kriging, but this computation-intensive procedure may not be suitable for high-resolution interpolation of spatial data. On the basis of a more effective serial approach, we propose an improved coarse-grained parallel algorithm to accelerate ordinary Kriging interpolation. In particular, the interpolation task of each unobserved point is considered as a basic parallel unit. To reduce time complexity and memory consumption, the large right hand side matrix in the Kriging linear system is transformed and fixed at only two columns and therefore no longer directly relevant to the number of unobserved points. The MPI (Message Passing Interface) model is employed to implement our parallel programs in a homogeneous distributed memory system. Experimentally, the improved parallel algorithm performs better than the traditional one in spatial interpolation of annual average precipitation in Victoria, Australia. For example, when the number of processors is 24, the improved algorithm keeps speed-up at 20.8 while the speed-up of the traditional algorithm only reaches 9.3. Likewise, the weak scaling efficiency of the improved algorithm is nearly 90% while that of the traditional algorithm almost drops to 40% with 16 processors. Experimental results also demonstrate that the performance of the improved algorithm is enhanced by increasing the problem size.
The impact of resolution upon entropy and information in coarse-grained models
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, SW, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into SW. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, −TSW is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models
Freeman, Gordon Samuel
DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence
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.
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model
Capdevila, Carlos; Miller, U; Jelenak, H; Bhadeshia, H. K. D. H.
2001-01-01
Mechanically alloyed iron-based ODS alloys have the potential for application in heat exchangers for biomass processing, with gas operating temperatures and pressures of approximately 1100°C and 15–30 bar. The yttria dispersion in such alloys improves the high-temperature creep and stress rupture life. The elevated temperature strength is enhanced by the development of a coarse-grained microstructure during recrystallisation. Factors controlling the evolution of this desirable micros...
Mechanism of the formation of peripheral coarse grain structure in hot extrusion of Al-4.5Zn-1Mg
Eivani, A. R.; Zhou, J.; Duszczyk, J.
2016-04-01
Microstructural evolution leading to peripheral coarse grain (PCG) structure in hot extruded Al-4.5Zn-1Mg rods is investigated. The extent of dynamic recrystallization (DRX) in the as-extruded product falls not in line with the basis over which the existing mechanisms for interpretation of PCG formation are built. A new mechanism is therefore proposed based on partial DRX during extrusion and nucleation and abnormal growth of statically recrsystallised grains.
Xiaoxu Li; Lianghui Gao; Weihai Fang
2016-01-01
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...
Chu, Jhih-Wei; Voth, Gregory A.
2007-01-01
In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle poi...
YAMAZAKI, Tamio
2011-01-01
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1) determination of bonded potentials, 2) scaling for time and solvent diffusivity, and 3) optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coef...
Poursina, Mohammad; Anderson, Kurt S.
2014-08-01
This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.
This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method
Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em
2016-07-01
We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.
Rui, Sun
2014-01-01
Coarse graining is an important ingredient in many multi-scale continuum-discrete solvers such as CFD--DEM (computational fluid dynamics--discrete element method) solvers for dense particle-laden flows. Although CFD--DEM solvers have become a mature technique that is widely used in multiphase flow research and industrial flow simulations, a flexible and easy-to-implement coarse graining algorithm that can work with CFD solvers of arbitrary meshes is still lacking. In this work, we proposed a new coarse graining algorithm for continuum--discrete solvers for dense particle-laden flows based on solving a transient diffusion equation. Via theoretical analysis we demonstrated that the proposed method is equivalent to the statistical kernel method with a Gaussian kernel, but the current method is much more straightforward to implement in CFD--DEM solvers. A priori numerical tests were performed to obtain the solid volume fraction fields based on given particle distributions, the results obtained by using the propos...
Sellers, Michael; Lisal, Martin; Schweigert, Igor; Larentzos, James; Brennan, John
2015-06-01
In discrete particle simulations, when an atomistic model is coarse-grained, a trade-off is made: a boost in computational speed for a reduction in accuracy. Dissipative Particle Dynamics (DPD) methods help to recover accuracy in viscous and thermal properties, while giving back a small amount of computational speed. One of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. Today, pairing the current evolution of DPD-RX with a coarse-grained potential and its chemical decomposition reactions allows for the simulation of the shock behavior of energetic materials at a timescale faster than an atomistic counterpart. In 2007, Maillet et al. introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We have recently extended the DPD-RX method and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its tranition to hot product gases within DPD-RX will be presented. Additionally, examples of the effect of microstructure on shock behavior will be shown. Approved for public release. Distribution is unlimited.
Sanyal, Tanmoy; Shell, M. Scott
2016-07-01
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.
Yang, Lee-Wei; Chng, Choon-Peng
2008-01-01
In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of 'open to close' (open-->close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764
Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.
Blanco, Marco A; Sahin, Erinc; Robinson, Anne S; Roberts, Christopher J
2013-12-19
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
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
On the Convergence of Adaptive Sequential Monte Carlo Methods
Beskos, Alexandros; Jasra, Ajay; Kantas, Nikolas; Thiery, Alexandre
2013-01-01
In several implementations of Sequential Monte Carlo (SMC) methods it is natural, and important in terms of algorithmic efficiency, to exploit the information of the history of the samples to optimally tune their subsequent propagations. In this article we provide a carefully formulated asymptotic theory for a class of such \\emph{adaptive} SMC methods. The theoretical framework developed here will cover, under assumptions, several commonly used SMC algorithms. There are only limited results a...
Rojas, Ana; Liwo, Adam; Browne, Dana; Scheraga, Harold A.
2010-01-01
The mechanism of growth of fibrils of the β-amyloid peptide (Aβ) was studied by means of a physics-based coarse-grained united-residue (UNRES) model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ1–40 fibril, an unstructured monomer was placed at a 20 Å distance from a fibril template, and allowed to interact freely with it. The monomer was not biased towards the fibril conformation, by either the force field or the MD algorithm. By using a coar...
Pandey, Ras B.; Kuang, Zhifeng; Farmer, Barry L.
2013-01-01
A hierarchical computational approach (all-atom residue to all-residue peptide) is introduced to study self-organizing structures of peptides as a function of temperature. A simulated residue-residue interaction involving all-atom description, analogous to knowledge-based analysis (with different input), is used as an input to a phenomenological coarse-grained interaction for large scales computer simulations. A set of short peptides P1 (1H 2S 3S 4Y 5W 6Y 7A 8F 9N 10N 11K 12T) is considered a...
Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems
In this work we propose a hierarchy of Markov chain Monte Carlo methods for sampling equilibrium properties of stochastic lattice systems with competing short and long range interactions. Each Monte Carlo step is composed by two or more sub-steps efficiently coupling coarse and finer state spaces. The method can be designed to sample the exact or controlled-error approximations of the target distribution, providing information on levels of different resolutions, as well as at the microscopic level. In both strategies the method achieves significant reduction of the computational cost compared to conventional Markov chain Monte Carlo methods. Applications in phase transition and pattern formation problems confirm the efficiency of the proposed methods.
Nozaki, Daijiro; Bustos-Marún, Raul; Cattena, Carlos J.; Cuniberti, Gianaurelio; Pastawski, Horacio M.
2016-04-01
Dephasing effects in electron transport in molecular systems connected between contacts average out the quantum characteristics of the system, forming a bridge to the classical behavior as the size of the system increases. For the evaluation of the conductance of the molecular systems which have sizes within this boundary domain, it is necessary to include these dephasing effects. These effects can be calculated by using the D'Amato-Pastawski model. However, this method is computationally demanding for large molecular systems since transmission functions for all pairs of atomic orbitals need to be calculated. To overcome this difficulty, we develop an efficient coarse-grained model for the calculation of conductance of molecular junctions including decoherence. By analyzing the relationship between chemical potential and inter-molecular coupling, we find that the chemical potential drops stepwise in the systems with weaker inter-unit coupling. Using this property, an efficient coarse-grained algorithm which can reduce computational costs considerably without losing the accuracy is derived and applied to one-dimensional organic systems as a demonstration. This model can be used for the study of the orientation dependence of conductivity in various phases (amorphous, crystals, and polymers) of large molecular systems such as organic semiconducting materials.
Non-Markovian coarse-grained modeling of polymeric fluids based on the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables based on the Mori-Zwanzig formalism. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons on both static and dynamic properties between the CG models with Markovian and non-Markovian approximations will be presented. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.
Implementation and analysis of an adaptive multilevel Monte Carlo algorithm
Hoel, Hakon
2014-01-01
We present an adaptive multilevel Monte Carlo (MLMC) method for weak approximations of solutions to Itô stochastic dierential equations (SDE). The work [11] proposed and analyzed an MLMC method based on a hierarchy of uniform time discretizations and control variates to reduce the computational effort required by a single level Euler-Maruyama Monte Carlo method from O(TOL-3) to O(TOL-2 log(TOL-1)2) for a mean square error of O(TOL2). Later, the work [17] presented an MLMC method using a hierarchy of adaptively re ned, non-uniform time discretizations, and, as such, it may be considered a generalization of the uniform time discretizationMLMC method. This work improves the adaptiveMLMC algorithms presented in [17] and it also provides mathematical analysis of the improved algorithms. In particular, we show that under some assumptions our adaptive MLMC algorithms are asymptotically accurate and essentially have the correct complexity but with improved control of the complexity constant factor in the asymptotic analysis. Numerical tests include one case with singular drift and one with stopped diusion, where the complexity of a uniform single level method is O(TOL-4). For both these cases the results con rm the theory, exhibiting savings in the computational cost for achieving the accuracy O(TOL) from O(TOL-3) for the adaptive single level algorithm to essentially O(TOL-2 log(TOL-1)2) for the adaptive MLMC algorithm. © 2014 by Walter de Gruyter Berlin/Boston 2014.
Vries, de R.
2011-01-01
A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large qu
Chushak, Y.; Travesset, A.
