The Martini Coarse-Grained Force Field
Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu
2013-01-01
The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical
The MARTINI force field : Coarse grained model for biomolecular simulations
Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.
2007-01-01
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To
Martini Coarse-Grained Force Field : Extension to Carbohydrates
Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.
2009-01-01
We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The
Martini Coarse-Grained Force Field : Extension to DNA
Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.
We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the
Improved Parameters for the Martini Coarse-Grained Protein Force Field
de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.
The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too
Martini Coarse-Grained Force Field : Extension to RNA
Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Marrink, Siewert J.; Faustino, Ignacio
2017-01-01
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain
Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case
DEFF Research Database (Denmark)
Rossi, G.; Monticelli, L.; Puisto, S. R.
2011-01-01
We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....
Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simblations with Implicit Solvent
Arnarez, Clement; Uusitalo, Jaakko J.; Masman, Marcelo F.; Ingolfsson, Helgi I.; de Jong, Djurre H.; Melo, Manuel N.; Periole, Xavier; de Vries, Alex H.; Marrink, Siewert J.
Coarse-grained (CG) models allow simulation of larger systems for longer times by decreasing the number of degrees of freedom compared with all-atom models. Here we introduce an implicit-solvent version of the popular CG Martini model, nicknamed Dry Martini. To account for the omitted solvent
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
Qi, Yifei; Ingolfsson, Helgi I.; Cheng, Xi; Lee, Jumin; Marrink, Siewert J.; Im, Wonpil
Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed
DEFF Research Database (Denmark)
Siani, Pablo; de Souza, R M; Dias, L G
2016-01-01
our new data of all-atom and coarse-grained simulations of hydroperoxidized lipid monolayer and bilayer systems and (iii) provide a comparison of the MARTINI and ELBA coarse grained force fields for lipid bilayer systems. We show that the better electrostatic treatment of interactions in ELBA is able...
Comparison of coarse-grained (MARTINI) and atomistic molecular ...
Indian Academy of Sciences (India)
Rajat Desikan
as the root mean square deviation (RMSD) histograms and the inner pore radius profiles from ... ever coarse-grained simulations of membrane-proteins ..... from the MARTINI simulations show greater fluctuations than the all-atom simulations.
Martini Force Field Parameters for Glycolipids
Lopez, Cesar A.; Sovova, Zofie; van Eerden, Floris J.; de Vries, Alex H.; Marrink, Siewert J.
We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its
Genheden, Samuel
2017-10-01
We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.
Genheden, Samuel
2017-10-01
We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.
International Nuclear Information System (INIS)
Vögele, Martin; Holm, Christian; Smiatek, Jens
2015-01-01
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
Energy Technology Data Exchange (ETDEWEB)
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.
Thermodynamic forces in coarse-grained simulations
Noid, William
Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.
Faustino, Ignacio; Marrink, S. J.
2017-01-01
Summary: We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of
Bayesian calibration of coarse-grained forces: Efficiently addressing transferability
International Nuclear Information System (INIS)
Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.
2016-01-01
Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f 0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f 0 . In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.
Bayesian calibration of coarse-grained forces: Efficiently addressing transferability
Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.
2016-04-01
Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.
Directory of Open Access Journals (Sweden)
Qingzhen Hou
Full Text Available Large-scale identification of native binding orientations is crucial for understanding the role of protein-protein interactions in their biological context. Measuring binding free energy is the method of choice to estimate binding strength and reveal the relevance of particular conformations in which proteins interact. In a recent study, we successfully applied coarse-grained molecular dynamics simulations to measure binding free energy for two protein complexes with similar accuracy to full-atomistic simulation, but 500-fold less time consuming. Here, we investigate the efficacy of this approach as a scoring method to identify stable binding conformations from thousands of docking decoys produced by protein docking programs. To test our method, we first applied it to calculate binding free energies of all protein conformations in a CAPRI (Critical Assessment of PRedicted Interactions benchmark dataset, which included over 19000 protein docking solutions for 15 benchmark targets. Based on the binding free energies, we ranked all docking solutions to select the near-native binding modes under the assumption that the native-solutions have lowest binding free energies. In our top 100 ranked structures, for the 'easy' targets that have many near-native conformations, we obtain a strong enrichment of acceptable or better quality structures; for the 'hard' targets without near-native decoys, our method is still able to retain structures which have native binding contacts. Moreover, in our top 10 selections, CLUB-MARTINI shows a comparable performance when compared with other state-of-the-art docking scoring functions. As a proof of concept, CLUB-MARTINI performs remarkably well for many targets and is able to pinpoint near-native binding modes in the top selections. To the best of our knowledge, this is the first time interaction free energy calculated from MD simulations have been used to rank docking solutions at a large scale.
Energy Technology Data Exchange (ETDEWEB)
Mustafa, Ghulam, E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org; Nandekar, Prajwal P.; Yu, Xiaofeng [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Wade, Rebecca C., E-mail: Ghulam.Mustafa@h-its.org, E-mail: rebecca.wade@h-its.org [Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg (Germany); Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120 Heidelberg (Germany); Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120 Heidelberg (Germany)
2015-12-28
An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.
International Nuclear Information System (INIS)
Mustafa, Ghulam; Nandekar, Prajwal P.; Yu, Xiaofeng; Wade, Rebecca C.
2015-01-01
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
Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian
2017-12-01
We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.
Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep
2014-10-16
Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of
Energy Technology Data Exchange (ETDEWEB)
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.
International Nuclear Information System (INIS)
Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr
2015-01-01
Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems
Energy Technology Data Exchange (ETDEWEB)
Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Katsoulakis, Markos A., E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716 (United States)
2015-08-28
Using the probabilistic language of conditional expectations, we reformulate the force matching method for coarse-graining of molecular systems as a projection onto spaces of coarse observables. A practical outcome of this probabilistic description is the link of the force matching method with thermodynamic integration. This connection provides a way to systematically construct a local mean force and to optimally approximate the potential of mean force through force matching. We introduce a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (e.g., reaction coordinates, end-to-end length of chains). Furthermore, we study the equivalence of force matching with relative entropy minimization which we derive for general non-linear coarse graining maps. We present in detail the generalized force matching condition through applications to specific examples in molecular systems.
The ELBA force field for coarse-grain modeling of lipid membranes.
Directory of Open Access Journals (Sweden)
Mario Orsi
Full Text Available A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r = 1. Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC and dioleoylphosphatidylethanolamine (DOPE in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids; this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.
Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.
Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this
Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field
DEFF Research Database (Denmark)
Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena
2013-01-01
The phase behavior of the coarse-grained MARTINI model for three-component lipid bilayers composed of dipalmytoyl-phosphatidylcholine (DPPC), cholesterol (Chol), and an unsaturated phosphatidylcholine (PC) was systematically investigated by molecular dynamics simulations. The aim of this study...... is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field...... PCs, such as dilinoleyl-phosphatidylcholine (DUPC) and diarachidonoyl-phosphatidylcholine (DAPC). Through systematic tweaking of the interactions between the hydrophobic groups of the PC molecules, we show that the appearance of phase separation in three-component lipid bilayers, as modeled through...
Perspective on the Martini model
Marrink, Siewert J.; Tieleman, D. Peter
2013-01-01
The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state
Adaptive Resolution Simulation of MARTINI Solvents
Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.; de Vries, Alex H.; Marrink, Siewert J.; Praprotnik, Matej
We present adaptive resolution dynamics simulations of aqueous and apolar solvents coarse-grained molecular models that are compatible with the MARTINI force field. As representatives of both classes solvents we have chosen liquid water and butane, respectively, at ambient temperature. The solvent
Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.
2017-03-01
We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.
Martini Force Field Parameters for Glycolipids
Czech Academy of Sciences Publication Activity Database
Lopéz, C. A.; Sovová, Žofie; van Eerden, F. J.; de Vries, H.; Marrink, S.
2013-01-01
Roč. 9, č. 3 (2013), s. 1694-1708 ISSN 1549-9618 Institutional support: RVO:67179843 Keywords : molecular-dynamics simulations * coarse-grained model * phase-behavior * lipid-bilayer * ganglioside GM1 * domain formation * head groups * membrane * Monogalactosyldiacylglycerol * X-RAY Subject RIV: BO - Biophysics Impact factor: 5.310, year: 2013
Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe
2013-10-08
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.
Energy Technology Data Exchange (ETDEWEB)
MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)
2015-12-28
The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.
Müller, Erich A; Jackson, George
2014-01-01
A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.
International Nuclear Information System (INIS)
Nishizawa, Manami; Nishizawa, Kazuhisa
2014-01-01
Interaction of transmembrane (TM) proteins is important in many biological processes. Large-scale computational studies using coarse-grained (CG) simulations are becoming popular. However, most CG model parameters have not fully been calibrated with respect to lateral interactions of TM peptide segments. Here, we compare the potential of mean forces (PMFs) of dimerization of TM helices obtained using a MARTINI CG model and an atomistic (AT) Berger lipids-OPLS/AA model (AT OPLS ). For helical, tryptophan-flanked, leucine-rich peptides (WL15 and WALP15) embedded in a parallel configuration in an octane slab, the AT OPLS PMF profiles showed a shallow minimum (with a depth of approximately 3 kJ/mol; i.e., a weak tendency to dimerize). A similar analysis using the CHARMM36 all-atom model (AT CHARMM ) showed comparable results. In contrast, the CG analysis generally showed steep PMF curves with depths of approximately 16–22 kJ/mol, suggesting a stronger tendency to dimerize compared to the AT model. This CG > AT discrepancy in the propensity for dimerization was also seen for dilauroylphosphatidylcholine (DLPC)-embedded peptides. For a WL15 (and WALP15)/DLPC bilayer system, AT OPLS PMF showed a repulsive mean force for a wide range of interhelical distances, in contrast to the attractive forces observed in the octane system. The change from the octane slab to the DLPC bilayer also mitigated the dimerization propensity in the CG system. The dimerization energies of CG (AALALAA) 3 peptides in DLPC and dioleoylphosphatidylcholine bilayers were in good agreement with previous experimental data. The lipid headgroup, but not the length of the lipid tails, was a key causative factor contributing to the differences between octane and DLPC. Furthermore, the CG model, but not the AT model, showed high sensitivity to changes in amino acid residues located near the lipid-water interface and hydrophobic mismatch between the peptides and membrane. These findings may help interpret
Energy Technology Data Exchange (ETDEWEB)
Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)
2010-09-15
We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
International Nuclear Information System (INIS)
Wang Zunjing; Deserno, Markus
2010-01-01
We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.
Energy Technology Data Exchange (ETDEWEB)
Schöberl, Markus, E-mail: m.schoeberl@tum.de [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany); Zabaras, Nicholas [Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748 Garching (Germany); Department of Aerospace and Mechanical Engineering, University of Notre Dame, 365 Fitzpatrick Hall, Notre Dame, IN 46556 (United States); Koutsourelakis, Phaedon-Stelios [Continuum Mechanics Group, Technical University of Munich, Boltzmannstraße 15, 85748 Garching (Germany)
2017-03-15
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo – Expectation–Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
International Nuclear Information System (INIS)
Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.
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 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
Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio
2015-02-10
Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.
Parameters for Martini sterols and hopanoids based on a virtual-site description
Melo, M. N.; Ingolfsson, H. I.; Marrink, S. J.
2015-01-01
Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the
Quantum theory of multiscale coarse-graining.
Han, Yining; Jin, Jaehyeok; Wagner, Jacob W; Voth, Gregory A
2018-03-14
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.
Quantum theory of multiscale coarse-graining
Han, Yining; Jin, Jaehyeok; Wagner, Jacob W.; Voth, Gregory A.
2018-03-01
Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.
Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary
2018-03-01
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.
Adaptive resolution simulation of an atomistic protein in MARTINI water
International Nuclear Information System (INIS)
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 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
Coarse-grained Simulations of Substrate Export through Multidrug Efflux Transporter AcrB
Jewel, Yead; Dutta, Prashanta; Liu, Jin
2017-11-01
The treatment of bacterial infectious diseases hampered by the overexpression of multidrug resistance (MDR) systems. The MDR system actively pumps the antibiotic drugs as well as other toxic compounds out of the cells. During the pumping, AcrB (one of the key MDR components) undergoes a series of large-scale proton/substrate dependent conformational changes. In this work, we implement a hybrid coarse-grained PACE force field that couples the united-atom protein model with the coarse-grained MARTINI water/lipid, to investigate the conformational changes of AcrB. We first develop the substrate force field which is compatible with PACE, then we implement the force field to explore large scale structural changes of AcrB in microsecond simulations. The effects of the substrate and the protonation states of two key residues: Asp407 and Asp408, are investigated. Our results show that the drug export through AcrB is proton as well as substrate dependent. Our simulations explain molecular mechanisms of substrate transport through AcrB complex, as well as provide valuable insights for designing proper antibiotic drugs. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM122081.
Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease
Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta
2016-11-01
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.
MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers
Lopez, Cesar A.; Bellesia, Giovanni; Redondo, Antonio; Langan, Paul; Chundawat, Shishir P. S.; Dale, Bruce E.; Marrink, Siewert J.; Gnanakaran, S.
2015-01-01
Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale and
Coarse-graining complex dynamics
DEFF Research Database (Denmark)
Sibani, Paolo
2013-01-01
Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat...... 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...
Hierarchical coarse-graining transform.
Pancaldi, Vera; King, Peter R; Christensen, Kim
2009-03-01
We present a hierarchical transform that can be applied to Laplace-like differential equations such as Darcy's equation for single-phase flow in a porous medium. A finite-difference discretization scheme is used to set the equation in the form of an eigenvalue problem. Within the formalism suggested, the pressure field is decomposed into an average value and fluctuations of different kinds and at different scales. The application of the transform to the equation allows us to calculate the unknown pressure with a varying level of detail. A procedure is suggested to localize important features in the pressure field based only on the fine-scale permeability, and hence we develop a form of adaptive coarse graining. The formalism and method are described and demonstrated using two synthetic toy problems.
Coarse graining for synchronization in directed networks
Zeng, An; Lü, Linyuan
2011-05-01
Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) 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 networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.
Parametrizing coarse grained models for molecular systems at equilibrium
Kalligiannaki, Evangelia; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plechá č, P.; Harmandaris, V.
2016-01-01
Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.
Parametrizing coarse grained models for molecular systems at equilibrium
Kalligiannaki, Evangelia
2016-10-18
Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.
Coarse-Grained Modeling of Polyelectrolyte Solutions
Denton, Alan R.; May, Sylvio
2014-03-01
Ionic mixtures, such as electrolyte and polyelectrolyte solutions, have attracted much attention recently for their rich and challenging combination of electrostatic and non-electrostatic interparticle forces and their practical importance, from battery technologies to biological systems. Hydration of ions in aqueous solutions is known to entail ion-specific effects, including variable solubility of organic molecules, as manifested in the classic Hofmeister series for salting-in and salting-out of proteins. The physical mechanism by which the solvent (water) mediates effective interactions between ions, however, is still poorly understood. Starting from a microscopic model of a polyelectrolyte solution, we apply a perturbation theory to derive a coarse-grained model of ions interacting through both long-range electrostatic and short-range solvent-induced pair potentials. Taking these effective interactions as input to molecular dynamics simulations, we calculate structural and thermodynamic properties of aqueous ionic solutions. This work was supported by the National Science Foundation under Grant No. DMR-1106331.
Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten
Wachtel, Artur; Rao, Riccardo; Esposito, Massimiliano
2018-04-01
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.
Hybrid continuum-coarse-grained modeling of erythrocytes
Lyu, Jinming; Chen, Paul G.; Boedec, Gwenn; Leonetti, Marc; Jaeger, Marc
2018-06-01
The red blood cell (RBC) membrane is a composite structure, consisting of a phospholipid bilayer and an underlying membrane-associated cytoskeleton. Both continuum and particle-based coarse-grained RBC models make use of a set of vertices connected by edges to represent the RBC membrane, which can be seen as a triangular surface mesh for the former and a spring network for the latter. Here, we present a modeling approach combining an existing continuum vesicle model with a coarse-grained model for the cytoskeleton. Compared to other two-component approaches, our method relies on only one mesh, representing the cytoskeleton, whose velocity in the tangential direction of the membrane may be different from that of the lipid bilayer. The finitely extensible nonlinear elastic (FENE) spring force law in combination with a repulsive force defined as a power function (POW), called FENE-POW, is used to describe the elastic properties of the RBC membrane. The mechanical interaction between the lipid bilayer and the cytoskeleton is explicitly computed and incorporated into the vesicle model. Our model includes the fundamental mechanical properties of the RBC membrane, namely fluidity and bending rigidity of the lipid bilayer, and shear elasticity of the cytoskeleton while maintaining surface-area and volume conservation constraint. We present three simulation examples to demonstrate the effectiveness of this hybrid continuum-coarse-grained model for the study of RBCs in fluid flows.
Coarse grained model for semiquantitative lipid simulations
Marrink, SJ; de Vries, AH; Mark, AE
2004-01-01
This paper describes the parametrization of a new coarse grained (CG) model for lipid and surfactant systems. Reduction of the number of degrees of freedom together with the use of short range potentials makes it computationally very efficient. Compared to atomistic models a gain of 3-4 orders of
Jewel, Yead; Dutta, Prashanta; Liu, Jin
2017-10-01
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H + symport process. Lactose/H + symport is a highly complex process that involves sugar translocation, H + transfer, and large-scale protein conformational changes. The complete picture of lactose/H + symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition. © 2017 Wiley Periodicals, Inc.
Spacetime coarse grainings in nonrelativistic quantum mechanics
International Nuclear Information System (INIS)
Hartle, J.B.
1991-01-01
Sum-over-histories generalizations of nonrelativistic quantum mechanics are explored in which probabilities are predicted, not just for alternatives defined on spacelike surfaces, but for alternatives defined by the behavior of spacetime histories with respect to spacetime regions. Closed, nonrelativistic systems are discussed whose histories are paths in a given configuration space. The action and the initial quantum state are assumed fixed and given. A formulation of quantum mechanics is used which assigns probabilities to members of sets of alternative coarse-grained histories of the system, that is, to the individual classes of a partition of its paths into exhaustive and exclusive classes. Probabilities are assigned to those sets which decohere, that is, whose probabilities are consistent with the sum rules of probability theory. Coarse graining by the behavior of paths with respect to regions of spacetime is described. For example, given a single region, the set of all paths may be partitioned into those which never pass through the region and those which pass through the region at least once. A sum-over-histories decoherence functional is defined for sets of alternative histories coarse-grained by spacetime regions. Techniques for the definition and effective computation of the relevant sums over histories by operator-product formulas are described and illustrated by examples. Methods based on Euclidean stochastic processes are also discussed and illustrated. Models of decoherence and measurement for spacetime coarse grainings are described. Issues of causality are investigated. Such spacetime generalizations of nonrelativistic quantum mechanics may be useful models for a generalized quantum mechanics of spacetime geometry
Coarse graining flow of spin foam intertwiners
Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian
2016-12-01
Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional 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 as they can be of use in other contexts. 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 two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.