2005-12-01
Multiblock polymers in aqueous solution, where one or several blocks are hydrophobic, exhibit a rich variety of phases and states of aggregation. In this paper, we investigate a pentablock system ABCBA, where the B block is always hydrophilic and the A and C blocks have varying degrees of hydrophobicity depending on external conditions. We report coarse-grained molecular-dynamics simulations where the solvent is included explicitly and monomers interact via a 6-9 Lennard Jones potential function. The hydrophobic interaction is modeled by tuning the parameter controlling the strength of the interaction between the hydrophobic monomers and the solvent. We investigate the structure and morphology of the micelles for two concrete situations representing changes in temperature and the pH level. The simulated system is directly relevant to a recently synthesized pentablock system consisting of a triblock Pluronic® with an added pH-sensitive end group [B. C. Anderson et al., Macromolecules 36, 1670 (2003)].
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea
2012-01-01
resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in...... solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to...... experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A...
Li, Xiaoxu; Gao, Lianghui; Fang, Weihai
2016-01-01
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. PMID:27137463
Haxton, Thomas K; Zuckermann, Ronald N; Whitelam, Stephen
2016-01-12
Peptoid polymers form extended two-dimensional nanostructures via an interface-mediated assembly process: the amphiphilic peptoids first adsorb to an air-water interface as a monolayer, then buckle and collapse into free-floating bilayer nanosheets when the interface is compressed. Here, we investigate the molecular mechanism of monolayer buckling by developing a method for incorporating interface fluctuations into an implicit-solvent coarse-grained model. Representing the interface with a triangular mesh controlled by surface tension and surfactant adsorption, we predict the direction of buckling for peptoids with a segregated arrangement of charged side chains and predict that peptoids with with an alternating charge pattern should buckle less easily than peptoids with a segregated charge pattern. PMID:26647143
Highlights: • Grain refinement of 304 stainless steel facilitated to the form more Cr2O3. • Grain refinement decreased electron work function of nano/ultrafine stainless steel. • Grain refinement facilitated redox reaction and promoted to form thicker passive film. - Abstract: The electron work function in coarse grained stainless steel was higher than that in nano/ultrafine grained one. More M2O3 types oxides and thicker passive film were observed in nano/ultrafine grained 304 stainless steel. The electrochemical impedance spectroscopy results showed that grain refinement improved corrosion resistance of 304 stainless steel. The results obtained indicated that the impedance increase was attributed to decreased electron work function. Lower electron work function facilitated to form thicker passive films. The same characteristics were observed with the increasing of chloride ion concentration
Li, Xiaoxu; Gao, Lianghui; Fang, Weihai
2016-01-01
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. PMID:27137463
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.
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.
Gui-long Xie; Yong-hong Zhang; Shi-ping Huang
2012-01-01
Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model,we have simulated the cooling process of liquid n-butanol.A new set of GB parameters are obtained by fitting the results of density functional theory calculations.The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K.The cooling characteristics are determined on the basis of the variations of the density,the potential energy and orientational order parameter with temperature,whose slopes all show discontinuity.Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak.Using the discontinuous change of these thermodynamic and structure properties,we obtain the glass transition at an estimate of temperature Tg=120±10 K,which is in good agreement with experimental results 110±1 K.
Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping
2012-04-01
Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.
Yamazaki, Tamio
2011-01-01
To evaluate shear viscosity of ehylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1)determination of bonded potentials, 2)scaling for time and solvent diffusivity, and 3)optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coefficient data. With the determined parameters and the scaling relations, we evaluated shear viscosities of EGO/water binary mixtures, which are in close agreement with the experimental data, without any further fitting procedure. The largest simulation in this article corresponds to a 1.2 microseconds atomistic simulation for 100,000 atoms. Our CG model with the parameterization scheme for CG particles may be useful to study the dynamic properties of a liquid which contains relatively low molecular weight polymers or oligomers...
Coarse-grained and fine-grained parallel optimization for real-time en-face OCT imaging
Kapinchev, Konstantin; Bradu, Adrian; Barnes, Frederick; Podoleanu, Adrian
2016-03-01
This paper presents parallel optimizations in the en-face (C-scan) optical coherence tomography (OCT) display. Compared with the cross-sectional (B-scan) imagery, the production of en-face images is more computationally demanding, due to the increased size of the data handled by the digital signal processing (DSP) algorithms. A sequential implementation of the DSP leads to a limited number of real-time generated en-face images. There are OCT applications, where simultaneous production of large number of en-face images from multiple depths is required, such as real-time diagnostics and monitoring of surgery and ablation. In sequential computing, this requirement leads to a significant increase of the time to process the data and to generate the images. As a result, the processing time exceeds the acquisition time and the image generation is not in real-time. In these cases, not producing en-face images in real-time makes the OCT system ineffective. Parallel optimization of the DSP algorithms provides a solution to this problem. Coarse-grained central processing unit (CPU) based and fine-grained graphics processing unit (GPU) based parallel implementations of the conventional Fourier domain (CFD) OCT method and the Master-Slave Interferometry (MSI) OCT method are studied. In the coarse-grained CPU implementation, each parallel thread processes the whole OCT frame and generates a single en-face image. The corresponding fine-grained GPU implementation launches one parallel thread for every data point from the OCT frame and thus achieves maximum parallelism. The performance and scalability of the CPU-based and GPU-based parallel approaches are analyzed and compared. The quality and the resolution of the images generated by the CFD method and the MSI method are also discussed and compared.
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
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
Rojas, Ana; Liwo, Adam; Browne, Dana; Scheraga, Harold A
2010-12-01
The growth mechanism of β-amyloid (Aβ) peptide fibrils was studied by a physics-based coarse-grained united-residue model and molecular dynamics (MD) simulations. To identify the mechanism of monomer addition to an Aβ(1-40) fibril, we placed an unstructured monomer at a distance of 20 Å from a fibril template and allowed it to interact freely with the latter. The monomer was not biased towards fibril conformation by either the force field or the MD algorithm. With the use of a coarse-grained model with replica-exchange molecular dynamics, a longer timescale was accessible, making it possible to observe how the monomers probe different binding modes during their search for the fibril conformation. Although different assembly pathways were seen, they all follow a dock-lock mechanism with two distinct locking stages, consistent with experimental data on fibril elongation. Whereas these experiments have not been able to characterize the conformations populating the different stages, we have been able to describe these different stages explicitly by following free monomers as they dock onto a fibril template and to adopt the fibril conformation (i.e., we describe fibril elongation step by step at the molecular level). During the first stage of the assembly ("docking"), the monomer tries different conformations. After docking, the monomer is locked into the fibril through two different locking stages. In the first stage, the monomer forms hydrogen bonds with the fibril template along one of the strands in a two-stranded β-hairpin; in the second stage, hydrogen bonds are formed along the second strand, locking the monomer into the fibril structure. The data reveal a free-energy barrier separating the two locking stages. The importance of hydrophobic interactions and hydrogen bonds in the stability of the Aβ fibril structure was examined by carrying out additional canonical MD simulations of oligomers with different numbers of chains (4-16 chains), with the fibril
Eisuke Chikayama
Full Text Available BACKGROUND: Metabolic phenotyping has become an important 'bird's-eye-view' technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of 'top-down' chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. METHODOLOGY/PRINCIPAL FINDINGS: The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 (1H and (13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each (13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient (13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. CONCLUSIONS/SIGNIFICANCE: Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities
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.
We investigate the volumetric glass transition temperature Tg 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 Tg increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition Tg 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 Tg 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
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
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.
Cipcigan, Flaviu S; Crain, Jason; Martyna, Glenn J
2016-01-01
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 was recognised early-on and described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086]. However, dispersion forces are still 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]. A way of treating both polarisation and dispersion on an equal basis is to coarse grain the electrons a molecular moiety to a single quantum harmonic oscillator, as suggested as early as the 1960s by Hirschfelder, Curtiss and Bird [The Molecular Theory of Gases and Liquids (1954)]. This treatment, when solved in the strong coupling ...
Endres, Stephan; Bleicher, Marcus
2016-01-01
Dilepton production in heavy-ion collisions at collider energies - i.e., for the Relativistic Heavy-Ion Collider (RHIC) and the Large Hadron Collider (LHC) - is studied within an approach that uses coarse-grained transport simulations to calculate thermal dilepton emission applying in-medium spectral functions from hadronic many-body theory and partonic production rates based on lattice calculations. The microscopic output from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model is hereby put on a grid of space-time cells which allows to extract the local temperature and chemical potential in each cell via an equation of state. The resulting dilepton spectra are in good agreement with the experimental results for the range of RHIC energies, $\\sqrt{s_{NN}}=19.6 - 200$ GeV. The comparison of data and model outcome shows that the newest measurements by the PHENIX and STAR collaborations are consistent and that the low-mass spectra can be described by a cocktail of hadronic decay contributions togethe...
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.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2011-09-01
A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces. PMID:21647929
The effects of membrane curvature on the free energy barrier for membrane fusion have been investigated using coarse-grained molecular dynamics (CG-MD) simulations, assuming that fusion takes place through a stalk intermediate. Free energy barriers were estimated for stalk formation as well as for fusion pore formation using the guiding potential method. Specifically, the three different geometries of two apposed membranes were considered: vesicle–vesicle, vesicle–planar, and planar–planar membranes. The free energy barriers for the resulting fusion were found to depend importantly on the fusing membrane geometries; the lowest barrier was obtained for vesicular membranes. Further, lipid sorting was observed in fusion of the mixed membranes of dimyristoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine (DOPE). Specifically, DOPE molecules were found to assemble around the stalk to support the highly negative curved membrane surface. A consistent result for lipid sorting was observed when a simple continuum model (CM) was used, where the Helfrich energy and mixing entropy of the lipids were taken into account. However, the CM predicts a much higher free energy barrier than found using CG-MD. This discrepancy originates from the conformational changes of lipids, which were not considered in the CM. The results of the CG-MD simulations reveal that a large conformational change in the lipid takes place around the stalk region, which results in a reduction of free energy barriers along the stalk mechanism of membrane fusion
High-temperature creep in a coarse-grained oxide-dispersion strengthened Ni{sub 3}Al alloy
Klotz, U.E. [Eidgenoessische Technische Hochschule, Zurich (Switzerland). Inst. fuer Metallforschung; Mason, R.P. [Metal Matrix Cast Composites, Unit 1, 101 Clematis Ave, Waltham, MA 02154 (United States); Goehring, E. [Max-Planck-Institut fuer Metallforschung, Stuttgart (Germany). Inst. fuer Werkstoffwissenschaft]|[Stuttgart Univ. (Germany). Inst. fuer Metallkunde; Arzt, E. [Max-Planck-Institut fuer Metallforschung, Stuttgart (Germany). Inst. fuer Werkstoffwissenschaft]|[Stuttgart Univ. (Germany). Inst. fuer Metallkunde
1997-07-15
An oxide-dispersion strengthened (ODS) Ni{sub 3}Al(B)-alloy containing 5 at.% chromium, produced by powder metallurgy, was zone-annealed to produce a coarse-grained microstructure. The creep properties were then investigated between 1000 and 1200 C at creep rates from 10{sup -7} to 10{sup -3} s{sup -1} and the resulting experimental data were compared with several models of creep deformation. As expected, the Roesler and Arzt model for the detachment of single dislocations from the dispersoids did not satisfactorily explain the measured data. The model of Goehring and Arzt, which considers superdislocations, as present in ordered Ni{sub 3}Al, provided a much better correlation. The measured creep strengths were approximately five to ten times higher than those of fine-grained ODS-Ni{sub 3}Al; however, they were about 1000 times lower than those of commercial Ni-based alloys such as MA 6000. Suggestions for further development and experiments are made. (orig.)
MacDermaid, Christopher M.; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.; Klein, Michael L.; Fiorin, Giacomo
2015-12-01
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.
Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)
2014-05-07
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.
Szklarczyk, Oliwia; Staroń, Krzysztof; Cieplak, Marek
2009-11-01
A coarse grained molecular dynamics model with an implicit solvent is used to elucidate properties of the human topoisomerase I. The model is defined through the native structure and it allows covering significantly longer time scales than in all atom simulations. Single residue and double residue motional characteristics are studied. The results are consistent with all atom simulations reported in the literature indicating usefulness of the model in further studies of this protein. Novel findings include broadening of the description of the dynamic behavior of the lip and hinge regions and a characterization of the motional properties of the RRM binding site of the enzyme. We also consider mechanical stretching of the protein and identify sources of the force peaks. The elastic properties of topoisomerase I are predicted to be average in comparison to other proteins, yielding a maximum force of resistance to pulling which should be of order 120 pN. The contact unraveling pattern is consistent with the understanding of the structure and function of the protein. We find supporting evidence for the hypothesis that the C-terminal domain acquires an ordered structure upon binding with the core enzyme even though it forms a molten globule when in isolation. PMID:19452556
Reasor, Daniel; Clausen, Jonathan; Aidun, Cyrus
2010-11-01
In small vessels, the cellular nature of blood is of utmost importance. The investigation of the non-Newtonian effects of blood for a complete range of hematocrit values and shear rates requires the direct numerical simulation (DNS) of individual red blood cells (RBCs) immersed in Newtonian blood plasma with hemoglobin within. Consequently, a coarse-grained spectrin-link (SL) RBC membrane model is coupled with a highly scalable lattice-Boltzmann (LB) flow solver to capture RBC dynamics in isolation and in dense suspensions of O(1,000) RBCs at realistic hematocrit values. Validation results include experimental comparisons with results for isolated RBCs tumbling, tank-treading, deforming in the wheel configuration, and parachuting in a microvessel-sized rigid tube. The rheology of blood is analyzed via LB-SL simulations of RBC suspensions at physiological concentrations. The results characterize the effect of the RBC deformation on the viscosity, normal stress differences, and particle pressure. Also, a demonstration of the Fahraeus effect is included which correlates the cell-depleted wall layer thickness with tube diameter for a variety of rigid microvessel-sized tube sizes. Lastly, the Fahraeus--Lindqvist effect is demonstrated using the apparent viscosity obtained from these simulations.
ZHANG Ying-qiao; ZHANG Han-qian; LI Jin-fu; LIU Wei-ming
2009-01-01
The influence of Nb on microstructure, mechanical property and the transformation kinetics of the coarse grain heat affected zone (CGHAZ) in HSLA steels for different heat inputs, has been investigated. When welded at higher heat inputs (100-60 kJ/cm), impact toughness values of the steel without Nb are much higher than those of the steel with Nb, and the lowest span is 153 J at 60 kJ/cm. But only a little higher values are observed at lower heat inputs (40-30 kJ/cm), and the highest span is 68 J at 30 kJ/cm. Dilatation studies indicate that continuous cooling transformation starting temperatures (Ts) of CGHAZ for the steel with Nb are approximately 15-30 ℃ which are lower than those of the steel without Nb at all heat inputs. For higher heat inputs, Nb in solid solution suppresses ferrite transformation and promotes the formation of granular bainite which has detrimental effect on impact tough-ness. For lower heat inputs higher Charpy impact energy values in the steel with Nb are associated with the formation of low carbon self-tempered martensite.
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 3H2O 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 3H2O (UPu/UT oxidative dissolution of Pu(IV) associated with the surfaces of 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 oxidative dissolution of colloid-associated Pu(IV) was observed in the aged suspensions.
Ghobadi, Ahmadreza F.; Jayaraman, Arthi
2015-03-01
Gene delivery involves successful transfection of therapeutic DNA by a vector into target cells and protein expression of that genetic material. Viral vectors are effective at gene delivery but elicit harmful immunogenic responses, thus motivating ongoing research on non-viral transfection agents. Cationic polymers are a promising class of non-viral vectors due to their low immugenic responses and low toxicity, and their ability to bind to the polyanionic DNA backbone to form a polycation-DNA complex (polyplex) that is then internalized in the target cell. While past studies have shown many polycations with differing DNA transfection efficacies, there is a need for general design guidelines that can relate the molecular features of the polycation to its DNA transfection efficiency. Using atomistic and coarse-grained molecular dynamics simulations we connect polycation design to polycation-DNA binding and experimentally observed transfection efficiency. Specifically in this presentation we will discuss our recent work looking into the effect of incorporating zwitterions into lysine based polycations on the resulting polyplex structure, shape, surface charge density and stability of DNA-polycation complexes.
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
Zheng, Wenjun
2012-04-21
This study aims to model a minimal dynein motor domain capable of motor function, which consists of the linker domain, six AAA+ modules (AAA1-AAA6), coiled coil stalk, and C-terminus domain. To this end, we have used the newly solved X-ray structures of dynein motor domain to perform a coarse-grained modeling of dynein's post- and pre-powerstroke conformation and the conformational transition between them. First, we have used normal mode analysis to identify a single normal mode that captures the coupled motions of AAA1-AAA2 closing and linker domain rotation, which enables the ATP-driven recovery stroke of dynein. Second, based on the post-powerstroke conformation solved crystallographically, we have modeled dynein's pre-powerstroke conformation by computationally inducing AAA1-AAA2 closing and sliding of coiled coil stalk, and the resulting model features a linker domain near the pre-powerstroke position and a slightly tilted stalk. Third, we have modeled the conformational transition from pre- to post-powerstroke conformation, which predicts a clear sequence of structural events that couple microtubule binding, powerstroke and product release, and supports a signaling path from stalk to AAA1 via AAA3 and AAA4. Finally, we have found that a closed AAA3-AAA4 interface (compatible with nucleotide binding) is essential to the mechano-chemical coupling in dynein. Our modeling not only offers unprecedented structural insights to the motor function of dynein as described by past single-molecule, fluorescence resonance energy transfer, and electron microscopy studies, but also provides new predictions for future experiments to test. PMID:22519354
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
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 3J(HNHCα)-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
Zhang, Peng; Gao, Chao; Zhang, Na; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
2014-01-01
We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions. PMID:25530818
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.
Mustafa, Ghulam; Nandekar, Prajwal P.; Yu, Xiaofeng; Wade, Rebecca C.
2015-12-01
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.
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.
Qingzhen Hou
Full Text Available Large-scale identification of native binding orientations is crucial for understanding the role of protein-protein interactions in their biological context. Measuring binding free energy is the method of choice to estimate binding strength and reveal the relevance of particular conformations in which proteins interact. In a recent study, we successfully applied coarse-grained molecular dynamics simulations to measure binding free energy for two protein complexes with similar accuracy to full-atomistic simulation, but 500-fold less time consuming. Here, we investigate the efficacy of this approach as a scoring method to identify stable binding conformations from thousands of docking decoys produced by protein docking programs. To test our method, we first applied it to calculate binding free energies of all protein conformations in a CAPRI (Critical Assessment of PRedicted Interactions benchmark dataset, which included over 19000 protein docking solutions for 15 benchmark targets. Based on the binding free energies, we ranked all docking solutions to select the near-native binding modes under the assumption that the native-solutions have lowest binding free energies. In our top 100 ranked structures, for the 'easy' targets that have many near-native conformations, we obtain a strong enrichment of acceptable or better quality structures; for the 'hard' targets without near-native decoys, our method is still able to retain structures which have native binding contacts. Moreover, in our top 10 selections, CLUB-MARTINI shows a comparable performance when compared with other state-of-the-art docking scoring functions. As a proof of concept, CLUB-MARTINI performs remarkably well for many targets and is able to pinpoint near-native binding modes in the top selections. To the best of our knowledge, this is the first time interaction free energy calculated from MD simulations have been used to rank docking solutions at a large scale.