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-Grained Model for Water Involving a Virtual Site.
Deng, Mingsen; Shen, Hujun
2016-02-04
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.
Information Theoretic Tools for Parameter Fitting in Coarse Grained Models
Kalligiannaki, Evangelia
2015-01-07
We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics and finding the optimal parameter set for which the relative entropy rate with respect to the atomistic dynamics is minimized. The minimization problem leads to a generalization of the force matching methods to non equilibrium systems. A multiplicative noise example reveals the importance of the diffusion coefficient in the optimization problem.
Multiscale coarse-graining of the protein energy landscape.
Directory of Open Access Journals (Sweden)
Ronald D Hills
2010-06-01
Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.
Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa
2015-04-14
We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.
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.
A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry.
Directory of Open Access Journals (Sweden)
Satyan Sharma
Full Text Available The resemblance of lipid membrane models to physiological membranes determines how well molecular dynamics (MD simulations imitate the dynamic behavior of cell membranes and membrane proteins. Physiological lipid membranes are composed of multiple types of phospholipids, and the leaflet compositions are generally asymmetric. Here we describe an approach for self-assembly of a Coarse-Grained (CG membrane model with physiological composition and leaflet asymmetry using the MARTINI force field. An initial set-up of two boxes with different types of lipids according to the leaflet asymmetry of mammalian cell membranes stacked with 0.5 nm overlap, reliably resulted in the self-assembly of bilayer membranes with leaflet asymmetry resembling that of physiological mammalian cell membranes. Self-assembly in the presence of a fragment of the plasma membrane protein syntaxin 1A led to spontaneous specific positioning of phosphatidylionositol(4,5bisphosphate at a positively charged stretch of syntaxin consistent with experimental data. An analogous approach choosing an initial set-up with two concentric shells filled with different lipid types results in successful assembly of a spherical vesicle with asymmetric leaflet composition. Self-assembly of the vesicle in the presence of the synaptic vesicle protein synaptobrevin 2 revealed the correct position of the synaptobrevin transmembrane domain. This is the first CG MD method to form a membrane with physiological lipid composition as well as leaflet asymmetry by self-assembly and will enable unbiased studies of the incorporation and dynamics of membrane proteins in more realistic CG membrane models.
Testing for entanglement with periodic coarse graining
Tasca, D. S.; Rudnicki, Łukasz; Aspden, R. S.; Padgett, M. J.; Souto Ribeiro, P. H.; Walborn, S. P.
2018-04-01
Continuous-variable systems find valuable applications in quantum information processing. To deal with an infinite-dimensional Hilbert space, one in general has to handle large numbers of discretized measurements in tasks such as entanglement detection. Here we employ the continuous transverse spatial variables of photon pairs to experimentally demonstrate entanglement criteria based on a periodic structure of coarse-grained measurements. The periodization of the measurements allows an efficient evaluation of entanglement using spatial masks acting as mode analyzers over the entire transverse field distribution of the photons and without the need to reconstruct the probability densities of the conjugate continuous variables. Our experimental results demonstrate the utility of the derived criteria with a success rate in entanglement detection of ˜60 % relative to 7344 studied cases.
FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS
Harmandaris, Vagelis
2017-10-03
The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from detailed atomistic representation for high dimensional molecular systems. Different methods are described based on (a) structural properties (inverse Boltzmann approaches), (b) forces (force matching), and (c) path-space information (relative entropy). Next, we present a detailed investigation concerning the application of these methods in systems under equilibrium and non-equilibrium conditions. Finally, we present results from the application of these methods to model molecular systems.
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.
Energy Technology Data Exchange (ETDEWEB)
Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)
2014-11-07
We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.
International Nuclear Information System (INIS)
Markutsya, Sergiy; Lamm, Monica H.
2014-01-01
We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems
De Sitter stability and coarse graining
International Nuclear Information System (INIS)
Markkanen, T.
2018-01-01
We present a 4-dimensional back reaction analysis of de Sitter space for a conformally coupled scalar field in the presence of vacuum energy initialized in the Bunch-Davies vacuum. In contrast to the usual semi-classical prescription, as the source term in the Friedmann equations we use expectation values where the unobservable information hidden by the cosmological event horizon has been neglected i.e. coarse grained over. It is shown that in this approach the energy-momentum is precisely thermal with constant temperature despite the dilution from the expansion of space due to a flux of energy radiated from the horizon. This leads to a self-consistent solution for the Hubble rate, which is gradually evolving and at late times deviates significantly from de Sitter. Our results hence imply de Sitter space to be unstable in this prescription. The solution also suggests dynamical vacuum energy: the continuous flux of energy is balanced by the generation of negative vacuum energy, which accumulatively decreases the overall contribution. Finally, we show that our results admit a thermodynamic interpretation which provides a simple alternate derivation of the mechanism. For very long times the solutions coincide with flat space. (orig.)
De Sitter stability and coarse graining
Energy Technology Data Exchange (ETDEWEB)
Markkanen, T. [Imperial College London, Department of Physics, London (United Kingdom); King' s College London, Department of Physics, London (United Kingdom)
2018-02-15
We present a 4-dimensional back reaction analysis of de Sitter space for a conformally coupled scalar field in the presence of vacuum energy initialized in the Bunch-Davies vacuum. In contrast to the usual semi-classical prescription, as the source term in the Friedmann equations we use expectation values where the unobservable information hidden by the cosmological event horizon has been neglected i.e. coarse grained over. It is shown that in this approach the energy-momentum is precisely thermal with constant temperature despite the dilution from the expansion of space due to a flux of energy radiated from the horizon. This leads to a self-consistent solution for the Hubble rate, which is gradually evolving and at late times deviates significantly from de Sitter. Our results hence imply de Sitter space to be unstable in this prescription. The solution also suggests dynamical vacuum energy: the continuous flux of energy is balanced by the generation of negative vacuum energy, which accumulatively decreases the overall contribution. Finally, we show that our results admit a thermodynamic interpretation which provides a simple alternate derivation of the mechanism. For very long times the solutions coincide with flat space. (orig.)
International Nuclear Information System (INIS)
Padding, J T; Briels, W J
2011-01-01
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review current and past computer simulation techniques and critically assess their ability to provide such a link between chemistry and rheology. We distinguish between two classes of coarse-graining levels, which we term coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics (CGSD). In CGMD the coarse-grained beads are still relatively hard, thus automatically preventing bond crossing. This also implies an upper limit on the number of atoms that can be lumped together (up to five backbone carbon atoms) and therefore on the longest chain lengths that can be studied. To reach a higher degree of coarse-graining, in CGSD many more atoms are lumped together (more than ten backbone carbon atoms), leading to relatively soft beads. In that case friction and stochastic forces dominate the interactions, and action must be undertaken to prevent bond crossing. We also review alternative methods that make use of the tube model of polymer dynamics, by obtaining the entanglement characteristics through a primitive path analysis and by simulation of a primitive chain network. We finally review super-coarse-grained methods in which an entire polymer is represented by a single particle, and comment on ways to include memory effects and transient forces. (topical review)
Information Theoretic Tools for Parameter Fitting in Coarse Grained Models
Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plechac, Petr
2015-01-01
We study the application of information theoretic tools for model reduction in the case of systems driven by stochastic dynamics out of equilibrium. The model/dimension reduction is considered by proposing parametrized coarse grained dynamics
Path-space variational inference for non-equilibrium coarse-grained systems
International Nuclear Information System (INIS)
Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr
2016-01-01
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.
Path-space variational inference for non-equilibrium coarse-grained systems
Energy Technology Data Exchange (ETDEWEB)
Harmandaris, Vagelis, E-mail: harman@uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion (Greece); Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr [Department of Mathematics and Applied Mathematics, University of Crete (Greece); Katsoulakis, Markos, E-mail: markos@math.umass.edu [Department of Mathematics and Statistics, University of Massachusetts at Amherst (United States); Plecháč, Petr, E-mail: plechac@math.udel.edu [Department of Mathematical Sciences, University of Delaware, Newark, Delaware (United States)
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.
A coarse-grained model for DNA origami.
Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D
2018-02-16
Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.
Entropies from Coarse-graining: Convex Polytopes vs. Ellipsoids
Directory of Open Access Journals (Sweden)
Nikos Kalogeropoulos
2015-09-01
Full Text Available We examine the Boltzmann/Gibbs/Shannon SBGS and the non-additive Havrda-Charvát/Daróczy/Cressie-Read/Tsallis Sq and the Kaniadakis κ-entropy Sκ from the viewpoint of coarse-graining, symplectic capacities and convexity. We argue that the functional form of such entropies can be ascribed to a discordance in phase-space coarse-graining between two generally different approaches: the Euclidean/Riemannian metric one that reflects independence and picks cubes as the fundamental cells in coarse-graining and the symplectic/canonical one that picks spheres/ellipsoids for this role. Our discussion is motivated by and confined to the behaviour of Hamiltonian systems of many degrees of freedom. We see that Dvoretzky’s theorem provides asymptotic estimates for the minimal dimension beyond which these two approaches are close to each other. We state and speculate about the role that dualities may play in this viewpoint.
Renormalization and Coarse-graining of Loop Quantum Gravity
Charles, Christoph
2017-01-01
The continuum limit of loop quantum gravity is still an open problem. Indeed, no proper dynamics in known to start with and we still lack the mathematical tools to study its would-be continuum limit. In the present PhD dissertation, we will investigate some coarse-graining methods that should become helpful in this enterprise. We concentrate on two aspects of the theory's coarse-graining: finding natural large scale observables on one hand and studying how the dynamics of varying graphs could...
Design of low-power coarse-grained reconfigurable architectures
Kim, Yoonjin
2010-01-01
Coarse-grained reconfigurable architecture (CGRA) has emerged as a solution for flexible, application-specific optimization of embedded systems. Helping you understand the issues involved in designing and constructing embedded systems, Design of Low-Power Coarse-Grained Reconfigurable Architectures offers new frameworks for optimizing the architecture of components in embedded systems in order to decrease area and save power. Real application benchmarks and gate-level simulations substantiate these frameworks.The first half of the book explains how to reduce power in the configuration cache. T
Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design
International Nuclear Information System (INIS)
Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.
2010-01-01
This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and
Generalized coarse-grained Becker-Doering equations
International Nuclear Information System (INIS)
Bolton, Colin D; Wattis, Jonathan A D
2003-01-01
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
International Nuclear Information System (INIS)
Edmunds, D. M.; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.
2015-01-01
We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C 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
Coarse graining of atactic polystyrene and its derivatives
Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2014-03-01
Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarse-grain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an all-atom atactic PS melts. The non-bonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly-(t-butyl-styrene) (PtBS). An additional coarse-grained bead is used to describe the t-butyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the non-bonded interactions for PS, we show that the IBI method for the non-bonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. We would like to acknowledge Prof. Kurt Kremer for helpful discussions during this work.
Variational approach to coarse-graining of generalized gradient flows
Duong, M.H.; Lamacz, A.; Peletier, M.A.; Sharma, U.
2017-01-01
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational evolutions, and which often arises from a large-deviations principle.
Loop overhead reduction techniques for coarse grained reconfigurable architectures
Vadivel, K.; Wijtvliet, M.; Jordans, R.; Corporaal, H.
2017-01-01
Due to their flexibility and high performance, Coarse Grained Reconfigurable Array (CGRA) are a topic of increasing research interest. However, CGRAs also have the potential to achieve very high energy efficiency in comparison to other reconfigurable architectures when hardware optimizations are
Time evolution as refining, coarse graining and entangling
International Nuclear Information System (INIS)
Dittrich, Bianca; Steinhaus, Sebastian
2014-01-01
We argue that refining, coarse graining and entangling operators can be obtained from time evolution operators. This applies in particular to geometric theories, such as spin foams. We point out that this provides a construction principle for the physical vacuum in quantum gravity theories and more generally allows construction of a (cylindrically) consistent continuum limit of the theory. (paper)
Time evolution as refining, coarse graining and entangling
Dittrich, Bianca; Steinhaus, Sebastian
2014-12-01
We argue that refining, coarse graining and entangling operators can be obtained from time evolution operators. This applies in particular to geometric theories, such as spin foams. We point out that this provides a construction principle for the physical vacuum in quantum gravity theories and more generally allows construction of a (cylindrically) consistent continuum limit of the theory.
Mineral Elements Content of some Coarse Grains used as staple ...
African Journals Online (AJOL)
Analysis of mineral elements were carried out on some coarse grains used as staple food in Kano metropolis. The levels of Magnesium, Calcium, Manganese, Iron, Copper and Zinc were determined using atomic absorption spectrophotometer (AAS), and that of Sodium and Potassium were obtained using flame photometer ...
Coarse-grain modelling of protein-protein interactions
Baaden, Marc; Marrink, Siewert J.
2013-01-01
Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are
Transferable coarse-grained model for perfluorosulfonic acid polymer membranes
Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru
2017-09-01
Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.
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.
MT-ADRES: Multithreading on Coarse-Grained Reconfigurable Architecture
DEFF Research Database (Denmark)
Wu, Kehuai; Kanstein, Andreas; Madsen, Jan
2007-01-01
The coarse-grained reconfigurable architecture ADRES (Architecture for Dynamically Reconfigurable Embedded Systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......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...
Coarse grainings and irreversibility in quantum field theory
International Nuclear Information System (INIS)
Anastopoulos, C.
1997-01-01
In this paper we are interested in studying coarse graining in field theories using the language of quantum open systems. Motivated by the ideas of Hu and Calzetta on correlation histories we employ the Zwanzig projection technique to obtain evolution equations for relevant observables in self-interacting scalar field theories. Our coarse-graining operation consists in concentrating solely on the evolution of the correlation functions of degree less than n, a treatment which corresponds to the familiar truncation of the BBKGY hierarchy at the nth level. We derive the equations governing the evolution of mean-field and two-point functions thus identifying the terms corresponding to dissipation and noise. We discuss possible applications of our formalism, the emergence of classical behavior, and the connection to the decoherent histories framework. copyright 1997 The American Physical Society
FROM ATOMISTIC TO SYSTEMATIC COARSE-GRAINED MODELS FOR MOLECULAR SYSTEMS
Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plechac, Petr
2017-01-01
The development of systematic (rigorous) coarse-grained mesoscopic models for complex molecular systems is an intense research area. Here we first give an overview of methods for obtaining optimal parametrized coarse-grained models, starting from
An Evaluation of Coarse-Grained Locking for Multicore Microkernels
Elphinstone, Kevin; Zarrabi, Amirreza; Danis, Adrian; Shen, Yanyan; Heiser, Gernot
2016-01-01
The trade-off between coarse- and fine-grained locking is a well understood issue in operating systems. Coarse-grained locking provides lower overhead under low contention, fine-grained locking provides higher scalability under contention, though at the expense of implementation complexity and re- duced best-case performance. We revisit this trade-off in the context of microkernels and tightly-coupled cores with shared caches and low inter-core migration latencies. We evaluate performance on ...
Superplastic behavior of coarse-grained aluminum alloys
Chezan, AR; De Hosson, JTM
2005-01-01
In this paper we concentrate on the superplastic behavior and the microstructural evolution of two coarse-grained Al alloys: Al-4.4w/oMg and Al-4.4w/oMg-0.4w/oCu. The values for the strain rate sensitivity index and activation energy suggest that solute drag on dislocation motion is an important
Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations
Energy Technology Data Exchange (ETDEWEB)
Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai [Los Alamos National Laboratory; Hengartner, Nick [Los Alamos National Laboratory
2008-01-01
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscoplc, non-Poissonian fluctuations of the slow ones. Our approach, which is similar to the Born-Oppenhelmer approximation in quantum mechanics, follows from the stochastic path Integral representation of the cumulant generating function of reaction events. In applications with a small number of chemIcal reactions, It produces analytical expressions for cumulants of chemical fluxes between the slow variables. This allows for a low-dimensional, Interpretable representation and can be used for coarse-grained numerical simulation schemes with a small computational complexity and yet high accuracy. As an example, we derive the coarse-grained description for a chain of biochemical reactions, and show that the coarse-grained and the microscopic simulations are in an agreement, but the coarse-gralned simulations are three orders of magnitude faster.
Hu, Mingyang; de Jong, Djurre H.; Marrink, Siewert J.; Deserno, Markus
2013-01-01
We calculate the Gaussian curvature modulus (k) over bar of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We
Coarse Grained Transport Model for Neutrals in Turbulent SOL Plasmas
Energy Technology Data Exchange (ETDEWEB)
Marandet, Y.; Mekkaoui, A.; Genesio, P.; Rosato, J.; Capes, H.; Godbert-Mouret, L.; Koubiti, M.; Stamm, R., E-mail: yannick.marandet@univ-amu.fr [PIIM, CNRS/Aix-Marseille University, Marseille (France); Reiter, D.; Boerner, P. [IEK4, FZJ, Juelich (Germany)
2012-09-15
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)
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.
An exactly solvable coarse-grained model for species diversity
International Nuclear Information System (INIS)
Suweis, Samir; Maritan, Amos; Rinaldo, Andrea
2012-01-01
We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth–death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology. (paper)
Shear localization and microstructure in coarse grained beta titanium alloy
Energy Technology Data Exchange (ETDEWEB)
Wang, Bingfeng, E-mail: biw009@ucsd.edu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Key Lab of Nonferrous Materials, Ministry of Education, Central South University, Changsha, Hunan (China); Wang, Xiaoyan [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Li, Zezhou [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Ma, Rui [School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhao, Shiteng [Department of Mechanical and Aerospace Engineering, University of California, San Diego, United States of America (United States); Xie, Fangyu [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China); School of Materials Science and Engineering, Central South University, Changsha, Hunan (China); Zhang, Xiaoyong [State Key Laboratory for Powder Metallurgy, Central South University, Changsha, Hunan (China)
2016-01-15
Adiabatic shear localization plays an important role in the deformation and failure of the coarse grained beta titanium alloy Ti-5 Al-5 Mo-5 V-1 Cr-1 Fe with grain size about 1 mm at high strain rate deformation. Hat shaped specimens with different nominal shear strains are used to induce the formation of shear bands under the controlled shock-loading experiments. The true stress in the specimens can reach about 1040 MPa where the strain is about 1.83. The whole shear localization process lasts about 35 μs. The microstructures within the shear band are investigated by optical microscopy, scanning electron microscopy / electron backscatter diffraction, and transmission electron microscopy. The results show that the width of the shear bands decreases with increasing nominal shear strain, and the grains in the transition region near the shear band are elongated along the shear band, and the core of the shear band consists of the ultrafine deformed grains with width of 0.1 μm and heavy dislocations. With the aims of accommodating the imposed shear strain and maintaining neighboring grain compatibility, the grain subdivision continues to take place within the band. A fiber texture is formed in the core of the shear band. The calculated temperature rise in the shear band can reach about 722 K. Dynamic recovery is responsible for the formation of the microstructure in coarse grained beta titanium alloy.