Ferreiro-Rangel, Carlos A; Gelb, Lev D
2013-06-13
Structural and mechanical properties of silica aerogels are studied using a flexible coarse-grained model and a variety of simulation techniques. The model, introduced in a previous study (J. Phys. Chem. C 2007, 111, 15792-15802), consists of spherical "primary" gel particles that interact through weak nonbonded forces and through microscopically motivated interparticle bonds that may break and form during the simulations. Aerogel models are prepared using a three-stage protocol consisting of separate simulations of gelation, aging, and a final relaxation during which no further bond formation is permitted. Models of varying particle size, density, and size dispersity are considered. These are characterized in terms of fractal dimensions and pore size distributions, and generally good agreement with experimental data is obtained for these metrics. The bulk moduli of these materials are studied in detail. Two different techniques for obtaining the bulk modulus are considered, fluctuation analysis and direct compression/expansion simulations. We find that the fluctuation result can be subject to systematic error due to coupling with the simulation barostat but, if performed carefully, yields results equivalent with those of compression/expansion experiments. The dependence of the bulk modulus on density follows a power law with an exponent between 3.00 and 3.15, in agreement with reported experimental results. The best correlate for the bulk modulus appears to be the volumetric bond density, on which there is also a power law dependence. Polydisperse models exhibit lower bulk moduli than comparable monodisperse models, which is due to lower bond densities in the polydisperse materials. PMID:23631801
Tsoumanis, A C; Kevrekidis, Yu G; Bafas, G V
2009-01-01
We focus at the interface between multiscale computations, bifurcation theory and social networks. In particular we address how the Equation-Free approach, a recently developed computational framework, can be exploited to systematically extract coarse-grained, emergent dynamical information by bridging detailed, agent-based models of social interactions on networks, with macroscopic, systems-level, continuum numerical analysis tools. For our illustrations we use a simple dynamic agent-based model describing the propagation of information between individuals interacting under mimesis in a social network with private and public information. We describe the rules governing the evolution of the agents emotional state dynamics and discover, through simulation, multiple stable stationary states as a function of the network topology. Using the Equation-Free approach we track the dependence of these stationary solutions on network parameters and quantify their stability in the form of coarse-grained bifurcation diagr...
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Panahi, Afra; Feig, Michael
2014-01-01
An extension of the recently developed PRIMO coarse-grained force field to membrane environments, PRIMO-M, is described. The membrane environment is modeled with the heterogeneous dielectric generalized Born (HDGB) methodology that simply replaces the standard generalized Born model in PRIMO without further parametrization. The resulting model was validated by comparing amino acid insertion free energy profiles and application in molecular dynamics simulations of membrane proteins and membran...
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.
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
We show how to implement stick boundary conditions for a spherical colloid in a solvent that is coarse-grained by the method of stochastic rotation dynamics. This allows us to measure colloidal rotational velocity auto-correlation functions by direct computer simulation. We find quantitative agreement with Enskog theory for short times and with hydrodynamic mode-coupling theory for longer times. For aqueous colloidal suspensions, the Enskog contribution to the rotational friction is larger than the hydrodynamic one when the colloidal radius drops below 35 nm
Meeker, G.P.
1995-01-01
Many coarse-grained calcium- aluminum-rich inclusions (CAIs) contain features that are inconsistent with equilibrium liquid crystallization models of origin. Spinel-free islands (SFIs) in spinel-rich cores of Type B CAIs are examples of such features. One model previously proposed for the origin of Allende 5241, a Type B1 CAI containing SFIs, involves the capture and assimilation of xenoliths by a liquid droplet in the solar nebula (El Goresy et al, 1985; MacPherson et al 1989). This study reports new textural and chemical zoning data from 5241 and identifies previously unrecognized chemical zoning patterns in the melilite mantle and in a SFI. -from Author
Strauch, Tobias
2015-01-01
The well known method C-Slow Retiming (CSR) can be used to automatically convert a given CPU into a multithreaded CPU with independent threads. These CPUs are then called streaming or barrel processors. System Hyper Pipelining (SHP) adds a new flexibility on top of CSR by allowing a dynamic number of threads to be executed and by enabling the threads to be stalled, bypassed and reordered. SHP is now applied on the programming elements (PE) of a coarse-grained reconfigurable architecture (CGRA...
Cao, R.; Li, J.; Liu, D. S.; Ma, J. Y.; Chen, J. H.
2015-07-01
This paper analyzes the micromechanism of decrease of impact toughness with increasing the welding heat input in coarse-grain heat-affected zone (CGHAZ) of a low-alloy high-strength ship-building steel plate. By comparing the microstructures, measuring the extending length of the fibrous crack, identifying the critical event of cleavage fracture, measuring the critical length, and calculating the local cleavage fracture stress σ f, and then using the basic principles of the micromechanism of cleavage fracture, this work reveals the essential causes of deteriorated toughness in the CGHAZ of high-strength steel welded joints.
Shimokawa, T.; Mortensen, Jens Jørgen; Schiøtz, Jakob; Jacobsen, Karsten Wedel
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...... 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....
Coarse-grained kinetic scheme-based simulation framework for solution growth of ZnO nanowires
Alvi, Farah, E-mail: falvi@mail.usf.edu [University of South Florida, Department of Electrical Engineering (United States); Joshi, Rakesh K. [University of South Florida, Department of Mechanical Engineering (United States); Huang, Qiang [University of Southern California, Daniel J. Epstein Department of Industrial and Systems Engineering (United States); Kumar, Ashok [University of South Florida, Department of Mechanical Engineering (United States)
2011-06-15
Kinetic Monte Carlo (KMC)-based stochastic model is used to understand the growth of zinc oxide nanowires from aqueous solution containing chemical precursors and capping agent. Through a hydrothermal growth mechanism, the average diameter of zinc oxide wires obtained is around 300 nm, whereas the length is order of several micrometers. Our Monte Carlo algorithm is based on the continuous-time Monte Carlo algorithm of Bortz, Kalos and Lebowitz (BKL) methodology. Both reactions and diffusion mechanisms assigning stochastic probabilities have been simulated. In algorithm, the ZnO atoms were treated as individual particles which diffuse in solution substrate and interact with other type of atoms. Once attached with growing nanowires, the diffusion rate of ZnO atom is considerably reduced. Since in a KMC algorithm each atom can be represented individually therefore, internal noise is automatically incorporated.
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.
Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de [Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt (Germany)
2014-12-14
Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.
Graphical abstract: EBSD results showing the inhomogeneous recrystallization behavior in FSS-A after final recrystallization annealing: (a) orientation map; (b) pole figures corresponding to partial-recrystallized region 1; (c and d) ODFs (φ2-constant sections) corresponding to distinct recrystallized regions 2 and 3, respectively and (e) pole figures corresponding to recovered region 4. . Research highlights: → Recrystallization of coarse-grained Nb-bearing ferritic stainless steels → important orientation and composition effects during primary recrystallization → distinct recrystallization textures depending on the chemical composition. - Abstract: Composition and orientation effects on the final recrystallization texture of three coarse-grained Nb-containing AISI 430 ferritic stainless steels (FSSs) were investigated. Hot-bands of steels containing distinct amounts of niobium, carbon and nitrogen were annealed at 1250 deg. C for 2 h to promote grain growth. In particular, the amounts of Nb in solid solution vary from one grade to another. For purposes of comparison, the texture evolution of a hot-band sheet annealed at 1030 deg. C for 1 min (finer grain structure) was also investigated. Subsequently, the four sheets were cold rolled up to 80% reduction and then annealed at 800 deg. C for 15 min. Texture was determined using X-ray diffraction and electron backscatter diffraction (EBSD). Noticeable differences regarding the final recrystallization texture and microstructure were observed in the four investigated grades. Results suggest that distinct nucleation mechanisms take place within these large grains leading to the development of different final recrystallization textures.
Siqueira, R.P. [Departamento de Engenharia de Materiais, Escola de Engenharia de Lorena, University of Sao Paulo, 12600-970, Lorena-SP (Brazil); Sandim, H.R.Z., E-mail: hsandim@demar.eel.usp.br [Departamento de Engenharia de Materiais, Escola de Engenharia de Lorena, University of Sao Paulo, 12600-970, Lorena-SP (Brazil); Oliveira, T.R. [Centro de Pesquisa da ArcelorMittal Inox Brasil S.A., 35180-000, Timoteo-MG (Brazil); Raabe, D. [Max-Planck Institut fuer Eisenforschung, D-40237, Duesseldorf (Germany)
2011-04-15
Graphical abstract: EBSD results showing the inhomogeneous recrystallization behavior in FSS-A after final recrystallization annealing: (a) orientation map; (b) pole figures corresponding to partial-recrystallized region 1; (c and d) ODFs ({phi}{sub 2}-constant sections) corresponding to distinct recrystallized regions 2 and 3, respectively and (e) pole figures corresponding to recovered region 4. . Research highlights: {yields} Recrystallization of coarse-grained Nb-bearing ferritic stainless steels {yields} important orientation and composition effects during primary recrystallization {yields} distinct recrystallization textures depending on the chemical composition. - Abstract: Composition and orientation effects on the final recrystallization texture of three coarse-grained Nb-containing AISI 430 ferritic stainless steels (FSSs) were investigated. Hot-bands of steels containing distinct amounts of niobium, carbon and nitrogen were annealed at 1250 deg. C for 2 h to promote grain growth. In particular, the amounts of Nb in solid solution vary from one grade to another. For purposes of comparison, the texture evolution of a hot-band sheet annealed at 1030 deg. C for 1 min (finer grain structure) was also investigated. Subsequently, the four sheets were cold rolled up to 80% reduction and then annealed at 800 deg. C for 15 min. Texture was determined using X-ray diffraction and electron backscatter diffraction (EBSD). Noticeable differences regarding the final recrystallization texture and microstructure were observed in the four investigated grades. Results suggest that distinct nucleation mechanisms take place within these large grains leading to the development of different final recrystallization textures.
Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics
Braun, Daniel; Boresch, Stefan; Steinhauser, Othmar
2014-02-01
Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.
The information-based complexity of approximation problem by adaptive Monte Carlo methods
2008-01-01
In this paper, we study the complexity of information of approximation problem on the multivariate Sobolev space with bounded mixed derivative MWpr,α(Td), 1 < p < ∞, in the norm of Lq(Td), 1 < q < ∞, by adaptive Monte Carlo methods. Applying the discretization technique and some properties of pseudo-s-scale, we determine the exact asymptotic orders of this problem.