Weak Galilean invariance as a selection principle for coarse-grained diffusive models.
Cairoli, Andrea; Klages, Rainer; Baule, Adrian
2018-05-29
How does the mathematical description of a system change in different reference frames? Galilei first addressed this fundamental question by formulating the famous principle of Galilean invariance. It prescribes that the equations of motion of closed systems remain the same in different inertial frames related by Galilean transformations, thus imposing strong constraints on the dynamical rules. However, real world systems are often described by coarse-grained models integrating complex internal and external interactions indistinguishably as friction and stochastic forces. Since Galilean invariance is then violated, there is seemingly no alternative principle to assess a priori the physical consistency of a given stochastic model in different inertial frames. Here, starting from the Kac-Zwanzig Hamiltonian model generating Brownian motion, we show how Galilean invariance is broken during the coarse-graining procedure when deriving stochastic equations. Our analysis leads to a set of rules characterizing systems in different inertial frames that have to be satisfied by general stochastic models, which we call "weak Galilean invariance." Several well-known stochastic processes are invariant in these terms, except the continuous-time random walk for which we derive the correct invariant description. Our results are particularly relevant for the modeling of biological systems, as they provide a theoretical principle to select physically consistent stochastic models before a validation against experimental data.
Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water
DEFF Research Database (Denmark)
Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore
2010-01-01
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 o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......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...
Coarse-grain parallelism using remote method invocation
Energy Technology Data Exchange (ETDEWEB)
Hebert, A. [Ecole Polytechnique de Montreal, Qc. (Canada)
2003-07-01
The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)
Coarse-grain parallelism using remote method invocation
International Nuclear Information System (INIS)
Hebert, A.
2003-01-01
The paper describes a user-oriented framework specifically designed to facilitate the development and supervision of coarse-grain parallel applications in reactor physics. The proposed user-oriented framework was designed and implemented in Java, in such a way to obtain a simple and robust application. The proposed approach is based on Java Native Interface(JNI) for integrating the Fortran legacy code and on Remote Method Invocation (RMI) for distributing the calculation load over the farm of processors. Dynamic code downloading over the network is possible. We are presenting the application of this approach to supervision of lattice calculations using the open source Dragon code. The Java layer surrounding Dragon can also be used to construct execution procedures, computational schemes and graphical user interfaces. This approach can be used with any existing legacy Fortran code, as soon as its input/output data structures are Dragon-compatible. (author)
Post-irradiation annealing of coarse-grained model alloys
Energy Technology Data Exchange (ETDEWEB)
Ray, P H.N.; Wilson, C; McElroy, R J [AEA Reactor Services, Harwell (United Kingdom)
1994-12-31
Thermal ageing and irradiation studies have been carried out on three model alloys (JPC, JPB, JPG) that have identical compositions except for different levels of phosphorus and/or copper. They have been irradiated in three conditions, as-received, heat treated to produce a coarse grained microstructure (similar to heat-affected-zone), and in this condition further aged at 450 C to produce a temper embrittled condition. One of the alloy have been subject to a post-irradiation anneal. The effect of these treatments on mechanical property changes has been characterized by Charpy testing and Vickers hardness measurements; the phosphorus segregation has been studied by a combination of STEM and Auger techniques.
Coarse-graining as a downward causation mechanism
Flack, Jessica C.
2017-11-01
Downward causation is the controversial idea that `higher' levels of organization can causally influence behaviour at `lower' levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties. I introduce a weak and strong notion of downward causation and discuss the role the strong form plays in the origins of new organizational levels. I illustrate these points with examples from the study of biological and social systems and deep neural networks. This article is part of the themed issue 'Reconceptualizing the origins of life'.
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...
Dynamics of Coarse-grained Model of Filled Rubber Composite under Deformation
Hagita, Katsumi; Ueno, Shinichi; Bito, Yasumasa; Takano, Hiroshi; Doi, Masao; Morita, Hiroshi
2010-03-01
We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Because all polymer chains are connected to one network gel, the size of simulation box under periodic boundary conditions (PBC) is set to about 33nm. We put 4 fillers, 80 polymer chains of 1024 particles, and many crosslink into the PBC box. One filler consists of 1280 particles of the C1280 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C1280 in order to make a sphere whose diameter is about 15nm. Some patterns of distribution of the fillers are examined. The stress-strain curves estimated by applying a deformation to the system in simulations qualitatively agree with those in experiments. It is successful to show hysteresis on the S-S curve between elongation / release of the filled rubber.
International Nuclear Information System (INIS)
Abbott, Lauren J.; Stevens, Mark J.
2015-01-01
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
Energy Technology Data Exchange (ETDEWEB)
Abbott, Lauren J.; Stevens, Mark J., E-mail: msteve@sandia.gov [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)
2015-12-28
A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.
Development of DPD coarse-grained models: From bulk to interfacial properties
Energy Technology Data Exchange (ETDEWEB)
Solano Canchaya, José G.; Dequidt, Alain, E-mail: alain.dequidt@univ-bpclermont.fr; Goujon, Florent; Malfreyt, Patrice [Institut de Chimie de Clermont-Ferrand, Université Blaise Pascal, Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand (France); CNRS, UMR 6296, ICCF, F-63178 Aubiere (France)
2016-08-07
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.
Energy Technology Data Exchange (ETDEWEB)
Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-09-01
Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects the measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.
Representing the Marginal Stability of Peptides in Coarse Grained Models
Sayar, Mehmet; Dalgicdir, Cahit; Ramezanghorbani, Farhad
Tertiary structure of proteins is only marginally stable; such that the folded structure is separated from local minima by as little as 10 kcal/mol. In particular for intrinsically disordered peptides, this marginal stability is key to understanding their complex behavior. Bottom-up coarse grained (CG) models for proteins/peptides which rely on structural and/or thermodynamic reference data from experiments or all atom simulations inherently focus on the equilibrium structure and fail to capture the conformational dynamics of the molecule. In this study, we present a CG model for a synthetic peptide, LK, which successfully captures the conformational flexibility of the molecule in different environments. LK peptide is composed of leucine and lysine residues and displays a stark conformational transition from a degenerate conformation in dilute solution to a fully stable alpha-helix at macroscopic and molecular interfaces. In this study we demonstrate that by carefully combining atomistic references from both the unfolded and folded states, one can create a CG model that can represent not only the folded state, but also the conformational transitions that the peptide exhibits in response to changes in the environment. M. Sayar thanks TÜBİTAK (Grant No. 212T184) and TÜBA Distinguished Young Scientist Award (2012 awardee) for financial support.
Fatigue damage in coarse-grained lean duplex stainless steels
Energy Technology Data Exchange (ETDEWEB)
Strubbia, R., E-mail: strubbia@ifir-conicet.gov.ar; Hereñú, S.; Marinelli, M.C.; Alvarez-Armas, I.
2016-04-06
The present investigation is focused on assessing the effect of a thermal treatment for grain coarsening on the low cycle fatigue damage evolution in two types of Lean Duplex Stainless Steels (LDSSs). The dislocation structure developed during cycling is observed by transmission electron microscopy (TEM). Additionally, a detailed analysis of short crack initiated and grown during low cycle fatigue (LCF) is performed by means of optical and scanning electron (SEM) microscopy in combination with automated electron back-scattered diffraction (EBSD) technique. Though in both coarse-grained LDSSs the short cracks nucleate in the ferrite phase, in each steels its origin is different. The embrittlement caused by the Cr{sub 2}N precipitation and the plastic activity sustained by each phase can explain this difference. The propagation behavior of the short cracks present two alternative growing mechanisms: the crack grows along a favorable slip plane with high Schmid Factor (SF) or the crack alternates between two slip systems. In both cases, the crack follows the path with the smallest tilt angle (β) at a grain boundary.
Improving the treatment of coarse-grain electrostatics: CVCEL
International Nuclear Information System (INIS)
Ceres, N.; Lavery, R.
2015-01-01
We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding
Improving the treatment of coarse-grain electrostatics: CVCEL.
Ceres, N; Lavery, R
2015-12-28
We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.
Improving the treatment of coarse-grain electrostatics: CVCEL
Energy Technology Data Exchange (ETDEWEB)
Ceres, N.; Lavery, R., E-mail: richard.lavery@ibcp.fr [Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367 (France)
2015-12-28
We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.
Coarse-grained molecular simulations of allosteric cooperativity
Energy Technology Data Exchange (ETDEWEB)
Nandigrami, Prithviraj; Portman, John J. [Department of Physics, Kent State University, Kent, Ohio 44242 (United States)
2016-03-14
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein’s functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca{sup 2+} ions to each domain of Calmodulin (CaM) through simulations of a simple coarse-grained model. In this model, the protein’s conformational transitions between open and closed conformational ensembles are simulated explicitly and ligand binding and unbinding are treated implicitly within the grand canonical ensemble. Ligand binding is cooperative because the binding sites are coupled through a shift in the dominant conformational ensemble upon binding. The classic Monod-Wyman-Changeux model of allostery with appropriate binding free energies to the open and closed ensembles accurately describes the simulated binding thermodynamics. The simulations predict that the two domains of CaM have distinct binding affinity and cooperativity. In particular, the C-terminal domain binds Ca{sup 2+} with higher affinity and greater cooperativity than the N-terminal domain. From a structural point of view, the affinity of an individual binding loop depends sensitively on the loop’s structural compatibility with the ligand in the bound ensemble, as well as the conformational flexibility of the binding site in the unbound ensemble.
Hou, Qingzhen; Lensink, Marc F; Heringa, Jaap; Feenstra, K Anton
2016-01-01
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
Coarse-grained debris flow dynamics on erodible beds
Lanzoni, Stefano; Gregoretti, Carlo; Stancanelli, Laura Maria
2017-03-01
A systematic set of flume experiments is used to investigate the features of velocity profiles within the body of coarse-grained debris flows and the dependence of the transport sediment concentration on the relevant parameters (runoff discharge, bed slope, grain size, and form). The flows are generated in a 10 m long laboratory flume, initially filled with a layer consisting of loose debris. After saturation, a prescribed water discharge is suddenly supplied over the granular bed, and the runoff triggers a debris flow wave that reaches nearly steady conditions. Three types of material have been used in the tests: gravel with mean grain size of 3 and 5 mm, and 3 mm glass spheres. Measured parameters included: triggering water discharge, volumetric sediment discharge, sediment concentration, flow depth, and velocity profiles. The dynamic similarity with full-sized debris flows is discussed on the basis of the relevant dimensionless parameters. Concentration data highlight the dependence on the slope angle and the importance of the quasi-static friction angle. The effects of flow rheology on the shape of velocity profiles are analyzed with attention to the role of different stress-generating mechanisms. A remarkable collapse of the dimensionless profiles is obtained by scaling the debris flow velocity with the runoff velocity, and a power law characterization is proposed following a heuristic approach. The shape of the profiles suggests a smooth transition between the different rheological regimes (collisional and frictional) that establish in the upper and lower regions of the flow and is compatible with the presence of multiple length scales dictated by the type of contacts (instantaneous or long lasting) between grains.
Directory of Open Access Journals (Sweden)
Animesh Agarwal
2017-09-01
Full Text Available We present a hierarchical coarse-graining framework for modeling semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC method. This framework forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even standard coarse-grained simulations. Previously, it was applied to simulations examining the structure of individual polymer chains in solution using up to four levels of coarse-graining (Ismail et al., J. Chem. Phys., 2005, 122, 234901 and Ismail et al., J. Chem. Phys., 2005, 122, 234902, recovering the correct scaling behavior in the coarse-grained representation. In the present work, we extend this method to the study of polymer solutions, deriving the bonded and non-bonded potentials between coarse-grained superatoms from the single chain statistics. A universal scaling function is obtained, which does not require recalculation of the potentials as the scale of the system is changed. To model semi-dilute polymer solutions, we assume the intermolecular potential between the coarse-grained beads to be equal to the non-bonded potential, which is a reasonable approximation in the case of semidilute systems. Thus, a minimal input of microscopic data is required for simulating the systems at the mesoscopic scale. We show that coarse-grained polymer solutions can reproduce results obtained from the more detailed atomistic system without a significant loss of accuracy.
Katsoulakis, Markos A.; Vlachos, Dionisios G.
2003-11-01
We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.
Coarse-grained modeling of hybrid block copolymer system
Su, Yongrui
This thesis is comprised of three major projects of my research. In the first project, I proposed a nanoparticle model and combined it with the Theoretically Informed Coarse Grained (TICG) model for pure polymer systems and the grand canonical slip springs model developed in our group to build a new model for entangled nanocomposites. With Molecule Dynamics(MD) simulation, I studied the mechanic properties of the nanocomposites, for example the influence of nanoparticles size and volume fraction on entanglements, the diffusion of polymers and nanoparticles, and the influence of nanoparticles size and volume fraction on viscosity et al.. We found that the addition of small-size nanoparticles reduces the viscosity of the nanocomposites, which is in contrary to what Einstein predicted a century ago. However, when particle increases its size to micrometers the Einstein predictions is recovered. From our simulation, we believe that small-size nanoparticles can more effectively decrease the entanglements of nanocomposites than larger particles. The free volume effect introduced by small-size nanoparticles also helps decrease the viscosity of the whole system. In the second project, I combined the Ohta-Kawasaki (OK) model [3] and the Covariance Matrix Adaptation Evolutionary Strategy(CMA-ES) to optimize the block copolymer blends self-assembly in the hole-shrink process. The aim is to predict the optimal composition and the optimal surface energy to direct the block copolymer blends self-assembly process in the confined hole. After optimization in the OK model, we calibrated the optimal results by the more reliable TICG model and got the same morphology. By comparing different optimization process, we found that the homopolymers which are comprised of the same monomers as either block of the block copolymer can form a perfect perforated hole and might have better performance than the pure block copolymer. While homopolymers which are comprised of a third-party monomers
Washizu, Hitoshi; Kajita, Seiji; Tohyama, Mamoru; Ohmori, Toshihide; Nishino, Noriaki; Teranishi, Hiroshi; Suzuki, Atsushi
2012-01-01
Coarse-grained Metropolis Monte Carlo Brownian Dynamics simulations are used to clarify the ultralow friction mechanism of a transfer film of multilayered graphene sheets. Each circular graphene sheet consists of 400 to 1,000,000 atoms confined between the upper and lower sliders and are allowed to move in 3 translational and 1 rotational directions due to thermal motion at 300 K. The sheet-sheet interaction energy is calculated by the sum of the pair potential of the sp2 carbons. The sliding simulations are done by moving the upper slider at a constant velocity. In the monolayer case, the friction force shows a stick-slip like curve and the average of the force is high. In the multilayer case, the friction force does not show any oscillation and the average of the force is very low. This is because the entire transfer film has an internal degree of freedom in the multilayer case and the lowest sheet of the layer is able to follow the equipotential surface of the lower slider.
Multi-scale coarse-graining of non-conservative interactions in molecular liquids
International Nuclear Information System (INIS)
Izvekov, Sergei; Rice, Betsy M.
2014-01-01
A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger
Multi-scale coarse-graining of non-conservative interactions in molecular liquids
Energy Technology Data Exchange (ETDEWEB)
Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M. [U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 (United States)
2014-03-14
A new bottom-up procedure for constructing non-conservative (dissipative and stochastic) interactions for dissipative particle dynamics (DPD) models is described and applied to perform hierarchical coarse-graining of a polar molecular liquid (nitromethane). The distant-dependent radial and shear frictions in functional-free form are derived consistently with a chosen form for conservative interactions by matching two-body force-velocity and three-body velocity-velocity correlations along the microscopic trajectories of the centroids of Voronoi cells (clusters), which represent the dissipative particles within the DPD description. The Voronoi tessellation is achieved by application of the K-means clustering algorithm at regular time intervals. Consistently with a notion of many-body DPD, the conservative interactions are determined through the multi-scale coarse-graining (MS-CG) method, which naturally implements a pairwise decomposition of the microscopic free energy. A hierarchy of MS-CG/DPD models starting with one molecule per Voronoi cell and up to 64 molecules per cell is derived. The radial contribution to the friction appears to be dominant for all models. As the Voronoi cell sizes increase, the dissipative forces rapidly become confined to the first coordination shell. For Voronoi cells of two and more molecules the time dependence of the velocity autocorrelation function becomes monotonic and well reproduced by the respective MS-CG/DPD models. A comparative analysis of force and velocity correlations in the atomistic and CG ensembles indicates Markovian behavior with as low as two molecules per dissipative particle. The models with one and two molecules per Voronoi cell yield transport properties (diffusion and shear viscosity) that are in good agreement with the atomistic data. The coarser models produce slower dynamics that can be appreciably attributed to unaccounted dissipation introduced by regular Voronoi re-partitioning as well as by larger
DEFF Research Database (Denmark)
Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit
2012-01-01
Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic...... resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...
Mutually unbiased coarse-grained measurements of two or more phase-space variables
Paul, E. C.; Walborn, S. P.; Tasca, D. S.; Rudnicki, Łukasz
2018-05-01
Mutual unbiasedness of the eigenstates of phase-space operators—such as position and momentum, or their standard coarse-grained versions—exists only in the limiting case of infinite squeezing. In Phys. Rev. Lett. 120, 040403 (2018), 10.1103/PhysRevLett.120.040403, it was shown that mutual unbiasedness can be recovered for periodic coarse graining of these two operators. Here we investigate mutual unbiasedness of coarse-grained measurements for more than two phase-space variables. We show that mutual unbiasedness can be recovered between periodic coarse graining of any two nonparallel phase-space operators. We illustrate these results through optics experiments, using the fractional Fourier transform to prepare and measure mutually unbiased phase-space variables. The differences between two and three mutually unbiased measurements is discussed. Our results contribute to bridging the gap between continuous and discrete quantum mechanics, and they could be useful in quantum-information protocols.
Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model
Invernizzi, Michele; Valsson, Omar; Parrinello, Michele
2017-01-01
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model
Invernizzi, Michele; Valsson, Omar; Parrinello, Michele
2017-03-01
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.
Coarse-graining free theories with gauge symmetries: the linearized case
International Nuclear Information System (INIS)
Bahr, Benjamin; Dittrich, Bianca; He Song
2011-01-01
Discretizations of continuum theories often do not preserve the gauge symmetry content. This occurs in particular for diffeomorphism symmetry in general relativity, which leads to severe difficulties in both canonical and covariant quantization approaches. We discuss here the method of perfect actions, which attempts to restore gauge symmetries by mirroring exactly continuum physics on a lattice via a coarse graining process. Analytical results can only be obtained via a perturbative approach, for which we consider the first step, namely the coarse graining of the linearized theory. The linearized gauge symmetries are exact also in the discretized theory; hence, we develop a formalism to deal with gauge systems. Finally, we provide a discretization of linearized gravity as well as a coarse graining map and show that with this choice the three-dimensional (3D) linearized gravity action is invariant under coarse graining.
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.
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.
Song, Bin; Molinero, Valeria
2013-08-07
Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.
A multi-state coarse grained modeling approach for an intrinsically disordered peptide
Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet
2017-09-01
Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.
Farrell, Kathryn; Oden, J. Tinsley
2014-07-01
Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and
Deformation and fracture of Coarse-grained Model of Filled Rubber Composites
Hagita, Katsumi; Morita, Hiroshi; Doi, Masao; Takano, Hiroshi
2011-03-01
We presented a result of coarse-grained Molecular Dynamics simulation of filled polymer melts with Sulfur-crosslink under deformation based on the Kremer-Grest Model. Under uni-axial deformation (extension) by setting Poisson's ratio to less than 0.5, facture of this polymer nanocomoposites occurs due to volume increase for increasing the strain. In order to study facture behavior, we use the original Lennard Jones potential formula (with attractive part) as interaction between polymers. The size of simulation box under periodic boundary conditions (PBC) is set to about 133nm. We put 2048 fillers, 5120 polymer chains of 1024 particles, and many crosslink into the PBC box. Due to the crosslink, all polymer chains are connected to one network gel. One filler consists of 320 particles of the C320 fullerene structure. A repulsive force from the center of the filler is applied to the particles of C320 in order to make a sphere whose diameter is about 7nm. We can observe the fracture occurs due to void created near surface of fillers for the case that interaction between polymer and filler is relatively non- attractive. Various cases of Poisson's ratio and interaction between polymer and filler are examined.
Directory of Open Access Journals (Sweden)
Denis V. Nazarov
2017-01-01
Full Text Available In this study, we present the detailed investigation of the influence of the etching medium (acidic or basic Piranha solutions and the etching time on the morphology and surface relief of ultrafine grained (UFG and coarse grained (CG titanium. The surface relief and morphology have been studied by means of scanning electron microscopy (SEM, atomic force microscopy (AFM, and the spectral ellipsometry. The composition of the samples has been determined by X-ray fluorescence analysis (XRF and X-ray Photoelectron Spectroscopy (XPS. Significant difference in the etching behavior of UFG and CG titanium has been found. UFG titanium exhibits higher etching activity independently of the etching medium. Formed structures possess higher homogeneity. The variation of the etching medium and time leads to micro-, nano-, or hierarchical micro/nanostructures on the surface. Significant difference has been found between surface composition for UFG titanium etched in basic and acidic Piranha solution. Based on the experimental data, the possible reasons and mechanisms are considered for the formation of nano- and microstructures. The prospects of etched UFG titanium as the material for implants are discussed.
Nazarov, Denis V; Zemtsova, Elena G; Solokhin, Alexandr Yu; Valiev, Ruslan Z; Smirnov, Vladimir M
2017-01-13
In this study, we present the detailed investigation of the influence of the etching medium (acidic or basic Piranha solutions) and the etching time on the morphology and surface relief of ultrafine grained (UFG) and coarse grained (CG) titanium. The surface relief and morphology have been studied by means of scanning electron microscopy (SEM), atomic force microscopy (AFM), and the spectral ellipsometry. The composition of the samples has been determined by X-ray fluorescence analysis (XRF) and X-ray Photoelectron Spectroscopy (XPS). Significant difference in the etching behavior of UFG and CG titanium has been found. UFG titanium exhibits higher etching activity independently of the etching medium. Formed structures possess higher homogeneity. The variation of the etching medium and time leads to micro-, nano-, or hierarchical micro/nanostructures on the surface. Significant difference has been found between surface composition for UFG titanium etched in basic and acidic Piranha solution. Based on the experimental data, the possible reasons and mechanisms are considered for the formation of nano- and microstructures. The prospects of etched UFG titanium as the material for implants are discussed.
Munafò, A; Panesi, M; Magin, T E
2014-02-01
A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.
Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam
2018-04-30
A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.
Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
Directory of Open Access Journals (Sweden)
Peter Spijker
2010-06-01
Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.
Directory of Open Access Journals (Sweden)
A. Bodego
2017-06-01
Full Text Available This is a field-based work that describes the stratigraphy and sedimentology of the Andatza Conglomerate Formation. Based on facies analysis three facies associations of a coarse-grained turbidite system and the related slope have been identified: (1 an inner fan of a turbidite system (or canyon and (2 a low- and (3 a high-gradient muddy slope respectively. The spatial distribution of the facies associations and the palaeocurrent analysis allow to interpret a depositional model for the Andatza Conglomerates consisting of an L-shaped, coarse-grained turbidite system, whose morphology was structurally controlled by synsedimentary basement-involved normal faults. The coarse-grained character of the turbidite system indicates the proximity of the source area, with the presence of a narrow shelf that fed the turbidite canyon from the north.
Energy Technology Data Exchange (ETDEWEB)
Cipcigan, Flaviu S., E-mail: flaviu.cipcigan@ed.ac.uk [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Sokhan, Vlad P. [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Crain, Jason [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Martyna, Glenn J. [IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 (United States)
2016-12-01
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a
International Nuclear Information System (INIS)
Cipcigan, Flaviu S.; Sokhan, Vlad P.; 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 in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a
Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study
International Nuclear Information System (INIS)
Yang, Delian; Wang, Qiang
2015-01-01
We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N m monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N m
Exact CTP renormalization group equation for the coarse-grained effective action
International Nuclear Information System (INIS)
Dalvit, D.A.; Mazzitelli, F.D.
1996-01-01
We consider a scalar field theory in Minkowski spacetime and define a coarse-grained closed time path (CTP) effective action by integrating quantum fluctuations of wavelengths shorter than a critical value. We derive an exact CTP renormalization group equation for the dependence of the effective action on the coarse-graining scale. We solve this equation using a derivative expansion approach. Explicit calculation is performed for the λφ 4 theory. We discuss the relevance of the CTP average action in the study of nonequilibrium aspects of phase transitions in quantum field theory. copyright 1996 The American Physical Society
Xu, Yinlin; Ma, Qianli D.Y.; Schmitt, Daniel T.; Bernaola-Galván, Pedro; Ivanov, Plamen Ch.
2011-01-01
We investigate how various coarse-graining methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find, that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and th...
Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.
2016-12-01
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230-233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeller through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO_MD.
Characterizing protein conformations by correlation analysis of coarse-grained contact matrices
Lindsay, Richard J.; Siess, Jan; Lohry, David P.; McGee, Trevor S.; Ritchie, Jordan S.; Johnson, Quentin R.; Shen, Tongye
2018-01-01
We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.
Power-Aware Rationale for Using Coarse-Grained Transponders in IP-Over-WDM Networks
DEFF Research Database (Denmark)
Saldaña Cercos, Silvia; Resendo, Leandro C.; Ribeiro, Moises R. N.
2015-01-01
.e., using 10 Gbps technology)? (2) What is the long-term cost of coarse-grained designs? We define a power-aware mixed integer linear programming (MILP) formulation based on actual modular architectures where modules are upgraded as the network traffic increases. We introduce, for the first time, important...
Lessons Learned from Designing the Montium a Coarse-Grained Reconfigurable Processing Tile
Smit, Gerardus Johannes Maria; Heysters, P.M.; Rosien, M.A.J.; Molenkamp, Egbert
2004-01-01
In this paper we describe in retrospective the main results of a four year project, called Chameleon. As part of this project we developed a coarse-grained reconfigurable core for DSP algorithms in wirelessdevices denoted MONTIUM. After presenting the main achievements within this project we present
DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model
DEFF Research Database (Denmark)
Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen
2012-01-01
We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can...
Network topology exploration of mesh-based coarse-grain reconfigurable architectures
Bansal, N.; Gupta, S.; Dutt, N.D.; Nicolau, A.; Gupta, R.
2004-01-01
Several coarse-grain reconfigurable architectures proposed recently consist of a large number of processing elements (PEs) connected in a mesh-like network topology. We study the effects of three aspects of network topology exploration on the performance of applications on these architectures: (a)
Implementing Non Power-of-Two FFTs on Coarse-Grain Reconfigurable Architectures
Rivaton, Arnaud; Quevremont, Jérôme; Zhang, Q.; Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Nurmi, J.; Takala, J.; Hamalainen, T.D.
2005-01-01
To improve power figures of a dual ARM9 RISC core architecture targeting low-power digital broadcasting applications, the addition of a coarse-grain architecture is considered. This paper introduces two of these structures: PACT's XPP technology and the Montium, developed by the University of
Energy Technology Data Exchange (ETDEWEB)
Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)
2015-01-21
The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.
Jämbeck, Joakim P M; Eriksson, Emma S E; Laaksonen, Aatto; Lyubartsev, Alexander P; Eriksson, Leif A
2014-01-14
Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous "droplet" through the liposome bilayer are reported herein.
International Nuclear Information System (INIS)
Antillon, Edwin; Banlusan, Kiettipong; Strachan, Alejandro
2014-01-01
We extend a thermally accurate model for coarse grain dynamics (Strachan and Holian 2005 Phys. Rev. Lett. 94 014301) to enable the description of stress-induced chemical reactions in the degrees of freedom internal to the mesoparticles. Similar to the breathing sphere model, we introduce an additional variable that describes the internal state of the particles and whose dynamics is governed both by an internal potential energy function and by interparticle forces. The equations of motion of these new variables are derived from a Hamiltonian and the model exhibits two desired features: total energy conservation and Galilean invariance. We use a simple model material with pairwise interactions between particles and study pressure-induced chemical reactions induced by hydrostatic and uniaxial compression. These examples demonstrate the ability of the model to capture non-trivial processes including the interplay between mechanical, thermal and chemical processes of interest in many applications. (paper)
Making coarse grained polymer simulations quantitatively predictive for statics and dynamics
Kremer, Kurt
2010-03-01
By combining input from short simulation runs of rather small systems with all atomistic details together with properly adapted coarse grained models we are able quantitatively predict static and especially dynamical properties of both pure polymer melts of long fully entangled but also of systems with low molecular weight additives. Comparisons to rather different experiments such as diffusion constant measurements or NMR relaxation experiments show a remarkable quantitative agreement without any adjustable parameter. Reintroduction of chemical details into the coarse grained trajectories allows the study of long time trajectories in all atomistic detail providing the opportunity for rather different means of data analysis. References: V. Harmandaris, K. Kremer, Macromolecules, in press (2009) V. Harmandaris et al, Macromolecules, 40, 7026 (2007) B. Hess, S. Leon, N. van der Vegt, K. Kremer, Soft Matter 2, 409 (2006) D. Fritz et al, Soft Matter 5, 4556 (2009)
Effect of cooling rates on the weld heat affected zone coarse grain microstructure
Directory of Open Access Journals (Sweden)
Roman Celin
2018-04-01
Full Text Available The effect of a cooling rate on the S690Q quenched and tempered steel welded joint coarse grain heat affected zone microstructure was investigated using a dilatometer with controlled heating and cooling fixture. Steel samples were heated to a peak temperature of 1350 °C and cooled at the different cooling time Dt8/5. A dilatometric analysis and hardness measurements of the simulated thermal cycle coarse grain samples were done. Transformation start and finish temperature were determined using dilatation vs. temperature data analysis. The microstructure of the sample with a cooling time 5 s consists of martensite, whereas at cooling time 80 s a bainitic microstructure was observed. The investigated steel cooling cycle using simulation approach makes possible to determine the range of an optimum CG HAZ cooling time for the welding.
Moving beyond Watson-Crick models of coarse grained DNA dynamics.
Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D
2011-11-28
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.
MT-ADRES: multi-threading on coarse-grained reconfigurable architecture
DEFF Research Database (Denmark)
Wu, Kehuai; Kanstein, Andreas; Madsen, Jan
2008-01-01
The coarse-grained reconfigurable architecture ADRES (architecture for dynamically reconfigurable embedded systems) and its compiler offer high instruction-level parallelism (ILP) to applications by means of a sparsely interconnected array of functional units and register files. As high-ILP archi......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...
Optimization of droplets for UV-NIL using coarse-grain simulation of resist flow
Sirotkin, Vadim; Svintsov, Alexander; Zaitsev, Sergey
2009-03-01
A mathematical model and numerical method are described, which make it possible to simulate ultraviolet ("step and flash") nanoimprint lithography (UV-NIL) process adequately even using standard Personal Computers. The model is derived from 3D Navier-Stokes equations with the understanding that the resist motion is largely directed along the substrate surface and characterized by ultra-low values of the Reynolds number. By the numerical approximation of the model, a special finite difference method is applied (a coarse-grain method). A coarse-grain modeling tool for detailed analysis of resist spreading in UV-NIL at the structure-scale level is tested. The obtained results demonstrate the high ability of the tool to calculate optimal dispensing for given stamp design and process parameters. This dispensing provides uniform filled areas and a homogeneous residual layer thickness in UV-NIL.
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.
Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas
2018-01-01
We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.
Multiblob coarse-graining for mixtures of long polymers and soft colloids
Locatelli, Emanuele; Capone, Barbara; Likos, Christos N.
2016-11-01
Soft nanocomposites represent both a theoretical and an experimental challenge due to the high number of the microscopic constituents that strongly influence the behaviour of the systems. An effective theoretical description of such systems invokes a reduction of the degrees of freedom to be analysed, hence requiring the introduction of an efficient, quantitative, coarse-grained description. We here report on a novel coarse graining approach based on a set of transferable potentials that quantitatively reproduces properties of mixtures of linear and star-shaped homopolymeric nanocomposites. By renormalizing groups of monomers into a single effective potential between a f-functional star polymer and an homopolymer of length N0, and through a scaling argument, it will be shown how a substantial reduction of the to degrees of freedom allows for a full quantitative description of the system. Our methodology is tested upon full monomer simulations for systems of different molecular weight, proving its full predictive potential.
Formation of incoherent deformation twin boundaries in a coarse-grained Al-7Mg alloy
Jin, S. B.; Zhang, K.; Bjørge, R.; Tao, N. R.; Marthinsen, K.; Lu, K.; Li, Y. J.
2015-08-01
Deformation twinning has rarely been observed in coarse grained Al and its alloys except under some extreme conditions such as ultrahigh deformation strain or strain rates. Here, we report that a significant amount of Σ3 deformation twins could be generated in a coarse-grained Al-7 Mg alloy by dynamic plastic deformation (DPD). A systematic investigation of the Σ3 boundaries shows that they are Σ3{112} type incoherent twin boundaries (ITBs). These ITBs have formed by gradual evolution from copious low-angle deformation bands through -twist Σ boundaries by lattice rotation. These findings provide an approach to generate deformation twin boundaries in high stacking fault energy metallic alloys. It is suggested that high solution content of Mg in the alloy and the special deformation mode of DPD played an important role in formation of the Σ and ITBs.
Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.
Das, Shankar P; Yoshimori, Akira
2013-10-01
Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.
Premelting, fluctuations, and coarse-graining of water-ice interfaces
Energy Technology Data Exchange (ETDEWEB)
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.
Premelting, fluctuations, and coarse-graining of water-ice interfaces
Limmer, David T.; Chandler, David
2014-11-01
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.
Premelting, fluctuations, and coarse-graining of water-ice interfaces
International Nuclear Information System (INIS)
Limmer, David T.; Chandler, David
2014-01-01
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
Premelting, fluctuations, and coarse-graining of water-ice interfaces.
Limmer, David T; Chandler, David
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.
Adhesion between a rutile surface and a polyimide: a coarse grained molecular dynamics study
Kumar, Arun; Sudarkodi, V.; Parandekar, Priya V.; Sinha, Nishant K.; Prakash, Om; Nair, Nisanth N.; Basu, Sumit
2018-04-01
Titanium, due to its high strength to weight ratio and polyimides, due to their excellent thermal stability are being increasingly used in aerospace applications. We investigate the bonding between a (110) rutile substrate and a popular commercial polyimide, PMR-15, starting from the known atomic structure of the rutile substrate and the architecture of the polymer. First, the long PMR-15 molecule is divided into four fragments and an all-atom non-bonded forcefield governing the interaction between PMR-15 and a rutile substrate is developed. To this end, parameters of Buckingham potential for interaction between each atom in the fragments and the rutile surface are fitted, so as to ensure that the sum of non-bonded and electrostatic interaction energy between the substrate and a large number of configurations of each fragment, calculated by the quantum mechanical route and obtained from the fitted potential, is closely matched. Further, two coarse grained models of PMR-15 are developed—one for interaction between two coarse grained PMR-15 molecules and another for that between a coarse grained PMR-15 and the rutile substrate. Molecular dynamics simulations with the coarse grained models yields a traction separation law—a very useful tool for conducting continuum level finite element simulations of rutile-PMR-15 joints—governing the normal separation of a PMR-15 block from a flat rutile substrate. Moreover, detailed information about the affinity of various fragments to the substrate are also obtained. In fact, though the separation energy between rutile and PMR-15 turns out to be rather low, our analysis—with merely the molecular architecture of the polyimide as the starting point—provides a scheme for in-silico prediction of adhesion energies for new polyimide formulations.
International Nuclear Information System (INIS)
Bonifacio, R.; Milan Univ.