V. Pujalte
2015-07-01
Full Text Available The Paleocene–Eocene thermal maximum (PETM is represented in numerous shallow and deep marine sections of the south-central and western Pyrenees by a 2–4 m thick unit (locally ca. 20 m of clays or marly clays intercalated within a carbonate-dominated succession. The massive input of fine-grained terrestrial siliciclastics into the Pyrenean Gulf recorded by that unit has been attributed to an abrupt hydrological change during the PETM. However, the nature of such change remains controversial. Here we show that, in addition to fine-grained deposits, large volumes of coarse-grained siliciclastics were brought into the basin that were mostly accumulated in incised valleys and a long-lived deep-sea channel, both spatially restricted settings. The occurrence of these coarse-grained deposits had been known for some time, but their correlation with the PETM is reported here for the first time. The bulk of incised valley PETM deposits are cross-bedded sands and pebbly sands, almost exclusively made of quartz, currently being actively quarried. Proof of their belonging to the PETM include: (1 their stratigraphic position, sandwiched between upper Thanetian and lower Ilerdian marine carbonates, (2 organic carbon isotope data, and (3 the fact that clay minerals from the sand matrix are more than 80 % kaolinite. The axially-flowing deep-sea channel existed throughout Paleocene times in the Pyrenean Basin, within which coarse-grained calciclastic turbidites, and lesser volumes of siliciclastic turbidites, were accumulated. This Paleocene succession is capped by thick-bedded turbiditic quartz sandstones and pebbly sandstones, here assigned to the PETM based on calcareous nannoplankton, clay mineral and organic carbon isotopic data. The large and simultaneous increase in coarse- and fine-grained terrestrial siliciclastic material delivered to the Pyrenean Gulf is related to an increased intra-annual humidity gradient. During the PETM longer and drier summer
Frusawa, Hiroshi, E-mail: frusawa.hiroshi@kochi-tech.ac.jp
2014-05-01
A coarse-grained system of one-dimensional (1D) hard spheres (HSs) is created using the Delaunay tessellation, which enables one to define the quasi-0D state. It is found from comparing the quasi-0D and 1D free energy densities that a frozen state due to the emergence of quasi-0D HSs is thermodynamically more favorable than fluidity with a large-scale heterogeneity above crossover volume fraction of ϕ{sub c}=e/(1+e)=0.731⋯ , at which the total entropy of the 1D state vanishes. The Delaunay-based lattice mapping further provides a similarity between the dense HS system above ϕ{sub c} and the jamming limit in the car parking problem.
A coarse-grained system of one-dimensional (1D) hard spheres (HSs) is created using the Delaunay tessellation, which enables one to define the quasi-0D state. It is found from comparing the quasi-0D and 1D free energy densities that a frozen state due to the emergence of quasi-0D HSs is thermodynamically more favorable than fluidity with a large-scale heterogeneity above crossover volume fraction of ϕc=e/(1+e)=0.731⋯ , at which the total entropy of the 1D state vanishes. The Delaunay-based lattice mapping further provides a similarity between the dense HS system above ϕc and the jamming limit in the car parking problem.
Brizuela, Jose; Katchadjian, Pablo; Garcia, Alejandro; Desimone, Carlos
2016-02-01
The aim of this work is to obtain a C-Scan view of an austenitic stainless steel weld from a nuclear use pipe. In order to obtain this result Sectorial Scans (S-Scan) from both sides of the weld are obtained by Ultrasonic Phase Array (UT-PA). Then, spatial image compounding is performed to generate a single image from the S-Scans acquired at the same circumferential position of the transducer. These joints have a coarse grain structure which significantly reduce the transmission of the ultrasonic wave due to attenuation characteristics and backscattered noise from microstructures inside the material. For this reason, phase coherence imaging technique has been also applied to reduce the structural noise and improve the image quality. To verify detected defects, and given the impossibility of cutting the component, gammagraphy were performed with Co60.
Adaptation of the B1 leakage model to Monte Carlo criticality calculations
This paper presents an attempt to consistently adapt the B1 homogeneous leakage model within Monte Carlo criticality calculations based on the power iteration method. Unlike deterministic lattice codes, most of Monte Carlo-based reactor physics codes perform lattice calculations without introducing leakage models. The critical flux is however required to accurately compute homogenized cross sections and diffusion coefficients in the context of lattice physics computation. In our proposed approach, a fundamental mode approximation is introduced in the Monte Carlo K-effective power iteration method. Similarly to the deterministic implementation of the lattice code DRAGON (typically the collision probability method), B1 equations are solved at each cycle, leading to Monte Carlo estimates for the critical buckling B2 and for the group-dependent leakage rates. These leakage reactions are then introduced in the neutron random walk. This approach is discussed on legacy PWR pin cell cases, by direct comparison with results obtained by the collision probability method. This approach leads to consistent results between the Monte Carlo and the deterministic computational ways of the DRAGON code. (author)
Lafitte, Thomas; Avendaño, Carlos; Papaioannou, Vasileios; Galindo, Amparo; Adjiman, Claire S.; Jackson, George; Müller, Erich A.
2012-06-01
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C.S. Adjiman, G. Jackson, and E.A. Müller, J. Phys. Chem. B 115, 11154 (2011)] our methodology for the development of accurate coarse-grained (CG) SAFT-γ force fields for the computer simulation of molecular fluids was introduced with carbon dioxide as a particular case study. The procedure involves the use of a molecular-based equation of state to obtain effective intermolecular parameters (from experimental fluid phase equilibrium data) appropriate for molecular simulation over a wide range of fluid conditions. We now extend the methodology to develop coarse-grained models for benzene (C6H6) that can be used in fluid phase simulations. Our SAFT-γ CG force fields for benzene consist of a simple single-segment spherical model, and a rigid three-segment ring structure of tangent spherical groups interacting via Mie (generalized Lennard-Jones) segment-segment interactions. The description of the fluid phase behaviour of benzene with our simplified CG force fields is found to be comparable to that obtained with the more sophisticated models commonly used in the field; a marked improvement is seen with our SAFT-γ models for the vapour pressure, particularly at lower temperatures. These models of benzene together with the previously developed SAFT-γ three-segment chain model of n-decane are used to develop hetero-group force fields for n-decylbenzene, in the spirit of a group contribution methodology. In our approach, the parameters of the phenyl and n-decyl groups are obtained transferably from the individual models of benzene and n-decane, respectively, and the unlike energetic parameters between the phenyl and decyl segments can be obtained from vapour-liquid equilibria data for n-decylbenzene using the SAFT-γ equation of state. The resulting CG hetero-group models are found to describe the fluid properties of n-decylbenzene over a wide range of conditions, exemplifying how our approach
Meyer, Sam
2014-01-01
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We apply the procedure on a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at the sites of histone-DNA contact, the DNA base-pairs are locally shifted outwards, consistent with locally repulsive forces exerted by the histones. In a second step, we show that the various force profiles of the analyzed structures derive locally from a unique, sequence-independent, quadratic repulsive force field, while the sequence preferences are entirely due to the internal DNA mechanics. We thus obtain the first knowledge-derived nanosca...
Meyer, Sam; Everaers, Ralf
2015-02-01
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.
Xu, Weixin; Wei, Guanghong; Su, Haibin; Nordenskiöld, Lars; Mu, Yuguang
2011-11-01
Disruption of the cellular membrane by the amyloidogenic peptide, islet amyloid polypeptide (IAPP), has been considered as one of the mechanisms of β-cell death during type 2 diabetes. The N-terminal region (residues 1-19) of the human version of IAPP is suggested to be primarily responsible for the membrane-disrupting effect of the full-length hIAPP peptide. However, the detailed assembly mode of hIAPP1-19 with membrane remains unclear. To gain insight into the interactions of hIAPP1-19 oligomer with the model membrane, we have employed coarse-grained molecular dynamics self-assembly simulations to study the aggregation of hIAPP1-19 fragments in the binary lipid made of zwitterionic dipalmitoylphosphatidylcholine (DPPC) and anionic dipalmitoylphosphatidylserine (DPPS) in the presence and absence of different levels of cholesterol content. The membrane-destabilizing effect of hIAPP1-19 is found to be modulated by the presence of cholesterol. In the absence of cholesterol, hIAPP1-19 aggregates prefer to locate inside the bilayer, forming pore-like assemblies. While in the presence of cholesterol molecules, the lipid bilayer becomes more ordered and stiff, and the hIAPP1-19 aggregates are dominantly positioned at the bilayer-water interface. The action of cholesterol may suggest a possible way to maintain the membrane integrity by small molecule interference.
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.
Dunn, Nicholas J. H.; Noid, W. G.
2016-05-01
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.
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.
Xiang-liang Wan; Kai-ming Wu; Gang Huang; Ran Wei; Lin Cheng
2014-01-01
The austenite grain growth behavior in a simulated coarse-grained heat-affected zone during thermal cycling was investigated via in situ observation. Austenite grains nucleated at ferrite grain boundaries and then grew in different directions through movement of grain boundaries into the ferrite phase. Subsequently, the adjacent austenite grains impinged against each other during theα→γtransformation. After theα→γtransformation, austenite grains coarsened via the coalescence of small grains and via boundary migration between grains. The growth process of austenite grains was a continuous process during heating, isothermal holding, and cooling in simulated thermal cy-cling. Abundant finely dispersed nanoscale TiN particles in a steel specimen containing 0.012wt%Ti effectively retarded the grain boundary migration, which resulted in refined austenite grains. When the Ti concentration in the steel was increased, the number of TiN particles de-creased and their size coarsened. The big particles were not effective in pinning the austenite grain boundary movement and resulted in coarse austenite grains.
Wood, I.; Martini, M. F.; Albano, J. M. R.; Cuestas, M. L.; Mathet, V. L.; Pickholz, M.
2016-04-01
The aim of this work is to understand the interactions of the poloxamer Pluronic F127, with lipid bilayers and its ability to self-associate in an aqueous environment. Molecular dynamics simulations at the coarse-grain scale were performed to address the behavior of single Pluronic F127 and shorter poloxamers unimers in palmitoyl-oleoyl-phosphatidyl-choline model membranes. According to the initial conditions and the poly-ethylene oxide/poly-propylene oxide composition, in water phase the unimer chain collapses into a coil conformation or adopts an interphacial U-shaped - or membrane spanning - distribution. A combination of poly-propylene oxide length, and the poly-ethylene oxide ability to cover poly-propylene oxide, is determinant for the conformation adopted by the unimer in each phase. Results of the simulations showed molecular evidence of strong interaction between Pluronic F127 and model membranes both in stable U-shaped and span conformations. The knowledge of this interaction could contribute to improve drug permeation. Additionally, we investigated the aggregation of one hundred Pluronic F127 unimers in water forming a micelle-like structure, suitable to be used as drug delivery system models.
We studied the microstructure and mechanical characteristics of spot welded specimens, fabricated from low carbon steel sheets with different microstructures. Both ultra-fine grained (UFG) steel sheet and coarse grained (CG) steel sheet were used. The refined microstructure of the UFG steel has been produced by severe plastic deformation (SPD) using the constrained groove pressing (CGP) method. The grain size of the base metals was approximately 260 nm and 30 µm in diameter, respectively, in the UFG and CG steels. Examining the microstructure of a cross section cut through the spot weld reveals a similar grain size and phase distribution in the nugget on both the sides of the initial interface between sheets. Some recrystallization is observed in the heat affected zone on the UFG side as previously reported after the welding of symmetrical UFG–UFG spot welded specimens. The same energy deposit produces larger nuggets after the spot welding of UFG steels. Moreover, the hardness distribution across the nugget changes after welding on both sides of the initial (UFG/CG) interface. This effect is presently attributed to a change in the solidification, cooling rate and tempering after welding, likely because the higher resistance of UFG steel sheets increases the heat release by the Joule effect during spot welding. These changes in the mechanical behavior modify the transition between the interfacial failure (IF) and pull out failure (PF) mode with respect to energy deposit
Yu, S. F.; Yan, N.; Chen, Y.
2016-06-01
In high heat-input multi-pass twin-wire submerged-arc welding, weld metal of previous pass will be affected by the heat input of subsequent one and form coarse-grained heat-affected zone (CGHAZ). This study focused on the effects of welding thermal cycle on the inclusions and microstructure of Ce-alloyed weld metal CGHAZ. According to the study of inclusions and microstructure of weld metal CGHAZ, it was found that the composition and type of the inclusions did not change under the effect of welding thermal cycle. Although the inclusions were coarsened slightly, the promoting ability to acicular ferrite (AF) was not deprived after thermal cycling. There are three types of AF in weld metal CGHAZ, which include oxy-sulfides of Ce inclusions-promoted AF, home-position-precipitated AF, and sympathetic AF. Results showed more than 80% of microstructure was AF, which greatly benefited the mechanical properties of weld metal CGHAZ, even though granular bainite and M-A constituents were generated.
Multiaxial creep of fine grained 0.5Cr-0.5Mo-0.25V and coarse grained 1Cr-0.5Mo steels
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)
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.
Dai, Xingxing; Yin, Qianqian; Wan, Guang; Wang, Ran; Shi, Xinyuan; Qiao, Yanjiang
2016-01-01
Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC) lipid bilayer comprised of Ceramide-N-sphingosine (CER NS) 24:0, cholesterol (CHOL) and free fatty acids (FFA) 24:0 (2:2:1) was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The “pull” effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM) experiments. PMID:27548141
Zhu, Zhixiong, E-mail: zhixiongzhu@gmail.com [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Kuzmikova, Lenka; Li, Huijun [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Barbaro, Frank [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); CBMM Technology Suisse, 14, Rue du Rhone, Geneva 1204 (Switzerland)
2014-05-01
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.
Schindler, Tanja; Kröner, Dietmar; Steinhauser, Martin O
2016-09-01
We present a molecular dynamics simulation study of the self-assembly of coarse-grained lipid molecules from unbiased random initial configurations. Our lipid model is based on a well-tried CG polymer model with an additional potential that mimics the hydrophobic properties of lipid tails. We find that several stages of self-organization of lipid clusters are involved in the dynamics of bilayer formation and that the resulting equilibrium structures sensitively depend on the strength of hydrophobic interactions hc of the lipid tails and on temperature T. The obtained stable lipid membranes are quantitatively analyzed with respect to their local structure and their degree of order. At equilibrium, we obtain self-stabilizing bilayer membrane structures that exhibit a bending stiffness κB and compression modulus KC comparable to experimental measurements under physiological conditions. We present a phase diagram of our lipid model which covers a sol-gel transition, a liquid (or gel-like) phase including stable bilayer structures and vesicle formation, as well as a quasi-crystalline phase. We also determine the exact conditions for temperature T and degree of hydrophobicity hc for stable bilayer formation including closed vesicles. PMID:27216316
Xingxing Dai
2016-08-01
Full Text Available Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC lipid bilayer comprised of Ceramide-N-sphingosine (CER NS 24:0, cholesterol (CHOL and free fatty acids (FFA 24:0 (2:2:1 was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The “pull” effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM experiments.
Joyeux, Marc
2014-01-01
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS protei...
Warchulski, R.; Gawęda, A.; Janeczek, J.; Kądziołka-Gaweł, M.
2016-03-01
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.
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
Dai, Xingxing; Yin, Qianqian; Wan, Guang; Wang, Ran; Shi, Xinyuan; Qiao, Yanjiang
2016-01-01
Borneol is a natural permeation enhancer that is effective in drugs used in traditional clinical practices as well as in modern scientific research. However, its molecular mechanism is not fully understood. In this study, a mixed coarse-grained model of stratum corneum (SC) lipid bilayer comprised of Ceramide-N-sphingosine (CER NS) 24:0, cholesterol (CHOL) and free fatty acids (FFA) 24:0 (2:2:1) was used to examine the permeation enhancing mechanism of borneol on the model drug osthole. We found two different mechanisms that were dependent on concentrations levels of borneol. At low concentrations, the lipid system maintained a bilayer structure. The addition of borneol made the lipid bilayer loosen and improved drug permeation. The "pull" effect of borneol also improved drug permeation. However, for a strongly hydrophobic drug like osthole, the permeation enhancement of borneol was limited. When most borneol molecules permeated into bilayers and were located at the hydrophobic tail region, the spatial competition effect inhibited drug molecules from permeating deeper into the bilayer. At high concentrations, borneol led to the formation of water pores and long-lived reversed micelles. This improved the permeation of osthole and possibly other hydrophobic or hydrophilic drugs through the SC. Our simulation results were supported by Franz diffusion tests and transmission electron microscope (TEM) experiments. PMID:27548141
Misra, R. D. K.; Venkatsurya, P. K. C.; Somani, M. C.; Karjalainen, L. P.
2012-12-01
We have used the recently adopted concept of phase reversion to obtain grain size from the nanograined/ultrafine-grained (NG/UFG) to fine grain (FG) regime by varying temperature-time annealing sequence of cold deformed metastable austenite. The phase-reversion induced NG/UFG structure was characterized by high strength-high ductility combination. The concept of phase reversion involves severe cold deformation of metastable austenite to generate strain-induced martensite. Upon annealing, martensite transforms back to austenite through a diffusional reversion mechanism with NG/UFG, sub-micron grains (SMG) or FG structure, depending on the annealing condition. Depth-sensing nanoindentation experiments were combined with electron microscopy to elucidate the dependence of grain size from nanograin/ultrafine-grain (NG/UFG) to coarse grain (CG) regime on the deformation mechanisms. There was distinct transition in the deformation mechanism from intense mechanical twinning and stacking faults in NG/UFG structure to strain-induced martensite formation at the intersection of shear bands in the CG structure. The transition in the deformation mechanism is discussed in terms of increase in austenite stability with decrease in grain size.
Y.T. Chen; X. Chen; Q.F. Ding; J. Zeng
2005-01-01
The microstructure and the characteristics of the inclusions embedded in ferrite matrix in simu lated coarse-grain heat affected zone (CGHAZ) of a Ti-Zr-treated high strength low alloy (HSLA) steel have been investigated. The microstructure of the simulated CGHAZ dominantly consisted of intragranular acicular ferrite (IAF) combining with a small amount of polygonal ferrite (PF), widmanstatten ferrite (WF), bainite ferrite (BF), pearlite and martensite-austenite (M-A) islands. The PF, WF and BF were generally observed at the prior austenite grain boundaries and the interlocking acicular ferrite was usually found intragranularly. It was found that the inclusions were composed of Ti2O3, ZrO2 Al2O3 locating at the center of the particles and MnS lying on the surface layer of the inclusions. The intragranular complex inclusions prornoted the acicular ferrite formation and the refinement of microstructure whilst those at prior austenite grain boundaries caused PF formation on the inclusions. The simulated CGHAZ con sisting of such complicated microstructure exhibited desired mechanical properties.
Mohseni, Peyman; Solberg, Jan Ketil; Karlsen, Morten; Akselsen, Odd Magne; Østby, Erling
2014-01-01
Local brittle zones, i.e., martensite-austenite (M-A) islands, are formed within the coarse-grained heat-affected zone (CGHAZ) and the intercritically reheated CGHAZ (ICCGHAZ) during welding of many HSLA steels. In the current study, the M-A constituents in the microstructure of simulated ICCGHAZ of an API X80 pipeline steel were investigated using transmission electron microscopy and scanning electron microscopy. The focused ion beam technique was applied to make TEM specimens of M-A constituents that were located in the initiation sites of cleavage cracks. The main purpose of the study was to identify crack-initiation sites of cleavage fracture in ICCGHAZ and to prove the presence of M-A constituents in such initiation sites. Twinned martensite was detected in all local brittle zones that were investigated in the current study, demonstrating that they are M-A constituents. It was also demonstrated that the fracture initiation occurred preferentially at M-A constituents by a debonding mechanism rather than cracking of the M-A constituents.