1983-05-01
We show that a proper coarse-grained description of time evolution leads to a finite difference equation with step tau for the density operator. This implies state reduction to the diagonal form in the energy representation and a quasi ergodic behaviour of quantum mechanical ensemble averages. An intrinsic time-energy relation tauΔE>=(h/2π)/2 is proposed, and its equivalence to a time quantization is discussed. (author)
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
Directory of Open Access Journals (Sweden)
Stovgaard Kasper
2010-08-01
Full Text Available Abstract Background Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. Results We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. Conclusion We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for
Flow structure of coarse-grained slurry in a horizontal pipe
Czech Academy of Sciences Publication Activity Database
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 Online Monitoring of BTI Aging by Reusing Power-Gating Infrastructure
Tenentes, V.; Rossi, D.; Sheng Yang,; Khursheed, S.; Al-Hashimi, B.M.; Gunn, S.R.
2017-01-01
In this paper, we present a novel coarse-grained technique for monitoring online the Bias Temperature Instability (BTI) aging of circuits by exploiting their power gating infrastructure. The proposed technique relies on monitoring the discharge time of the virtual-power-network during stand-by operations, the value of which depends on the threshold voltage of the CMOS devices in the power-gated design (PGD). It does not require any distributed sensors, because the virtual-power network is alr...
Coarse-grained simulation of a real-time process control network under peak load
International Nuclear Information System (INIS)
George, A.D.; Clapp, N.E. Jr.
1992-01-01
This paper presents a simulation study on the real-time process control network proposed for the new ANS reactor system at ORNL. A background discussion is provided on networks, modeling, and simulation, followed by an overview of the ANS process control network, its three peak-load models, and the results of a series of coarse-grained simulation studies carried out on these models using implementations of 802.3, 802.4, and 802.5 standard local area networks
Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid
Directory of Open Access Journals (Sweden)
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.
Effects of Particle Size on the Shear Behavior of Coarse Grained Soils Reinforced with Geogrid.
Kim, Daehyeon; Ha, Sungwoo
2014-02-07
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.
Pazzona, Federico G.; Pireddu, Giovanni; Gabrieli, Andrea; Pintus, Alberto M.; Demontis, Pierfranco
2018-05-01
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely accepted approach, in which the contributions to the free energy given by the molecules located in two neighboring pores are estimated through Monte Carlo simulations where the two pores are kept separated from the rest of the system, leads to inaccurate results at high sorbate densities. In the coarse-graining strategy that we propose, which is based on the Bethe-Peierls approximation, density-independent interaction terms are instead computed according to local effective potentials that take into account the correlations between the pore pair and its surroundings by means of mean-field correction terms without the need for simulating the pore pair separately. Use of the interaction parameters obtained this way allows the coarse-grained system to reproduce more closely the equilibrium properties of the original one. Results are shown for lattice-gases where the local free energy can be computed exactly and for a system of Lennard-Jones particles under the effect of a static confining field.
Energy Technology Data Exchange (ETDEWEB)
Garrido, J. M. [Departamento de Ingeniería Química, Universidad de Concepción, POB 160-C Concepción (Chile); Algaba, J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Míguez, J. M. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et Leurs Reservoirs, Université de Pau et des Pays de l’Adour, CNRS, TOTAL–UMR 5150, Avenue de l’Université, B.P. 1155, Pau F-64013 (France); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain); Piñeiro, M. M. [Departamento de Física Aplicada, Universidade de Vigo, E36310 Vigo (Spain)
2016-04-14
We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with
International Nuclear Information System (INIS)
Garrido, J. M.; Algaba, J.; Blas, F. J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.
2016-01-01
We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with
Lubecka, Emilia A.; Liwo, Adam
2017-09-01
Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all
Xu, Yinlin; Ma, Qianli D Y; Schmitt, Daniel T; Bernaola-Galván, Pedro; Ivanov, Plamen Ch
2011-11-01
We investigate how various coarse-graining (signal quantization) methods affect the scaling properties of long-range power-law correlated and anti-correlated signals, quantified by the detrended fluctuation analysis. Specifically, for coarse-graining in the magnitude of a signal, we consider (i) the Floor, (ii) the Symmetry and (iii) the Centro-Symmetry coarse-graining methods. We find that for anti-correlated signals coarse-graining in the magnitude leads to a crossover to random behavior at large scales, and that with increasing the width of the coarse-graining partition interval Δ, this crossover moves to intermediate and small scales. In contrast, the scaling of positively correlated signals is less affected by the coarse-graining, with no observable changes when Δ 1 a crossover appears at small scales and moves to intermediate and large scales with increasing Δ. For very rough coarse-graining (Δ > 3) based on the Floor and Symmetry methods, the position of the crossover stabilizes, in contrast to the Centro-Symmetry method where the crossover continuously moves across scales and leads to a random behavior at all scales; thus indicating a much stronger effect of the Centro-Symmetry compared to the Floor and the Symmetry method. For coarse-graining in time, where data points are averaged in non-overlapping time windows, we find that the scaling for both anti-correlated and positively correlated signals is practically preserved. The results of our simulations are useful for the correct interpretation of the correlation and scaling properties of symbolic sequences.
International Nuclear Information System (INIS)
Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der
2014-01-01
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
Energy Technology Data Exchange (ETDEWEB)
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.
The random phase transducer in ultrasonic NDT of coarse grain stainless steel
International Nuclear Information System (INIS)
Bordier, J.M.; Fink, M.; Le Brun, A.; Cohen-Tenoudji, F.
1993-11-01
Ultrasonic NDT of cast stainless steel is known to be difficult due to a huge loss of focussing of the ultrasonic beam, and to a high level speckle noise generated by the coarse grain structure. In this paper, we describe the principle of the ultrasonic random phase transducer. Experimental results are compared with those obtained with a standard spatial compound technique. We show that the random phase transducer is a good tool to characterize the multiple scattering process generated by these materials. (authors). 7 figs., 11 refs
Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.
Fačkovec, B; Vanden-Eijnden, E; Wales, D J
2015-07-28
A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.
Deformation bands in ⟨120⟩ grains in coarse-grained aluminium
DEFF Research Database (Denmark)
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......)[011](111) and (a/2)[011](111). The Schmid factor for the highest stressed secondary systems has a local minimum of 0.245 at [120]. The application of Frank's equation shows that the only boundaries without long-range stresses that can be formed by combination of the two sets of dislocations, (a/2)- [011...
Energy Technology Data Exchange (ETDEWEB)
Español, Pep [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Donev, Aleksandar [Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid (Spain); Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012 (United States)
2015-12-21
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our “bottom-up” and previous “top-down” approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a “linear for spiky” weak approximation which replaces microscopic “fields” with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics
Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).
Sinitskiy, Anton V; Voth, Gregory A
2018-01-07
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.
Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry
2018-04-01
The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.
Lardner, Timothy; Li, Minghui; Gachagan, Anthony
2014-02-01
Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.
Evaluation of ultrasonic array imaging algorithms for inspection of a coarse grained material
Van Pamel, A.; Lowe, M. J. S.; Brett, C. R.
2014-02-01
Improving the ultrasound inspection capability for coarse grain metals remains of longstanding interest to industry and the NDE research community and is expected to become increasingly important for next generation power plants. A test sample of coarse grained Inconel 625 which is representative of future power plant components has been manufactured to test the detectability of different inspection techniques. Conventional ultrasonic A, B, and C-scans showed the sample to be extraordinarily difficult to inspect due to its scattering behaviour. However, in recent years, array probes and Full Matrix Capture (FMC) imaging algorithms, which extract the maximum amount of information possible, have unlocked exciting possibilities for improvements. This article proposes a robust methodology to evaluate the detection performance of imaging algorithms, applying this to three FMC imaging algorithms; Total Focusing Method (TFM), Phase Coherent Imaging (PCI), and Decomposition of the Time Reversal Operator with Multiple Scattering (DORT MSF). The methodology considers the statistics of detection, presenting the detection performance as Probability of Detection (POD) and probability of False Alarm (PFA). The data is captured in pulse-echo mode using 64 element array probes at centre frequencies of 1MHz and 5MHz. All three algorithms are shown to perform very similarly when comparing their flaw detection capabilities on this particular case.
On the representability problem and the physical meaning of coarse-grained models
Energy Technology Data Exchange (ETDEWEB)
Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States)
2016-07-28
In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable’s dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.
Systematic hierarchical coarse-graining with the inverse Monte Carlo method
Energy Technology Data Exchange (ETDEWEB)
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.
Energy Technology Data Exchange (ETDEWEB)
Lardner, Timothy; Gachagan, Anthony [Centre for Ultrasonic Engineering, University of Strathclyde, Glasgow, G1 1XW (United Kingdom); Li, Minghui [School of Engineering, University of Glasgow, Glasgow, G12 8QQ (United Kingdom)
2014-02-18
Materials with a coarse grain structure are becoming increasingly prevalent in industry due to their resilience to stress and corrosion. These materials are difficult to inspect with ultrasound because reflections from the grains lead to high noise levels which hinder the echoes of interest. Spatially Averaged Sub-Aperture Correlation Imaging (SASACI) is an advanced array beamforming technique that uses the cross-correlation between images from array sub-apertures to generate an image weighting matrix, in order to reduce noise levels. This paper presents a method inspired by SASACI to further improve imaging using phase information to refine focusing and reduce noise. A-scans from adjacent array elements are cross-correlated using both signal amplitude and phase to refine delay laws and minimize phase aberration. The phase-based and amplitude-based corrected images are used as inputs to a two-dimensional cross-correlation algorithm that will output a weighting matrix that can be applied to any conventional image. This approach was validated experimentally using a 5MHz array a coarse grained Inconel 625 step wedge, and compared to the Total Focusing Method (TFM). Initial results have seen SNR improvements of over 20dB compared to TFM, and a resolution that is much higher.
On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies
Degiacomi, Matteo T.
2018-05-01
Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
Energy Technology Data Exchange (ETDEWEB)
Heinemann, Thomas, E-mail: thomas.heinemann@tu-berlin.de; Klapp, Sabine H. L., E-mail: klapp@physik.tu-berlin.de [Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin (Germany); Palczynski, Karol, E-mail: karol.palczynski@helmholtz-berlin.de; Dzubiella, Joachim, E-mail: joachim.dzubiella@helmholtz-berlin.de [Institut für Physik, Humboldt Universität zu Berlin, Newtonstraße 15, 12489 Berlin (Germany); Institut für Weiche Materie und Funktionale Materialen, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany)
2015-11-07
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
International Nuclear Information System (INIS)
Heinemann, Thomas; Klapp, Sabine H. L.; Palczynski, Karol; Dzubiella, Joachim
2015-01-01
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 model for the interconversion between different crystalline cellulose allomorphs
Energy Technology Data Exchange (ETDEWEB)
Langan, Paul [ORNL
2012-01-01
We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.
Multiscale modeling, coarse-graining and shock wave computer simulationsin materials science
Directory of Open Access Journals (Sweden)
Martin O. Steinhauser
2017-12-01
Full Text Available My intention in this review article is to briefly discuss several major topics of presentdaycomputational materials science in order to show their importance for state-of-the-art materialsmodeling and computer simulation. The topics I discuss are multiscale modeling approaches forhierarchical systems such as biological macromolecules and related coarse-graining techniques, whichprovide an effcient means to investigate systems on the mesoscale, and shock wave physics whichhas many important and interesting multi- and interdisciplinary applications in research areas wherephysics, biology, chemistry, computer science, medicine and even engineering meet. In fact, recently,as a new emerging field, the use of coarse-grained approaches for the simulation of biologicalmacromolecules such as lipids and bilayer membranes and the investigation of their interaction withshock waves has become very popular. This emerging area of research may contribute not only toan improved understanding of the microscopic details of molecular self-assembly but may also leadto enhanced medical tumor treatments which are based on the destructive effects of High IntensityFocused Ultrasound (HIFU or shock waves when interacting with biological cells and tissue; theseare treatments which have been used in medicine for many years, but which are not well understoodfrom a fundamental physical point of view.
Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM)
Sinitskiy, Anton V.; Voth, Gregory A.
2018-01-01
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used. However, the QM/MM approach often faces a number of challenges, including the high cost of repetitive QM computations, the slow sampling even for the MM part in those cases where a system under investigation has a complex dynamics, and a difficulty in providing a simple, qualitative interpretation of numerical results in terms of the influence of the molecular environment upon the active QM region. In this paper, we address these issues by combining QM/MM modeling with the methodology of "bottom-up" coarse-graining (CG) to provide the theoretical basis for a systematic quantum-mechanical/coarse-grained molecular mechanics (QM/CG-MM) mixed resolution approach. A derivation of the method is presented based on a combination of statistical mechanics and quantum mechanics, leading to an equation for the effective Hamiltonian of the QM part, a central concept in the QM/CG-MM theory. A detailed analysis of different contributions to the effective Hamiltonian from electrostatic, induction, dispersion, and exchange interactions between the QM part and the surroundings is provided, serving as a foundation for a potential hierarchy of QM/CG-MM methods varying in their accuracy and computational cost. A relationship of the QM/CG-MM methodology to other mixed resolution approaches is also discussed.
Energy Technology Data Exchange (ETDEWEB)
Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)
2015-12-28
We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.
International Nuclear Information System (INIS)
Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian; Sugii, Taisuke
2015-01-01
We investigate the volumetric glass transition temperature T 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 g increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T 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 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
Energy Technology Data Exchange (ETDEWEB)
Li, Chunhua [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States); Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin [College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124 (China); Su, Jiguo, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [College of Science, Yanshan University, Qinhuangdao 066004 (China); Zhang, Yang, E-mail: jiguosu@ysu.edu.cn, E-mail: zhng@umich.edu [Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 45108 (United States)
2016-07-07
Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.
A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties
Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.
2012-10-01
Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of
Polwaththe-Gallage, Hasitha-Nayanajith; Sauret, Emilie; Nguyen, Nam-Trung; Saha, Suvash C.; Gu, YuanTong
2018-01-01
Liquid marbles are liquid droplets coated with superhydrophobic powders whose morphology is governed by the gravitational and surface tension forces. Small liquid marbles take spherical shapes, while larger liquid marbles exhibit puddle shapes due to the dominance of gravitational forces. Liquid marbles coated with hydrophobic magnetic powders respond to an external magnetic field. This unique feature of magnetic liquid marbles is very attractive for digital microfluidics and drug delivery systems. Several experimental studies have reported the behavior of the liquid marbles. However, the complete behavior of liquid marbles under various environmental conditions is yet to be understood. Modeling techniques can be used to predict the properties and the behavior of the liquid marbles effectively and efficiently. A robust liquid marble model will inspire new experiments and provide new insights. This paper presents a novel numerical modeling technique to predict the morphology of magnetic liquid marbles based on coarse grained molecular dynamics concepts. The proposed model is employed to predict the changes in height of a magnetic liquid marble against its width and compared with the experimental data. The model predictions agree well with the experimental findings. Subsequently, the relationship between the morphology of a liquid marble with the properties of the liquid is investigated. Furthermore, the developed model is capable of simulating the reversible process of opening and closing of the magnetic liquid marble under the action of a magnetic force. The scaling analysis shows that the model predictions are consistent with the scaling laws. Finally, the proposed model is used to assess the compressibility of the liquid marbles. The proposed modeling approach has the potential to be a powerful tool to predict the behavior of magnetic liquid marbles serving as bioreactors.
Anomalous g-Factors for Charged Leptons in a Fractional Coarse-Grained Approach
International Nuclear Information System (INIS)
Helayël-Neto, J. A.; Weberszpil, J.
2014-01-01
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
Experimental study on waves propagation over a coarse-grained sloping beach
Hsu, Tai-Wen; Lai, Jian-Wu
2013-04-01
This study investigates velocity fields of wave propagation over a coarse-grained sloping beach using laboratory experiments. The experiment was conducted in a wave flume of 25 m long, 0.5 m wide and 0.6 m high in which a coarse-grained sloping 1:5 beach was placed with two layers ball. The glass ball is D=7.9 cm and the center to center distance of each ball is 8.0 cm. The test section for observing wave and flow fields is located at the middle part of the flume. A piston type wave maker driven by an electromechanical hydraulic serve system is installed at the end of the flume. The intrinsic permeability Kp and turbulent drag coefficient Cf were obtained from steady flow water-head experiments. The flow velocity was measured by the particle image velocimeter (PIV) and digital image process (DIP) techniques. Eleven fields of view (FOVS) were integrated into a complete representation including the outer, surf and swash zone. Details of the definition sketch of the coarse-grained sloping beach model as well as experimental setup are referred to Lai et al. (2008). A high resolution of CCD camera was used to capture the images which was calibrated by the direct linear transform (DCT) algorithm proposed by Abed El-Aziz and Kar-Ara (1971). The water surface between the interface of air and water at each time step are calculated by Otsu' (1978) detect algorithm. The comparison shows that the water surface elevation observed by integrated image agrees well with that of Otsu' detection results. For the flow field measurement, each image pair was cross correlated with 32X32 pixel inter rogation window and a half overlap between adjacent windows. The repeatability and synchronization are the key elements for both wave motion and PIV technique. The wave profiles and flow field were compared during several wave periods to ensure that they can be reproduced by the present system. The water depth is kept as a constant of h=32 cm. The incident wave conditions are set to be wave
Hsu, David D.
Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational
Probing finite coarse-grained virtual Feynman histories with sequential weak values
Georgiev, Danko; Cohen, Eliahu
2018-05-01
Feynman's sum-over-histories formulation of quantum mechanics has been considered a useful calculational tool in which virtual Feynman histories entering into a coherent quantum superposition cannot be individually measured. Here we show that sequential weak values, inferred by consecutive weak measurements of projectors, allow direct experimental probing of individual virtual Feynman histories, thereby revealing the exact nature of quantum interference of coherently superposed histories. Because the total sum of sequential weak values of multitime projection operators for a complete set of orthogonal quantum histories is unity, complete sets of weak values could be interpreted in agreement with the standard quantum mechanical picture. We also elucidate the relationship between sequential weak values of quantum histories with different coarse graining in time and establish the incompatibility of weak values for nonorthogonal quantum histories in history Hilbert space. Bridging theory and experiment, the presented results may enhance our understanding of both weak values and quantum histories.