Zhang, Y.Q. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China)], E-mail: yingqiaozhang@yahoo.com.cn; Zhang, H.Q. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China); Research Institute for Advanced Structural Steel, R and D Center, Baoshan Iron and Steel Limited Company, Shanghai 201900 (China); Liu, W.M. [Department of Materials Science and Engineering, Shanghai Jiaotong University, Shanghai 200030 (China); Hou, H. [Research Institute for Advanced Structural Steel, R and D Center, Baoshan Iron and Steel Limited Company, Shanghai 201900 (China)
2009-01-15
Continuous cooling transformation diagrams of the coarse grain heat-affected zone and microstructure after continuous cooling were investigated for 610 MPa class high-strength low-alloy (HSLA) structural steels with and without niobium. For the steel without Nb, grain boundary ferrite, degenerate pearlite and acicular ferrite are produced at slower cooling rates. Bainite phase is formed at faster cooling rates. However, for the steel with Nb, granular bainite is dominant at a large range of cooling rates. At cooling rates <32 K/s, transformation start temperature is decreased by 20 K approximately in the steel with Nb compared with that without Nb. Ferrite nucleation at prior austenite grain boundaries is suppressed and the cooling rate region for granular bainite transformation is broadened. At cooling rates >32 K/s, Nb addition has no obvious influence on transformation start temperature, but it influences microstructure transformation significantly. Martensite is observed in steel with Nb at faster cooling rates, but not produced in steel without Nb.
Khodabakhshi, F.; Kazeminezhad, M., E-mail: mkazemi@sharif.edu; Kokabi, A.H.
2015-06-18
We studied the microstructure and mechanical characteristics of spot welded specimens, fabricated from low carbon steel sheets with different microstructures. Both ultra-fine grained (UFG) steel sheet and coarse grained (CG) steel sheet were used. The refined microstructure of the UFG steel has been produced by severe plastic deformation (SPD) using the constrained groove pressing (CGP) method. The grain size of the base metals was approximately 260 nm and 30 µm in diameter, respectively, in the UFG and CG steels. Examining the microstructure of a cross section cut through the spot weld reveals a similar grain size and phase distribution in the nugget on both the sides of the initial interface between sheets. Some recrystallization is observed in the heat affected zone on the UFG side as previously reported after the welding of symmetrical UFG–UFG spot welded specimens. The same energy deposit produces larger nuggets after the spot welding of UFG steels. Moreover, the hardness distribution across the nugget changes after welding on both sides of the initial (UFG/CG) interface. This effect is presently attributed to a change in the solidification, cooling rate and tempering after welding, likely because the higher resistance of UFG steel sheets increases the heat release by the Joule effect during spot welding. These changes in the mechanical behavior modify the transition between the interfacial failure (IF) and pull out failure (PF) mode with respect to energy deposit.
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
Quan, Xuebo; Peng, ChunWang; Dong, Jiaqi; Zhou, Jian
2016-04-14
In this work, the structural properties of amphiphilic polymer-brush-grafted gold nanoparticles (AuNPs) at the oil-water interface were investigated by coarse-grained simulations. The effects of grafting architecture (diblock, mixed and Janus brush-grafted AuNPs) and hydrophilicity of polymer brushes are discussed. Simulation results indicate that functionalized AuNPs present abundant morphologies including typical core-shell, Janus-type, jellyfish-like, etc., in a water or oil-water solvent environment. It is found that hydrophobic/weak hydrophilic polymer-brush-grafted AuNPs have better phase transfer performance, especially for AuNPs modified with hydrophobic chains as outer blocks and weak hydrophilic chains as inner blocks. This kind of AuNP can cross the interface region and move into the oil phase completely. For hydrophobic/strong hydrophilic polymer-brush-grafted AuNPs, they are trapped in the interface region instead of moving into any phase. The mechanism of phase transfer is ascribed to the flexibility and mobility of outer blocks. Besides, we study the desorption energy by PMF analysis. The results demonstrate that Janus brush-grafted AuNPs show the highest interfacial stability and activity, which can be further strengthened by increasing the hydrophilicity of grafted polymer brushes. This work will promote the industrial applications of polymer-brush-grafted NPs such as phase transfer catalysis and Pickering emulsion catalysis. PMID:26954721
Adaptive resolution simulation of an atomistic protein in MARTINI water
We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations
Adaptive Multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model
Navarro, C A; Deng, Youjin
2015-01-01
The study of disordered spin systems through Monte Carlo simulations has proven to be a hard task due to the adverse energy landscape present at the low temperature regime, making it difficult for the simulation to escape from a local minimum. Replica based algorithms such as the Exchange Monte Carlo (also known as parallel tempering) are effective at overcoming this problem, reaching equilibrium on disordered spin systems such as the Spin Glass or Random Field models, by exchanging information between replicas of neighbor temperatures. In this work we present a multi-GPU Exchange Monte Carlo method designed for the simulation of the 3D Random Field Model. The implementation is based on a two-level parallelization scheme that allows the method to scale its performance in the presence of faster and GPUs as well as multiple GPUs. In addition, we modified the original algorithm by adapting the set of temperatures according to the exchange rate observed from short trial runs, leading to an increased exchange rate...
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 (ATOPLS). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the ATOPLS 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 (ATCHARMM) 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, ATOPLS 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 CG and
Ghelichi, Mahdi; Qazvini, Nader Taheri
2016-05-18
We present the results of a Langevin dynamics simulation study of micellar organization and hydrogel formation in the solutions of coarse-grained ABA copolymer chains. Polymer chains are modeled as bead-spring chains of Lennard-Jones particles by explicit treatment of ionic species in implicit solvent. The studied copolymer is composed of a polyelectrolyte midblock flanked by two hydrophobic endblocks. We explore the self-assembly of copolymer solutions at a fixed polymer concentration and temperature upon systematic variation of the midblock charge fraction, valency of neutralizing counterions, and the stiffness and length of hydrophobic endblocks. Minimization of the surface energy, conformational entropy of the midblock chains, electrostatic repulsion of midblock charges, and the translational entropy of counterions are found to play central roles in controlling the self-organization features of copolymer solutions. Flower-like micelles with A-blocks forming the core of spherical aggregates and B-blocks constituting the micelle corona are established for the neutral midblocks. Increasing the charge content of B chains lowers the fraction of loop conformations and yields a spanning hydrogel network with midblocks bridging the hydrophobic clusters. Counterion valence is shown to exert a strong effect on the micelle size and network structure. The increase in the rigidity of terminal A-blocks increases the fraction of bridging chains and results in the formation of a hydrogel network with bundle-like hydrophobic domains. Longer endblocks are shown to increase the hydrophobic cluster size and enhance the bridged midblock fraction. The qualitative agreement between the experimental and theoretical studies is also discussed. The comprehensive molecular picture provides a framework for the future studies of stimuli-responsive copolymer systems. PMID:27116478
Andrea N Kravats
2016-01-01
Full Text Available Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation.
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.
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.
Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM
2008-01-01
Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.
Multidimensional stochastic approximation Monte Carlo.
Zablotskiy, Sergey V; Ivanov, Victor A; Paul, Wolfgang
2016-06-01
Stochastic Approximation Monte Carlo (SAMC) has been established as a mathematically founded powerful flat-histogram Monte Carlo method, used to determine the density of states, g(E), of a model system. We show here how it can be generalized for the determination of multidimensional probability distributions (or equivalently densities of states) of macroscopic or mesoscopic variables defined on the space of microstates of a statistical mechanical system. This establishes this method as a systematic way for coarse graining a model system, or, in other words, for performing a renormalization group step on a model. We discuss the formulation of the Kadanoff block spin transformation and the coarse-graining procedure for polymer models in this language. We also apply it to a standard case in the literature of two-dimensional densities of states, where two competing energetic effects are present g(E_{1},E_{2}). We show when and why care has to be exercised when obtaining the microcanonical density of states g(E_{1}+E_{2}) from g(E_{1},E_{2}). PMID:27415383
Qian, Guangqiang; Yang, Zhuanling; Dong, Zhibao; Luo, Wanyin; Zhang, Zhengcai; Lu, Junfeng
2016-04-01
The aeolian process over fine to medium sand beds has been thoroughly discussed based on short-term, in-situ observations and wind tunnel tests. However, little is known about the long period variation of aeolian sediment transport as well as the geomorphological significance of saltating process, in particular, on the coarse-grained surface. By means of a segmented, eight-directional sand trap (SEDST) designed by the authors, the aeolian sediment transport on zibar surface was measured in the Kumtagh Desert of NW China. The SEDST has eight sub-traps faced to eight directions, each sub-trap contains a vertical array of samplers with four openings at 0 - 0.1 m, 0.1 - 0.2 m, 0.2 - 0.4 m and 0.4 - 1.0 m, respectively. Each opening is connected with an underground sand chamber. During the 1-yr field observation since May 2014, sediments were collected for six times with an interval of 1 to 3 months depending on the wind strength. The total weight of the captured sediments is 314.76 kg and most of them (54%) were transported within 0.1 m above the ground. The sediment transport rate ranges from 0.43 to 64.47 g/m.min for the six runs, the maximum transport rate occurred during the period of Aug to Oct 2014 with sediments from the north direction. The annual mean transport rate changes between 11.81 and 28.49 g/m.min and the sediments are mainly blown from the N, NE and NW directions. The resultant sediment transport direction (net transport) is SSE (172.92°), which implies the major sediment source direction. The sediment flux profiles can be fitted with the exponential decay function for six runs and all directions. Three groups can be identified from the gradients of the fitting curves, i.e. the N, NE and NW cluster, the S and SE cluster, as well as the E, SE and W cluster. Each cluster represents a particular combination of sediment source features and geomorphological settings that may significantly affect the formation process of zibars. The sediment transport
Nishizawa, Manami; Nishizawa, Kazuhisa, E-mail: kazunet@med.teikyo-u.ac.jp [Teikyo University School of Medical Technology, Itabashi, Tokyo (Japan)
2014-08-21
Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT{sup OPLS}). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT{sup OPLS} PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT{sup CHARMM}) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT{sup OPLS} PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA){sub 3} peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These
Le Bris, C.; Rouchon, P.; Roussel, J.