A Coarse-Grained Reconfigurable Architecture with Compilation for High Performance
Directory of Open Access Journals (Sweden)
Lu Wan
2012-01-01
Full Text Available We propose a fast data relay (FDR mechanism to enhance existing CGRA (coarse-grained reconfigurable architecture. FDR can not only provide multicycle data transmission in concurrent with computations but also convert resource-demanding inter-processing-element global data accesses into local data accesses to avoid communication congestion. We also propose the supporting compiler techniques that can efficiently utilize the FDR feature to achieve higher performance for a variety of applications. Our results on FDR-based CGRA are compared with two other works in this field: ADRES and RCP. Experimental results for various multimedia applications show that FDR combined with the new compiler deliver up to 29% and 21% higher performance than ADRES and RCP, respectively.
A coarse-grained model for synergistic action of multiple enzymes on cellulose
Directory of Open Access Journals (Sweden)
Asztalos Andrea
2012-08-01
Full Text Available Abstract Background Degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing β-1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, β-glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. Results We present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. Conclusions Our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures
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.
Archie's Saturation Exponent for Natural Gas Hydrate in Coarse-Grained Reservoirs
Cook, Ann E.; Waite, William F.
2018-03-01
Accurately quantifying the amount of naturally occurring gas hydrate in marine and permafrost environments is important for assessing its resource potential and understanding the role of gas hydrate in the global carbon cycle. Electrical resistivity well logs are often used to calculate gas hydrate saturations, Sh, using Archie's equation. Archie's equation, in turn, relies on an empirical saturation parameter, n. Though n = 1.9 has been measured for ice-bearing sands and is widely used within the hydrate community, it is highly questionable if this n value is appropriate for hydrate-bearing sands. In this work, we calibrate n for hydrate-bearing sands from the Canadian permafrost gas hydrate research well, Mallik 5L-38, by establishing an independent downhole Sh profile based on compressional-wave velocity log data. Using the independently determined Sh profile and colocated electrical resistivity and bulk density logs, Archie's saturation equation is solved for n, and uncertainty is tracked throughout the iterative process. In addition to the Mallik 5L-38 well, we also apply this method to two marine, coarse-grained reservoirs from the northern Gulf of Mexico Gas Hydrate Joint Industry Project: Walker Ridge 313-H and Green Canyon 955-H. All locations yield similar results, each suggesting n ≈ 2.5 ± 0.5. Thus, for the coarse-grained hydrate bearing (Sh > 0.4) of greatest interest as potential energy resources, we suggest that n = 2.5 ± 0.5 should be applied in Archie's equation for either marine or permafrost gas hydrate settings if independent estimates of n are not available.
Embrittlement of Intercritically Reheated Coarse Grain Heat-Affected Zone of ASTM4130 Steel
Li, Liying; Han, Tao; Han, Bin
2018-04-01
In this investigation, a thermal welding simulation technique was used to investigate the microstructures and mechanical properties of the intercritically reheated coarse grain heat-affected zone (IR CGHAZ) of ASTM4130 steel. The effect of post weld heat treatment (PWHT) on the toughness of IR CGHAZ was also analyzed. The toughness of IR CGHAZ was measured by means of Charpy impact, and it is found that IR CGHAZ has the lowest toughness which is much lower than that of the base metal regardless of whether PWHT is applied or not. The as-welded IR CGHAZ is mainly composed of ferrite, martensite, and many blocky M-A constituents distributing along grain boundaries and subgrain boundaries in a near-connected network. Also, the prior austenite grains are still as coarse as those in the coarse grain heat-affected zone (CGHAZ). The presence of the blocky M-A constituents and the coarsened austenite grains result in the toughness deterioration of the as-welded IR CGHAZ. Most of the blocky M-A constituents are decomposed to granular bainite due to the effect of the PWHT. However, PWHT cannot refine the prior austenite grains. Thus, the low toughness of IR CGHAZ after PWHT can be attributed to two factors, i.e., the coarsened austenite grains, and the presence of the remaining M-A constituents and granular bainite, which are located at grain boundaries and subgrain boundaries in a near-connected network. The absorbed energy of the IR CGHAZ was increased by about 3.75 times, which means that the PWHT can effectively improve the toughness but it cannot be recovered to the level of base metal.
Hydrogen accumulation in nanostructured as compared to the coarse-grained tungsten
International Nuclear Information System (INIS)
Gonzalez-Arrabal, R.; Panizo-Laiz, M.; Gordillo, N.; Tejado, E.; Munnik, F.; Rivera, A.; Perlado, J.M.
2014-01-01
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 × 10 20 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
Sharma, Govind K; Kumar, Anish; Jayakumar, T; Purnachandra Rao, B; Mariyappa, N
2015-03-01
A signal processing methodology is proposed in this paper for effective reconstruction of ultrasonic signals in coarse grained high scattering austenitic stainless steel. The proposed methodology is comprised of the Ensemble Empirical Mode Decomposition (EEMD) processing of ultrasonic signals and application of signal minimisation algorithm on selected Intrinsic Mode Functions (IMFs) obtained by EEMD. The methodology is applied to ultrasonic signals obtained from austenitic stainless steel specimens of different grain size, with and without defects. The influence of probe frequency and data length of a signal on EEMD decomposition is also investigated. For a particular sampling rate and probe frequency, the same range of IMFs can be used to reconstruct the ultrasonic signal, irrespective of the grain size in the range of 30-210 μm investigated in this study. This methodology is successfully employed for detection of defects in a 50mm thick coarse grain austenitic stainless steel specimens. Signal to noise ratio improvement of better than 15 dB is observed for the ultrasonic signal obtained from a 25 mm deep flat bottom hole in 200 μm grain size specimen. For ultrasonic signals obtained from defects at different depths, a minimum of 7 dB extra enhancement in SNR is achieved as compared to the sum of selected IMF approach. The application of minimisation algorithm with EEMD processed signal in the proposed methodology proves to be effective for adaptive signal reconstruction with improved signal to noise ratio. This methodology was further employed for successful imaging of defects in a B-scan. Copyright © 2014. Published by Elsevier B.V.
Thermal dileptons from coarse-grained transport as fireball probes at SIS energies
International Nuclear Information System (INIS)
Galatyuk, Tetyana; Seck, Florian; Hohler, Paul M.; Rapp, Ralf; Stroth, Joachim
2016-01-01
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 ρ spectral function that describes available spectra at ultrarelativistic collision energies. In particular, we analyze 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 evolution alone would suggest. We furthermore find that the total dilepton yield radiated into the invariant-mass window of M = 0.3-0.7 GeV/c 2 normalized to the number of charged pions, follows a relation to the lifetime found earlier in the (ultra-)relativistic regime of heavy-ion collisions, and thus corroborates the versatility of this tool. The spectral slopes of the invariant-mass spectra above the φ -meson mass provide a thermometer of the hottest phases of the collision, and agree well with the maximal temperatures extracted from the coarse-grained hadron spectra. (orig.)
Bore, Thierry; Bhuyan, Habibullah; Bittner, Tilman; Murgan, Vignesh; Wagner, Norman; Scheuermann, Alexander
2018-01-01
Knowledge of the frequency-dependent electromagnetic properties of coarse-grained materials is imperative for the successful application of high frequency electromagnetic measurement techniques for near and subsurface monitoring. This paper reports the design, calibration and application of a novel one-port large coaxial cell for broadband complex permittivity measurements of civil engineering materials. It was designed to allow the characterization of heterogeneous material with large aggregate dimensions (up to 28 mm) over a frequency range from 1 MHz-860 MHz. In the first step, the system parameters were calibrated using the measured scattering function in a perfectly known dielectric material in an optimization scheme. In the second step, the method was validated with measurements made on standard liquids. Then the performance of the cell was evaluated on a compacted coarse-grained soil. The dielectric spectra were obtained by means of fitting the measured scattering function using a transverse electromagnetic mode propagation model considering the frequency-dependent complex permittivity. Two scenarios were systematically analyzed and compared. The first scenario consisted of a broadband generalized dielectric relaxation model with two Cole-Cole type relaxation processes related to the interaction of the aqueous phase and the solid phase, a constant high frequency contribution as well as an apparent direct current conductivity term. The second scenario relied on a three-phase theoretical mixture equation which was used in a forward approach in order to calibrate the model. Both scenarios provide almost identical results for the broadband effective complex relative permittivity. The combination of both scenarios suggests the simultaneous estimation of water content, density, bulk and pore water conductivity for road base materials for in situ applications.
Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.
Directory of Open Access Journals (Sweden)
Frank C Pickard
2014-07-01
Full Text Available A lesson utilizing a coarse-grained (CG Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing web portal (www.charmming.org to the Chemistry at HARvard Macromolecular Mechanics (CHARMM molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.
On the second law of thermodynamics: The significance of coarse-graining and the role of decoherence
International Nuclear Information System (INIS)
Noorbala, Mahdiyar
2014-01-01
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
International Nuclear Information System (INIS)
Toth, Gergely
2007-01-01
The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car-Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions (Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well. We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method
International Nuclear Information System (INIS)
Wan, X.L.; Wei, R.; Wu, K.M.
2010-01-01
The microstructure of acicular ferrite and its formation for the grain refinement of coarse-grained region of heat-affected zone of high strength low-alloy bainite steels were studied using three-dimensional reconstruction technique. Crystallographic grain size was analyzed by means of electron backscatter diffraction. It was revealed that the microstructure in the coarse-grained region of the heat-affected zone consisted of predominantly bainite packets and a small proportion of acicular ferrite. Acicular ferrite was of lath or plate-like rather than needle or rod-like morphology. Tempering of the coarse-grained region of heat-affected zone showed that the acicular ferrite was more stable than the bainite, indicating that the acicular ferrite was formed prior to bainite. The acicular ferrite laths or plates divided the prior austenite grains into smaller and separate regions, and confining the bainite transformed at lower temperatures in the smaller regions and hence leading to the grain refinement in the coarse-grained region of the heat-affected zone.
Energy Technology Data Exchange (ETDEWEB)
Wan, X.L.; Wei, R. [Institute of Advanced Steels and Welding Technology, Hubei Provincial Key Laboratory for Systems Science on Metallurgical Processing, Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan 430081 (China); Wu, K.M., E-mail: wukaiming@wust.edu.cn [Institute of Advanced Steels and Welding Technology, Hubei Provincial Key Laboratory for Systems Science on Metallurgical Processing, Key Laboratory for Ferrous Metallurgy and Resources Utilization of Ministry of Education, Wuhan University of Science and Technology, Wuhan 430081 (China)
2010-07-15
The microstructure of acicular ferrite and its formation for the grain refinement of coarse-grained region of heat-affected zone of high strength low-alloy bainite steels were studied using three-dimensional reconstruction technique. Crystallographic grain size was analyzed by means of electron backscatter diffraction. It was revealed that the microstructure in the coarse-grained region of the heat-affected zone consisted of predominantly bainite packets and a small proportion of acicular ferrite. Acicular ferrite was of lath or plate-like rather than needle or rod-like morphology. Tempering of the coarse-grained region of heat-affected zone showed that the acicular ferrite was more stable than the bainite, indicating that the acicular ferrite was formed prior to bainite. The acicular ferrite laths or plates divided the prior austenite grains into smaller and separate regions, and confining the bainite transformed at lower temperatures in the smaller regions and hence leading to the grain refinement in the coarse-grained region of the heat-affected zone.
Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF
2006-01-01
Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model
Tatsumi, Eri; Sugita, Seiji
2018-01-01
Remote sensing observations made by the spacecraft Hayabusa provided the first direct evidence of a rubble-pile asteroid: 25143 Itokawa. Itokawa was found to have a surface structure very different from other explored asteroids; covered with coarse pebbles and boulders ranging at least from cm to meter size. The cumulative size distribution of small circular depressions on Itokawa, most of which may be of impact origin, has a significantly shallower slope than that on the Moon; small craters are highly depleted on Itokawa compared to the Moon. This deficiency of small circular depressions and other features, such as clustered fragments and pits on boulders, suggest that the boulders on Itokawa might behave like armor, preventing crater formation: the ;armoring effect;. This might contribute to the low number density of small crater candidates. In this study, the cratering efficiency reduction due to coarse-grained targets was investigated based on impact experiments at velocities ranging from ∼ 70 m/s to ∼ 6 km/s using two vertical gas gun ranges. We propose a scaling law extended for cratering on coarse-grained targets (i.e., target grain size ≳ projectile size). We have found that the crater efficiency reduction is caused by energy dissipation at the collision site where momentum is transferred from the impactor to the first-contact target grain, and that the armoring effect can be classified into three regimes: (1) gravity scaled regime, (2) reduced size crater regime, or (3) no apparent crater regime, depending on the ratio of the impactor size to the target grain size and the ratio of the impactor kinetic energy to the disruption energy of a target grain. We found that the shallow slope of the circular depressions on Itokawa cannot be accounted for by this new scaling law, suggesting that obliteration processes, such as regolith convection and migration, play a greater role in the depletion of circular depressions on Itokawa. Based on the new extended
Representing environment-induced helix-coil transitions in a coarse grained peptide model
Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine
2016-10-01
Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that
Short- and medium-term response to storms on three Mediterranean coarse-grained beaches
Grottoli, Edoardo; Bertoni, Duccio; Ciavola, Paolo
2017-10-01
The storm response of three Italian coarse-grained beaches was investigated to better understand the morphodynamics of coarse-clastic beaches in a microtidal context. Two of the studied sites are located on the eastern side of the country (Portonovo and Sirolo) and the third one (Marina di Pisa) is on the western side. Portonovo and Sirolo are mixed sand and gravel beaches where the storms approach from two main directions, SE and NE. Marina di Pisa is a coarse-grained, gravel-dominated beach, exposed to storms driven by SW winds. Gravel nourishments were undertaken in recent years on the three sites. Beach topography was monitored measuring the same network of cross sections at a monthly (i.e. short-term) to seasonal frequency (i.e. medium-term). Geomorphic changes were examined before and after storm occurrences by means of profile analyses and shoreline position evaluations. The beach orientation and the influence of hard structures are the main factors controlling the transport and accumulation of significant amount of sediments and the consequent high variability of beach morphology over the medium-term. For Marina di Pisa, storms tend to accumulate material towards the upper part of the beach with no shoreline rotation and no chance to recover the initial configuration. Sirolo and Portonovo showed a similar behaviour that is more typical of pocket beaches. Both beaches show shoreline rotation after storms in a clockwise or counter-clockwise direction according to the incoming wave direction. The wider and longer beach at Sirolo allows the accumulation of a thin layer of sediment during storms, rather than at Portonovo where, given its longshore and landward boundaries, the beach material tends to accumulate in greater thickness. After storms, Sirolo and especially Portonovo can quickly recover the initial beach configuration, as soon as another storm of comparable energy approaches from the opposite direction of the previous one. Large morphological
A Coarse-grain Force Field for RDX: Density Dependent and Eergy Conserving.
Czech Academy of Sciences Publication Activity Database
Moore, J.D.; Barnes, B.C.; Izvekov, S.; Lísal, Martin; Sellers, M.S.; Taylor, D.E.; Brennan, J.K.
2016-01-01
Roč. 144, č. 10 (2016), s. 104501 ISSN 0021-9606 R&D Projects: GA ČR(CZ) GA13-02938S Grant - others:ARL(US) W911NF-10-2-0039 Institutional support: RVO:67985858 Keywords : dissipative particle dynamics * cyclotrimethylele-trinitramine * biomolecular systems Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.965, year: 2016
Houjou, Hirohiko
2011-10-01
Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m-1 for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.
Directory of Open Access Journals (Sweden)
Liang Cao
2009-01-01
Full Text Available This paper presents SmartCell, a novel coarse-grained reconfigurable architecture, which tiles a large number of processor elements with reconfigurable interconnection fabrics on a single chip. SmartCell is able to provide high performance and energy efficient processing for stream-based applications. It can be configured to operate in various modes, such as SIMD, MIMD, and systolic array. This paper describes the SmartCell architecture design, including processing element, reconfigurable interconnection fabrics, instruction and control process, and configuration scheme. The SmartCell prototype with 64 PEs is implemented using 0.13 m CMOS standard cell technology. The core area is about 8.5 , and the power consumption is about 1.6 mW/MHz. The performance is evaluated through a set of benchmark applications, and then compared with FPGA, ASIC, and two well-known reconfigurable architectures including RaPiD and Montium. The results show that the SmartCell can bridge the performance and flexibility gap between ASIC and FPGA. It is also about 8% and 69% more energy efficient than Montium and RaPiD systems for evaluated benchmarks. Meanwhile, SmartCell can achieve 4 and 2 times more throughput gains when comparing with Montium and RaPiD, respectively. It is concluded that SmartCell system is a promising reconfigurable and energy efficient architecture for stream processing.
Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer
Yang, Shaorui; Qu, Jianmin
2014-07-01
Using a previously developed coarse-grained model, we conducted large-scale (˜85×85×85nm3) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ˜60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.
Gu, Yan; Wang, Jiao
1997-02-01
We study relaxation of an ensemble of cat maps with initially localized phase-space distributions. Calculations of the coarse-grained entropy Sɛ ( t) for both classical and quantum motions are presented. It is shown that, within the relaxation period, both classical and quantum entropies increase with a nearly constant rate which can be identified as the largest Lyapunov exponent of the classical cat. After an empirical relaxation time, the time behavior for two entropies becomes different. While the classical entropy increases to the equilibrium entropy Seqm and stays there, its quantum analogue fluctuates incessantly around a mean overlineSɛ which is less than Seqm. We regard the entropy difference ΔS = S eqm - overlineSɛ as a measure of nonergodicity of the quantum motion of strongly chaotic systems and investigate its dependence on the Planck constant h. For fixed initial phase-space distributions, numerical results suggest that there is a scaling law ΔSαhβ with β ≈ 0.72 in the semiclassical regime.
Hagita, Katsumi; Morita, Hiroshi; Takano, Hiroshi
We performed coarse grained molecular dynamics (MD) simulations based on Kremer-Grest model in order to investigate a fracture of polymer nanocomposites filled with spherical nanoparticles (NPs) under uniaxial elongation with a Poisson ratio of 0.4. In our model, the NP consists of 320 surface beads and one center bead. In order to make the NP spherical, a harmonic potential is applied to the surface particles from the center of the NP. Here, the initial volume fraction of the NPs is about 20%. The dependences of the fracture on the interactions between the NPs and polymers were examined. In order to observe the creation of nanovoids, the interaction among the polymers was set to be attractive. When the NP-polymer interaction is attractive, nanovoids appear in the bulk of polymers. On the other hand, for repulsive NP-polymer interaction, nanovoids are created at the surface between the polymers and NPs. At the same time, segregation of NPs is observed. We found that these behaviors depend on crosslink densities.