2015-12-01
We present a twofold contribution to the numerical simulation of Lindblad equations. First, an adaptive numerical approach to approximate Lindblad equations using low-rank dynamics is described: a deterministic low-rank approximation of the density operator is computed, and its rank is adjusted dynamically, using an on-the-fly estimator of the error committed when reducing the dimension. On the other hand, when the intrinsic dimension of the Lindblad equation is too high to allow for such a deterministic approximation, we combine classical ensemble averages of quantum Monte Carlo trajectories and a denoising technique. Specifically, a variance reduction method based on the consideration of a low-rank dynamics as a control variate is developed. Numerical tests for quantum collapse and revivals show the efficiency of each approach, along with the complementarity of the two approaches.
An adaptive Monte-Carlo Markov chain algorithm for inference from mixture signals
Adaptive Metropolis (AM) is a powerful recent algorithmic tool in numerical Bayesian data analysis. AM builds on a well-known Markov Chain Monte Carlo algorithm but optimizes the rate of convergence to the target distribution by automatically tuning the design parameters of the algorithm on the fly. Label switching is a major problem in inference on mixture models because of the invariance to symmetries. The simplest (non-adaptive) solution is to modify the prior in order to make it select a single permutation of the variables, introducing an identifiability constraint. This solution is known to cause artificial biases by not respecting the topology of the posterior. In this paper we describe an online relabeling procedure which can be incorporated into the AM algorithm. We give elements of convergence of the algorithm and identify the link between its modified target measure and the original posterior distribution of interest. We illustrate the algorithm on a synthetic mixture model inspired by the muonic water Cherenkov signal of the surface detectors in the Pierre Auger Experiment.
Kink, Dimitri; Bast, Alexander; Meyer, Christine; Meier, Wolfgang; Egli, Markus; Gärtner, Holger
2014-05-01
. In order to confirm this assumption and possibly find more important root properties which have an influence on soil stabilization, the root systems of seven trees (three grey alder, four mountain maple) were excavated and analyzed. The study site is a catchment, where shallow landslides are common. It is located in the Prättigau valley in the Eastern Swiss Alps and was eco-engineered in 1997. The substrate is coarse-grained morainic material, mean annual air temperature reaches 4.64°C, average precipitation is 1170 mm, and the altitude is about 1000 m a.s.l.. The root system of each tree was uncovered carefully by hand to keep the roots undamaged, before removal it was photographed in situ to document the root distribution. The root systems were then cut into single root pieces of about 20 cm length and the position of each sample was documented. The root samples were then hierarchically classified in several root classes. The tensile strength of more than 500 samples was determined. In addition, the values for age, diameter, and root moisture were ascertained. Since it was assumed, that the cellular structure of the roots has an influence on the tensile strength, two microscopic thin-sections were prepared from all successfully tested root samples. The microscopic analysis focused on anatomical parameters such as the size and number of vessels, their distribution as well as their conductivity. The results for the final correlation between the anatomical characteristics and the root's tensile strength are presented for both tree species.
Adaptive resolution simulation of an atomistic protein in MARTINI water
Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej
2014-01-01
We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coa
Kreis, K.; Fogarty, A. C.; Kremer, K.; Potestio, R.
2015-09-01
In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One of the main advantages of such approaches is the computational efficiency gained in the coarse-grained region. In this respect the best coarse-grained system to employ in the low resolution region would be the ideal gas, making intermolecular force calculations in the coarse-grained subdomain redundant. In this case, however, a smooth coupling is challenging due to the high energetic imbalance between typical liquids and a system of non-interacting particles. In the present work, we investigate this approach, using as a test case the most biologically relevant fluid, water. We demonstrate that a successful coupling of water to the ideal gas can be achieved with current adaptive resolution methods, and discuss the issues that remain to be addressed.
Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej
2016-01-01
The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to
The mechanical properties of the coarse grained (CG) Ni-18.75 at.% Fe alloy (the average grain size is 35 mkm) were studied in uniaxial compression with a constant rate in the temperature range 4.2-350 K. The temperature dependence of yield stress was measured, and the shape of the stress-strain curves was analyzed. The temperature dependences of flow stress, strain rate sensitivity of flow stress and activation volume of plastic deformation were measured for plastic strain of 2 %. The thermal activation analysis of the experimental data was carried out. It is shown that the plastic deformation of coarse grained alloy in the temperature range 35-350 K has a thermally activated type and it is controlled by the single deformation mechanism. Empirical estimates of the parameters of dislocation interaction with local barriers and the values of effective and internal stresses were obtained. The comparable analysis was carried out of the regularities of the low-temperature thermally activated plastic deformation of the alloy in CG and nanocrystalline (NC) states. It is concluded that the microscopic barriers, controlling the thermally activated plastic flow, are different in NC and CG states. The range of local barriers, which can determine the thermally activated dis-location plasticity in NC and CG states, is discussed.
Jagoda-Cwiklik, Barbara; Cwiklik, Lukasz
2007-01-01
Roč. 445, 1/3 (2007), s. 42-46. ISSN 0009-2614 Institutional research plan: CEZ:AV0Z40550506 Keywords : Monte Carlo * adsorption * difusion Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.207, year: 2007
Basden, Alastair
2015-01-01
The performance of a wide-field adaptive optics system depends on input design parameters. Here we investigate the performance of a multi-conjugate adaptive optics system design for the European Extremely Large Telescope, using an end-to-end Monte-Carlo adaptive optics simulation tool, DASP. We consider parameters such as the number of laser guide stars, sodium layer depth, wavefront sensor pixel scale, number of deformable mirrors, mirror conjugation and actuator pitch. We provide potential areas where costs savings can be made, and investigate trade-offs between performance and cost. We conclude that a 6 laser guide star system using 3 DMs seems to be a sweet spot for performance and cost compromise.
Moon, Joonoh; Lee, Tae-Ho; Park, Seong-Jun; Jang, Jae-il; Jang, Min-Ho; Ha, Heon-Young; Hwang, Byoungchul
2013-07-01
The tensile deformation behavior and phase transformation in the weld coarse-grained heat-affected zone (CGHAZ) of a metastable high-nitrogen austenitic stainless steel was explored through tensile tests, nanoindentation experiments, and transmission electron microscopy analysis. True stress-strain response during tensile test was found to be seriously affected by δ-ferrite fraction, which depends on peak temperature of the CGHAZs. The strain-induced martensitic transformation (SIMT) occurred in base steel, whereas the SIMT disappeared and deformation twinning occurred predominantly in the CGHAZs. The relationship among true stress-strain response, nanoindentation hardness, and deformed microstructures was carefully investigated and discussed in terms of changes of stacking fault energy.
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.
Kroonblawd, Matthew P.; Sewell, Thomas D., E-mail: sewellt@missouri.edu [Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600 (United States); Maillet, Jean-Bernard, E-mail: jean-bernard.maillet@cea.fr [CEA, DAM, DIF, F-91297 Arpajon (France)
2016-02-14
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.
Kroonblawd, Matthew P; Sewell, Thomas D; Maillet, Jean-Bernard
2016-02-14
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. PMID:26874491
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
Wetting of polymer liquids: Monte Carlo simulations and self-consistent field calculations
Müller, M
2003-01-01
Using Monte Carlo simulations and self-consistent field (SCF) theory we study the surface and interface properties of a coarse grained off-lattice model. In the simulations we employ the grand canonical ensemble together with a reweighting scheme in order to measure surface and interface free energies and discuss various methods for accurately locating the wetting transition. In the SCF theory, we use a partial enumeration scheme to incorporate single-chain properties on all length scales and use a weighted density functional for the excess free energy. The results of various forms of the density functional are compared quantitatively to the simulation results. For the theory to be accurate, it is important to decompose the free energy functional into a repulsive and an attractive part, with different approximations for the two parts. Measuring the effective interface potential for our coarse grained model we explore routes for controlling the equilibrium wetting properties. (i) Coating of the substrate by an...
Fast Lattice Monte Carlo Simulations of Polymers
Wang, Qiang; Zhang, Pengfei
2014-03-01
The recently proposed fast lattice Monte Carlo (FLMC) simulations (with multiple occupancy of lattice sites (MOLS) and Kronecker δ-function interactions) give much faster/better sampling of configuration space than both off-lattice molecular simulations (with pair-potential calculations) and conventional lattice Monte Carlo simulations (with self- and mutual-avoiding walk and nearest-neighbor interactions) of polymers.[1] Quantitative coarse-graining of polymeric systems can also be performed using lattice models with MOLS.[2] Here we use several model systems, including polymer melts, solutions, blends, as well as confined and/or grafted polymers, to demonstrate the great advantages of FLMC simulations in the study of equilibrium properties of polymers.
Rached, Nadhir B.
2013-12-01
The Monte Carlo forward Euler method with uniform time stepping is the standard technique to compute an approximation of the expected payoff of a solution of an Itô SDE. For a given accuracy requirement TOL, the complexity of this technique for well behaved problems, that is the amount of computational work to solve the problem, is O(TOL-3). A new hybrid adaptive Monte Carlo forward Euler algorithm for SDEs with non-smooth coefficients and low regular observables is developed in this thesis. This adaptive method is based on the derivation of a new error expansion with computable leading-order terms. The basic idea of the new expansion is the use of a mixture of prior information to determine the weight functions and posterior information to compute the local error. In a number of numerical examples the superior efficiency of the hybrid adaptive algorithm over the standard uniform time stepping technique is verified. When a non-smooth binary payoff with either GBM or drift singularity type of SDEs is considered, the new adaptive method achieves the same complexity as the uniform discretization with smooth problems. Moreover, the new developed algorithm is extended to the MLMC forward Euler setting which reduces the complexity from O(TOL-3) to O(TOL-2(log(TOL))2). For the binary option case with the same type of Itô SDEs, the hybrid adaptive MLMC forward Euler recovers the standard multilevel computational cost O(TOL-2(log(TOL))2). When considering a higher order Milstein scheme, a similar complexity result was obtained by Giles using the uniform time stepping for one dimensional SDEs. The difficulty to extend Giles\\' Milstein MLMC method to the multidimensional case is an argument for the flexibility of our new constructed adaptive MLMC forward Euler method which can be easily adapted to this setting. Similarly, the expected complexity O(TOL-2(log(TOL))2) is reached for the multidimensional case and verified numerically.