Lyu, Dandan; Li, Shaofan
2017-10-01
Crystal defects have microstructure, and this microstructure should be related to the microstructure of the original crystal. Hence each type of crystals may have similar defects due to the same failure mechanism originated from the same microstructure, if they are under the same loading conditions. In this work, we propose a multiscale crystal defect dynamics (MCDD) model that models defects by considering its intrinsic microstructure derived from the microstructure or material genome of the original perfect crystal. The main novelties of present work are: (1) the discrete exterior calculus and algebraic topology theory are used to construct a scale-up (coarse-grained) dual lattice model for crystal defects, which may represent all possible defect modes inside a crystal; (2) a higher order Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed constitutive relations for various defect process zones, and (3) an hierarchical strain gradient theory based finite element formulation is developed to support an hierarchical multiscale cohesive (process) zone model for various defects in a unified formulation. The efficiency of MCDD computational algorithm allows us to simulate dynamic defect evolution at large scale while taking into account atomistic interaction. The MCDD model has been validated by comparing of the results of MCDD simulations with that of molecular dynamics (MD) in the cases of nanoindentation and uniaxial tension. Numerical simulations have shown that MCDD model can predict dislocation nucleation induced instability and inelastic deformation, and thus it may provide an alternative solution to study crystal plasticity.
A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.
Sinitskiy, Anton V; Voth, Gregory A
2015-09-07
Computational modeling of the condensed phase based on classical statistical mechanics has been rapidly developing over the last few decades and has yielded important information on various systems containing up to millions of atoms. However, if a system of interest contains important quantum effects, well-developed classical techniques cannot be used. One way of treating finite temperature quantum systems at equilibrium has been based on Feynman's imaginary time path integral approach and the ensuing quantum-classical isomorphism. This isomorphism is exact only in the limit of infinitely many classical quasiparticles representing each physical quantum particle. In this work, we present a reductionist perspective on this problem based on the emerging methodology of coarse-graining. This perspective allows for the representations of one quantum particle with only two classical-like quasiparticles and their conjugate momenta. One of these coupled quasiparticles is the centroid particle of the quantum path integral quasiparticle distribution. Only this quasiparticle feels the potential energy function. The other quasiparticle directly provides the observable averages of quantum mechanical operators. The theory offers a simplified perspective on quantum statistical mechanics, revealing its most reductionist connection to classical statistical physics. By doing so, it can facilitate a simpler representation of certain quantum effects in complex molecular environments.
Directory of Open Access Journals (Sweden)
Noah S Bieler
Full Text Available The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are generated. We report Dynamical Monte Carlo simulations that allow us to study the early stages of amyloid formation. We use a generic, coarse-grained model of an amyloidogenic peptide that has two internal states: the first one representing the soluble random coil structure and the second one the [Formula: see text]-sheet conformation. We find that this system exhibits a propensity towards fibrillar self-assembly following the formation of a critical nucleus. Our calculations establish connections between the early nucleation events and the kinetic information available in the later stages of the aggregation process that are commonly probed in experiments. We analyze the kinetic behaviour in our simulations within the framework of the theory of classical nucleated polymerisation, and are able to connect the structural events at the early stages in amyloid growth with the resulting macroscopic observables such as the effective nucleus size. Furthermore, the free-energy landscapes that emerge from these simulations allow us to identify pertinent properties of the monomeric state that could be targeted to suppress oligomer formation.
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.
Twist-writhe partitioning in a coarse-grained DNA minicircle model
Sayar, Mehmet; Avşaroǧlu, Barış; Kabakçıoǧlu, Alkan
2010-04-01
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 dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.
Demixing by a Nematic Mean Field: Coarse-Grained Simulations of Liquid Crystalline Polymers
Energy Technology Data Exchange (ETDEWEB)
Ramírez-Hernández, Abelardo; Hur, Su-Mi; Armas-Pérez, Julio; Cruz, Monica; de Pablo, Juan
2017-03-01
Liquid crystalline polymers exhibit a particular richness of behaviors that stems from their rigidity and their macromolecular nature. On the one hand, the orientational interaction between liquid-crystalline motifs promotes their alignment, thereby leading to the emergence of nematic phases. On the other hand, the large number of configurations associated with polymer chains favors formation of isotropic phases, with chain stiffness becoming the factor that tips the balance. In this work, a soft coarse-grained model is introduced to explore the interplay of chain stiffness, molecular weight and orientational coupling, and their role on the isotropic-nematic transition in homopolymer melts. We also study the structure of polymer mixtures composed of stiff and flexible polymeric molecules. We consider the effects of blend composition, persistence length, molecular weight and orientational coupling strength on the melt structure at the nano-and mesoscopic levels. Conditions are found where the systems separate into two phases, one isotropic and the other nematic. We confirm the existence of non-equilibrium states that exhibit sought-after percolating nematic domains, which are of interest for applications in organic photovoltaic and electronic devices.
Coarse-Grain QoS-Aware Dynamic Instance Provisioning for Interactive Workload in the Cloud
Directory of Open Access Journals (Sweden)
Jianxiong Wan
2014-01-01
Full Text Available Cloud computing paradigm renders the Internet service providers (ISPs with a new approach to deliver their service with less cost. ISPs can rent virtual machines from the Infrastructure-as-a-Service (IaaS provided by the cloud rather than purchasing them. In addition, commercial cloud providers (CPs offer diverse VM instance rental services in various time granularities, which provide another opportunity for ISPs to reduce cost. We investigate a Coarse-grain QoS-aware Dynamic Instance Provisioning (CDIP problem for interactive workload in the cloud from the perspective of ISPs. We formulate the CDIP problem as an optimization problem where the objective is to minimize the VM instance rental cost and the constraint is the percentile delay bound. Since the Internet traffic shows a strong self-similar property, it is hard to get an analytical form of the percentile delay constraint. To address this issue, we purpose a lookup table structure together with a learning algorithm to estimate the performance of the instance provisioning policy. This approach is further extended with two function approximations to enhance the scalability of the learning algorithm. We also present an efficient dynamic instance provisioning algorithm, which takes full advantage of the rental service diversity, to determine the instance rental policy. Extensive simulations are conducted to validate the effectiveness of the proposed algorithms.
Superplasticity-like deformation of a coarse-grained Al5052 alloy
International Nuclear Information System (INIS)
Chow, K.K.; Chan, K.C.
2000-01-01
In the present paper, hot forming properties of a commercially available coarse-grained Al5052 alloy under uniaxial and biaxial stress states were examined. In hot tensile tests, the alloy exhibits a superplastic-like behaviour with a maximum tensile elongation of 194% at a temperature of 873 K and at an initial strain rate of 2.08 x 10 -1 s -1 . Dislocation slip and grain boundary sliding were considered to be the deformation mechanisms. The alloy was also bulged at a constant polar strain-rate of 2.0 x 10 -1 s -1 and at an optimum temperature of 873 K using elliptical dies with aspect ratios of 1:1, 4:3, 2:1, 8:3 and 4:1. The strain distributions revealed that the strain gradient obtained in the minor axis was much greater than that in major axis. Moreover, it was shown that the deformation behavior of the alloy was basically isotropic and the volume strain of the alloy sheet did not equal to zero which was considered to relate to its cavitation behaviour. (orig.)
Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining
International Nuclear Information System (INIS)
Khasin, M.; Kosloff, R.
2010-01-01
An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n 3/2 (ln n) -1 compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10 4 and 2x10 6 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.
Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer.
Yang, Shaorui; Qu, Jianmin
2014-07-01
Using a previously developed coarse-grained model, we conducted large-scale (∼ 85 × 85 × 85 nm(3)) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ∼ 60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.
Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.
Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni
2018-06-11
We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.
Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.
2017-05-01
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
Energy Technology Data Exchange (ETDEWEB)
Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K., E-mail: jonathan.doye@chem.ox.ac.uk [Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ (United Kingdom); Randisi, Ferdinando [Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU (United Kingdom); Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Šulc, Petr [Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065 (United States); Ouldridge, Thomas E. [Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ (United Kingdom); Tsukanov, Roman; Nir, Eyal [Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva (Israel); Louis, Ard A. [Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP (United Kingdom)
2015-06-21
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
International Nuclear Information System (INIS)
Snodin, Benedict E. K.; Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.
2015-01-01
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na + ] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA
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.
Extension of 239+240Pu sediment geochronology to coarse-grained marine sediments
Kuehl, Steven A.; Ketterer, Michael E.; Miselis, Jennifer L.
2012-01-01
Sediment geochronology of coastal sedimentary environments dominated by sand has been extremely limited because concentrations of natural and bomb-fallout radionuclides are often below the limit of measurement using standard techniques. ICP-MS analyses of 239+240Pu from two sites representative of traditionally challenging (i.e., low concentration) environments provide a "proof of concept" and demonstrate a new application for bomb-fallout radiotracers in the study of sandy shelf-seabed dynamics. A kasten core from the New Zealand shelf in the Southern Hemisphere (low fallout), and a vibracore from the sandy nearshore of North Carolina (low particle surface area) both reveal measurable 239+240Pu activities at depth. In the case of the New Zealand site, independently verified steady-state sedimentation results in a 239+240Pu profile that mimics the expected atmospheric fallout. The depth profile of 239+240Pu in the North Carolina core is more uniform, indicating significant sediment resuspension, which would be expected in this energetic nearshore environment. This study, for the first time, demonstrates the utility of 239+240Pu in the study of sandy environments, significantly extending the application of bomb-fallout isotopes to coarse-grained sediments, which compose the majority of nearshore regions.
International Nuclear Information System (INIS)
Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine
2013-01-01
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
Energy Technology Data Exchange (ETDEWEB)
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.
The attachment of α -synuclein to a fiber: A coarse-grain approach
Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.
2017-03-01
We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.
Hammond, Nathan A; Kamm, Roger D
2008-07-01
The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long beta-sheets that pair together to form filaments; filaments form bundles approximately 30-60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two beta-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials.
Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers.
Rahimi, Ali; Amjad-Iranagh, Sepideh; Modarress, Hamid
2016-03-01
Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.
International Nuclear Information System (INIS)
Pereira, Claudio M.N.A.; Lapa, Celso M.F.
2003-01-01
This work extends the research related to generic algorithms (GA) in core design optimization problems, which basic investigations were presented in previous work. Here we explore the use of the Island Genetic Algorithm (IGA), a coarse-grained parallel GA model, comparing its performance to that obtained by the application of a traditional non-parallel GA. The optimization problem consists on adjusting several reactor cell parameters, such as dimensions, enrichment and materials, in order to minimize the average peak-factor in a 3-enrichment zone reactor, considering restrictions on the average thermal flux, criticality and sub-moderation. Our IGA implementation runs as a distributed application on a conventional local area network (LAN), avoiding the use of expensive parallel computers or architectures. After exhaustive experiments, taking more than 1500 h in 550 MHz personal computers, we have observed that the IGA provided gains not only in terms of computational time, but also in the optimization outcome. Besides, we have also realized that, for such kind of problem, which fitness evaluation is itself time consuming, the time overhead in the IGA, due to the communication in LANs, is practically imperceptible, leading to the conclusion that the use of expensive parallel computers or architecture can be avoided
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.
An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.
Directory of Open Access Journals (Sweden)
Levan Tsereteli
Full Text Available Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.
An accurate coarse-grained model for chitosan polysaccharides in aqueous solution.
Tsereteli, Levan; Grafmüller, Andrea
2017-01-01
Computational models can provide detailed information about molecular conformations and interactions in solution, which is currently inaccessible by other means in many cases. Here we describe an efficient and precise coarse-grained model for long polysaccharides in aqueous solution at different physico-chemical conditions such as pH and ionic strength. The Model is carefully constructed based on all-atom simulations of small saccharides and metadynamics sampling of the dihedral angles in the glycosidic links, which represent the most flexible degrees of freedom of the polysaccharides. The model is validated against experimental data for Chitosan molecules in solution with various degree of deacetylation, and is shown to closely reproduce the available experimental data. For long polymers, subtle differences of the free energy maps of the glycosidic links are found to significantly affect the measurable polymer properties. Therefore, for titratable monomers the free energy maps of the corresponding links are updated according to the current charge of the monomers. We then characterize the microscopic and mesoscopic structural properties of large chitosan polysaccharides in solution for a wide range of solvent pH and ionic strength, and investigate the effect of polymer length and degree and pattern of deacetylation on the polymer properties.
Systematic methods for defining coarse-grained maps in large biomolecules.
Zhang, Zhiyong
2015-01-01
Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.
A new algorithm for construction of coarse-grained sites of large biomolecules.
Li, Min; Zhang, John Z H; Xia, Fei
2016-04-05
The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.
Optimal number of coarse-grained sites in different components of large biomolecular complexes.
Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A
2012-07-26
The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.
A coarse-grained model for the simulations of biomolecular interactions in cellular environments
International Nuclear Information System (INIS)
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2014-01-01
The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments
Li, Minghui; Hayward, Gordon
2018-04-01
Over the recent decades, there has been a growing demand on reliable and robust non-destructive evaluation (NDE) of structures and components made from coarse grained materials such as alloys, stainless steels, carbon-reinforced composites and concrete; however, when inspected using ultrasound, the flaw echoes are usually contaminated by high-level, time-invariant, and correlated grain noise originating from the microstructure and grain boundaries, leading to pretty low signal-to-noise ratio (SNR) and the flaw information being obscured or completely hidden by the grain noise. In this paper, the fractal dimension analysis of the A-scan echoes is investigated as a measure of complexity of the time series to distinguish the echoes originating from the real defects and the grain noise, and then the normalized fractal dimension coefficients are applied to the amplitudes as the weighting factor to enhance the SNR and defect detection. Experiments on industrial samples of the mild steel and the stainless steel are conducted and the results confirm the great benefits of the method.
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.
Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni
2018-02-28
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.
A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals
International Nuclear Information System (INIS)
Sinitskiy, Anton V.; Voth, Gregory A.
2015-01-01
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
Synthetic Aperture Focusing Technique in Ultrasonic Inspection of Coarse Grained Materials
Energy Technology Data Exchange (ETDEWEB)
Stepinski, Tadeusz (Uppsala Univ., Signals and Systems, Box 528, SE-751 20 Uppsala (Sweden))
2007-12-15
Experience from the ultrasonic inspection of nuclear power plants has shown that large focused transducers are relatively effective in suppressing grain (structure) noise. Operation of a large focused transducer can be thought of as an integration (coherent summation) of individual beams reflected from the target and received by individual points at the transducer surface. Synthetic aperture focusing technique (SAFT), in its simplest version mimics an acoustic lens used for focusing beams at a desired point in the region of interest. Thus, SAFT should be able to suppress the grain noise in the similar way as the focused transducer does. This report presents the results of investigation of SAFT algorithms applied for post-processing of ultrasonic data acquired in inspection of coarse grained metals. The performance of SAFT in terms of its spatial (cross-range) resolution and grain noise suppression is studied. The evaluation is made based on the experimental data obtained from the ultrasonic inspection of test specimens with artificial defects (side drilled holes). SAFT algorithms for both contact and immersion mode are introduced and experimentally verified
International Nuclear Information System (INIS)
Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro
2013-01-01
This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)
Directory of Open Access Journals (Sweden)
Chi Wai Yu
2008-01-01
Full Text Available This paper examines the interface between fine-grained and coarse-grained programmable logic in FPGAs. Specifically, it presents an empirical study that covers the location, pin arrangement, and interconnect between embedded floating point units (FPUs and the fine-grained logic fabric in FPGAs. It also studies this interface in FPGAs which contain both FPUs and embedded memories. The results show that (1 FPUs should have a square aspect ratio; (2 they should be positioned near the center of the FPGA; (3 their I/O pins should be arranged around all four sides of the FPU; (4 embedded memory should be located between the FPUs; and (5 connecting higher I/O density coarse-grained blocks increases the demand for routing resources. The hybrid FPGAs with embedded memory required 12% wider channels than the case where embedded memory is not used.
Coarse graining of entanglement classes in 2 ×m ×n systems
Hebenstreit, M.; Gachechiladze, M.; Gühne, O.; Kraus, B.
2018-03-01
We consider three-partite pure states in the Hilbert space C2⊗Cm⊗Cn and investigate to which states a given state can be locally transformed with a nonvanishing probability. Whenever the initial and final states are elements of the same Hilbert space, the problem can be solved via the characterization of the entanglement classes which are determined via stochastic local operations and classical communication (SLOCC). In the particular case considered here, the matrix pencil theory can be utilized to address this point. In general, there are infinitely many SLOCC classes. However, when considering transformations from higher to lower dimensional Hilbert spaces, an additional hierarchy among the classes can be found. This hierarchy of SLOCC classes coarse grains SLOCC classes which can be reached from a common resource state of higher dimension. We first show that a generic set of states in C2⊗Cm⊗Cn for n =m is the union of infinitely many SLOCC classes, which can be parameterized by m -3 parameters. However, for n ≠m there exists a single SLOCC class which is generic. Using this result, we then show that there is a full-measure set of states in C2⊗Cm⊗Cn such that any state within this set can be transformed locally to a full measure set of states in any lower dimensional Hilbert space. We also investigate resource states, which can be transformed to any state (not excluding any zero-measure set) in the smaller dimensional Hilbert space. We explicitly derive a state in C2⊗Cm⊗C2 m -2 which is the optimal common resource of all states in C2⊗Cm⊗Cm . We also show that for any n m .
Influence of High Temperature Treatment on Mechanical Behavior of a Coarse-grained Marble
Rong, G.; Peng, J.; Jiang, M.
2017-12-01
High temperature has a significant influence on the physical and mechanical behavior of rocks. With increasing geotechnical engineering structures concerning with high temperature problems such as boreholes for oil or gas production, underground caverns for storage of radioactive waste, and deep wells for injection of carbon dioxides, etc., it is important to study the influence of temperature on the physical and mechanical properties of rocks. This paper experimentally investigates the triaxial compressive properties of a coarse-grained marble after exposure to different high temperatures. The rock specimens were first heated to a predetermined temperature (200, 400, and 600 oC) and then cooled down to room temperature. Triaxial compression tests on these heat-treated specimens subjected to different confining pressures (i.e., 0, 5, 10, 15, 20, 25, 30, 35, and 40 MPa) were then conducted. Triaxial compression tests on rock specimens with no heat treatment were also conducted for comparison. The results show that the high temperature treatment has a significant influence on the microstructure, porosity, P-wave velocity, stress-strain relation, strength and deformation parameters, and failure mode of the tested rock. As the treatment temperature gradually increases, the porosity slightly increases and the P-wave velocity dramatically decreases. Microscopic observation on thin sections reveals that many micro-cracks will be generated inside the rock specimen after high temperature treatment. The rock strength and Young's modulus show a decreasing trend with increase of the treatment temperature. The ductility of the rock is generally enhanced as the treatment temperature increases. In general, the high temperature treatment weakens the performance of the tested rock. Finally, a degradation parameter is defined and a strength degradation model is proposed to characterize the strength behavior of heat-treated rocks. The results in this study provide useful data for
Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing
Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.
2015-03-01
Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor 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 infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.
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
De determination for young samples using the standardised OSL response of coarse-grain quartz
International Nuclear Information System (INIS)
Burbidge, C.I.; Duller, G.A.T.; Roberts, H.M.
2006-01-01
It has recently been shown that it is possible to construct standardised curves of the sensitivity corrected growth in optically stimulated luminescence (OSL) with exposure to ionising radiation, and that they may be used in the dating of quartz and polymineral samples. Standardised growth curves are particularly advantageous where measurement time is limited, as once they have been defined, only the natural signal and the response to a subsequent test dose are required in order to determine the equivalent dose of a sub-sample. The present study is concerned with the application of the standardised growth curve approach to OSL dating of Holocene age samples. Systematic changes in the shape of the standardised growth curve of coarse-grain quartz are identified as the size of the test dose is varied, because of non-proportionality between the test dose and the luminescence test response. The effect is characterised by fitting the change in gradient of the standardised growth curve as test dose is varied. An equation is defined to describe standardised growth as a function of regenerative dose and test dose. Regenerative dose responses of other samples in this study are treated as unknowns and recovered through different growth curves to compare precision and accuracy of various methods of D e determination. The standardised growth curve is found to yield similar precision to conventional fits of single aliquot regenerative data, but slightly poorer accuracy. The standardised growth curve approach was refined by incorporating the measurement of one regenerative response for each aliquot as well as its natural signal. Measurements of this additional data point for aliquots of 22 samples were used to adjust the standardised growth equation, improving its accuracy. The incorporation of this additional data point also indicated a systematic uncertainty of 2.4% in the estimates of D e
Into the deep: A coarse-grained carbonate turbidite thalweg generated by gigantic submarine chutes
Mulder, Thierry; Gillet, Hervé; Reijmer, John; Droxler, André; cavailhes, Thibault; Hanquiez, Vincent; Fauquembergue, Kelly; Bujan, Stéphane; Blanck, David; bashah, Sara; Guiastrennec, Léa; Fabregas, Natacha; Recouvreur, Audrey; Seibert, Chloé
2017-04-01
New high-resolution multibeam mapping, in the Southeastern Bahamas, images in exquisite details the southern part of Exuma Sound, and its unchartered transition area to the deep abyssal plain of the Western North Atlantic bounded by the Bahama Escarpment (BE) between San Salvador Island and Samana Cay, referred here to the San Salvador abyssal plain. The transition area is locally referred to as Crooked Island Passage, loosely delineated by Crooked, Long, and Conception Islands, Rum and Samana Cays. Surprisingly in such a pure carbonate landscape, the newly established map reveals the detailed and complex morphology of a giant valley formed by numerous gravity flows originated in Exuma Sound itself, in addition to many secondary slope gullies and smaller tributaries draining the surrounding upper slopes. The valley referred here as the Exuma canyon system starts with a perched valley with low sinuosity, characterized by several flow restrictions and knickpoints initiated by the presence of drowned isolated platforms and merging tributaries. The valley abruptly transforms itself into a deep incised canyon, rivaling the depth of the Colorado Grand Canyon, through two major knickpoints with outsized chutes exceeding several hundred of meters in height, a total of 1600-1800 m. The sudden transformation of the wide valley into a deep narrow canyon, occurring when the flows incised deep into an underlying lower Cretaceous drowned carbonate platform, generates a huge hydraulic jump and creates an enormous plunge pool and related deposits with mechanisms comparable to the ones operating along giant subaerial waterfalls. The high kinetic flow energy, constrained by this narrow and deeply incised canyon, formed, when it is released at its mouth in the abyssal plain, a wide deep-sea channel with well-developed levees and fan, made of coarse-grained carbonate defined layers separated by fine carbonate sediments mixed with fine siliciclastics transported along the BE by the
Energy-efficient specialization of functional units in a Coarse-Grained Reconfigurable Array
International Nuclear Information System (INIS)
Van Essen, B.; Panda, R.; Wood, A.; Ebeling, C.; Hauck, S.
2010-01-01
Functional units provide the backbone of any spatial accelerator by providing the computing resources. The desire for having rich and expensive functional units is in tension with producing a regular and energy-efficient computing fabric. This paper explores the design trade-off between complex, universal functional units and simpler, limited functional units. We show that a modest amount of specialization reduces the area-delay-energy product of an optimized architecture to 0.86x a baseline architecture. Furthermore, we provide a design guideline that allows an architect to customize the contents of the computing fabric just by examining the profile of benchmarks within the application domains. Functional units are the core of compute-intensive spatial accelerators. They perform the computation of interest with support from local storage and communication structures. Ideally, the functional units will provide rich functionality, supporting operations ranging from simple addition, to fused multiply-adds, to advanced transcendental functions and domain specific operations like add-compare-select. However, the total opportunity cost to support the more complex operations is a function of the cost of the hardware, the rate of occurrence of the operation in the application domain, and the inefficiency of emulating the operation with simpler operators. Examples of operations that are typically emulated in spatial accelerators are division and trigonometric functions, which can be solved using table-lookup based algorithms and the CORDIC algorithm. One reason to avoid having direct hardware support for complex operations in a tiled architecture like a Coarse-Grained Reconfigurable Array (CGRA) is that the expensive hardware will typically need to be replicated in some or all of the architecture's tiles. Tiled architecture are designed such that their tiles are either homogeneous or heterogeneous. Homogeneous architectures are simpler to design but heterogeneous
HIGH-FIDELITY SIMULATION-DRIVEN MODEL DEVELOPMENT FOR COARSE-GRAINED COMPUTATIONAL FLUID DYNAMICS
Energy Technology Data Exchange (ETDEWEB)
Hanna, Botros N.; Dinh, Nam T.; Bolotnov, Igor A.
2016-06-01
Nuclear reactor safety analysis requires identifying various credible accident scenarios and determining their consequences. For a full-scale nuclear power plant system behavior, it is impossible to obtain sufficient experimental data for a broad range of risk-significant accident scenarios. In single-phase flow convective problems, Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES) can provide us with high fidelity results when physical data are unavailable. However, these methods are computationally expensive and cannot be afforded for simulation of long transient scenarios in nuclear accidents despite extraordinary advances in high performance scientific computing over the past decades. The major issue is the inability to make the transient computation parallel, thus making number of time steps required in high-fidelity methods unaffordable for long transients. In this work, we propose to apply a high fidelity simulation-driven approach to model sub-grid scale (SGS) effect in Coarse Grained Computational Fluid Dynamics CG-CFD. This approach aims to develop a statistical surrogate model instead of the deterministic SGS model. We chose to start with a turbulent natural convection case with volumetric heating in a horizontal fluid layer with a rigid, insulated lower boundary and isothermal (cold) upper boundary. This scenario of unstable stratification is relevant to turbulent natural convection in a molten corium pool during a severe nuclear reactor accident, as well as in containment mixing and passive cooling. The presented approach demonstrates how to create a correction for the CG-CFD solution by modifying the energy balance equation. A global correction for the temperature equation proves to achieve a significant improvement to the prediction of steady state temperature distribution through the fluid layer.
International Nuclear Information System (INIS)
Anderson, Michael T.; Cumblidge, Stephen E.; Doctor, Steven R.
2003-01-01
Pacific Northwest Laboratory is evaluating the capabilities and limitations of phased array (PA) technology to detect service-type flaws in coarse-grained austenitic piping structures. The work is being sponsored by the U.S. Nuclear Regulatory Commission, Office of Research. This paper presents initial work involving the use of PA technology to determine the effectiveness of detecting and accurately characterizing flaws on the far-side of austenitic piping welds
Energy Technology Data Exchange (ETDEWEB)
Farrell, Kathryn, E-mail: kfarrell@ices.utexas.edu; Oden, J. Tinsley, E-mail: oden@ices.utexas.edu; Faghihi, Danial, E-mail: danial@ices.utexas.edu
2015-08-15
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.
Farrell, Kathryn; Oden, J. Tinsley; Faghihi, Danial
2015-08-01
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.
International Nuclear Information System (INIS)
Poursina, Mohammad; Anderson, Kurt S.
2014-01-01
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
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.
International Nuclear Information System (INIS)
Tabachnikova, E D; Podolskiy, A V; Smirnov, S N; Psaruk, I A; Liao, P K
2014-01-01
Mechanical properties of Ni-18.75 at.% Fe in coarse grained (average grain size 15 gm) and nanocrystalline (average grain size 22 nm) states were studied in uniaxial compression in the temperature range 4.2-350 K. Temperature dependences of the flow stress, strain rate sensitivity and activation volume of plastic deformation were measured. The thermal activation analysis of the experimental data has been fulfilled for the the plastic deformation value of 2 %. It was shown that plastic deformation in temperature range from 35 to 350 K in both studied structural states has the thermally activated type. Comparative analysis of low temperature thermal activation plastic deformation was carried out for the alloy in coarse grained and nanocrystalline states. Empirical estimates of parameters of the dislocation interaction with local barriers and internal stress value estimates were obtained for the both studied structural states. Analysis of the results indicates that different mechanisms control the thermal activation plasticity of the Ni-18.75 at.% Fe alloy in coarse grained and nanocrystalline states. Possible mechanisms, which control plactisity of the studied states, are disscussed
International Nuclear Information System (INIS)
Sanyal, Tanmoy; Shell, M. Scott
2016-01-01
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
Macdonald, R. L.; Grover, M. S.; Schwartzentruber, T. E.; Panesi, M.
2018-02-01
This work presents the analysis of non-equilibrium energy transfer and dissociation of nitrogen molecules (N2(g+1Σ) ) using two different approaches: the direct molecular simulation (DMS) method and the coarse-grain quasi-classical trajectory (CG-QCT) method. The two methods are used to study thermochemical relaxation in a zero-dimensional isochoric and isothermal reactor in which the nitrogen molecules are heated to several thousand degrees Kelvin, forcing the system into strong non-equilibrium. The analysis considers thermochemical relaxation for temperatures ranging from 10 000 to 25 000 K. Both methods make use of the same potential energy surface for the N2(g+1Σ ) -N2(g+1Σ ) system taken from the NASA Ames quantum chemistry database. Within the CG-QCT method, the rovibrational energy levels of the electronic ground state of the nitrogen molecule are lumped into a reduced number of bins. Two different grouping strategies are used: the more conventional vibrational-based grouping, widely used in the literature, and energy-based grouping. The analysis of both the internal state populations and concentration profiles show excellent agreement between the energy-based grouping and the DMS solutions. During the energy transfer process, discrepancies arise between the energy-based grouping and DMS solution due to the increased importance of mode separation for low energy states. By contrast, the vibrational grouping, traditionally considered state-of-the-art, captures well the behavior of the energy relaxation but fails to consistently predict the dissociation process. The deficiency of the vibrational grouping model is due to the assumption of strict mode separation and equilibrium of rotational energy states. These assumptions result in errors predicting the energy contribution to dissociation from the rotational and vibrational modes, with rotational energy actually contributing 30%-40% of the energy required to dissociate a molecule. This work confirms the
Abberton, Brendan C.; Liu, Wing Kam; Keten, Sinan
2013-12-01
Thermally actuated shape-memory polymers (SMPs) are capable of being programmed into a temporary shape and then recovering their permanent reference shape upon exposure to heat, which facilitates a phase transition that allows dramatic increase in molecular mobility. Experimental, analytical, and computational studies have established empirical relations of the thermomechanical behavior of SMPs that have been instrumental in device design. However, the underlying mechanisms of the recovery behavior and dependence on polymer microstructure remain to be fully understood for copolymer systems. This presents an opportunity for bottom-up studies through molecular modeling; however, the limited time-scales of atomistic simulations prohibit the study of key performance metrics pertaining to recovery. In order to elucidate the effects of phase fraction, recovery temperature, and deformation temperature on shape recovery, here we investigate the shape-memory behavior in a copolymer model with coarse-grained potentials using a two-phase molecular model that reproduces physical crosslinking. Our simulation protocol allows observation of upwards of 90% strain recovery in some cases, at time-scales that are on the order of the timescale of the relevant relaxation mechanism (stress relaxation in the unentangled soft-phase). Partial disintegration of the glassy phase during mechanical deformation is found to contribute to irrecoverable strain. Temperature dependence of the recovery indicates nearly full elastic recovery above the trigger temperature, which is near the glass-transition temperature of the rubbery switching matrix. We find that the trigger temperature is also directly correlated with the deformation temperature, indicating that deformation temperature influences the recovery temperatures required to obtain a given amount of shape recovery, until the plateau regions overlap above the transition region. Increasing the fraction of glassy phase results in higher strain
Protein folding simulations: from coarse-grained model to all-atom model.
Zhang, Jian; Li, Wenfei; Wang, Jun; Qin, Meng; Wu, Lei; Yan, Zhiqiang; Xu, Weixin; Zuo, Guanghong; Wang, Wei
2009-06-01
Protein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL
Reaction and relaxation in a coarse-grained fluvial system following catchment-wide disturbance
Tunnicliffe, Jon; Brierley, Gary; Fuller, Ian C.; Leenman, Anya; Marden, Mike; Peacock, Dave
2018-04-01
The Waiapu River catchment (drainage area of 1734-km2) is one of the most prolific conveyors of sediment in the world, annually delivering roughly 35 Mt of fine material to the ocean from eroding gullies, hillslopes, and reworked sediment on valley floors. Tectonic and geologic influences, in combination with a dynamic climate influenced by tropical cyclones and clearance of vegetation from steep hillslopes, predisposes this region to high rates of erosion. The bedload sediment regime of the river is strongly influenced by several exceptionally large gullies and gully complexes that produce a coarse-grained, poorly sorted sediment mixture. Rapid abrasion and breakdown leads to high rates of suspended sediment yield. A wave of bedload material, manifesting as elevated bed levels and significant widening of active alluvial fills, has been triggered by large inputs of hillslope material from a few key tributary catchments following Cyclone Bola in 1988. We review the evidence for the relaxation process of the sedimentary system in the subsequent 29 years, appraising some of the legacy effects that may endure, as associated with reworking of the considerable alluvial stores within the Waiapu system. We use Structure-from-Motion (SfM) techniques and archival aerial photos to quantify changes in sediment storage at the base of two major gully systems in recent decades. A record of over 850 cross section surveys at 62 sites on 10 rivers throughout the catchment (1958-2017) indicates recent transition from a trend of continuous accumulation to downcutting and remobilisation of valley-bottom deposits. The channel cross sections provide a minimum estimate of sediment flux from source areas to the lower reaches of the river, giving a rudimentary but spatially extensive picture of the wave of material cascading through the drainage network. The largest impacts occur in the upper steepland rivers, closest to the landslide-derived sediment supply. Transport rates here, as
International Nuclear Information System (INIS)
Pumir, Alain; Naso, Aurore
2010-01-01
A proper description of the velocity gradient tensor is crucial for understanding the dynamics of turbulent flows, in particular the energy transfer from large to small scales. Insight into the statistical properties of the velocity gradient tensor and into its coarse-grained generalization can be obtained with the help of a stochastic 'tetrad model' that describes the coarse-grained velocity gradient tensor based on the evolution of four points. Although the solution of the stochastic model can be formally expressed in terms of path integrals, its numerical determination in terms of the Monte-Carlo method is very challenging, as very few configurations contribute effectively to the statistical weight. Here, we discuss a strategy that allows us to solve the tetrad model numerically. The algorithm is based on the importance sampling method, which consists here of identifying and sampling preferentially the configurations that are likely to correspond to a large statistical weight, and selectively rejecting configurations with a small statistical weight. The algorithm leads to an efficient numerical determination of the solutions of the model and allows us to determine their qualitative behavior as a function of scale. We find that the moments of order n≤4 of the solutions of the model scale with the coarse-graining scale and that the scaling exponents are very close to the predictions of the Kolmogorov theory. The model qualitatively reproduces quite well the statistics concerning the local structure of the flow. However, we find that the model generally tends to predict an excess of strain compared to vorticity. Thus, our results show that while some physical aspects are not fully captured by the model, our approach leads to a very good description of several important qualitative properties of real turbulent flows.
Nehyba, Slavomír
2018-02-01
Two coarse-grained Gilbert-type deltas in the Lower Badenian deposits along the southern margin of the Western Carpathian Foredeep (peripheral foreland basin) were newly interpreted. Facies characterizing a range of depositional processes are assigned to four facies associations — topset, foreset, bottomset and offshore marine pelagic deposits. The evidence of Gilbert deltas within open marine deposits reflects the formation of a basin with relatively steep margins connected with a relative sea level fall, erosion and incision. Formation, progradation and aggradation of the thick coarse-grained Gilbert delta piles generally indicate a dramatic increase of sediment supply from the hinterland, followed by both relatively continuous sediment delivery and an increase in accommodation space. Deltaic deposition is terminated by relatively rapid and extended drowning and is explained as a transgressive event. The lower Gilbert delta was significantly larger, more areally extended and reveals a more complicated stratigraphic architecture than the upper one. Its basal surface represents a sequence boundary and occurs around the Karpatian/Badenian stratigraphic limit. Two coeval deltaic branches were recognized in the lower delta with partly different stratigraphic arrangements. This different stratigraphic architecture is mostly explained by variations in the sediment delivery and /or predisposed paleotopography and paleobathymetry of the basin floor. The upper delta was recognized only in a restricted area. Its basal surface represents a sequence boundary probably reflecting a higher order cycle of a relative sea level rise and fall within the Lower Badenian. Evidence of two laterally and stratigraphically separated coarse-grained Gilbert deltas indicates two regional/basin wide transgressive/regressive cycles, but not necessarily of the same order. Provenance analysis reveals similar sources of both deltas. Several partial source areas were identified (Mesozoic
Urbanowicz, Krzysztof; Hołyst, Janusz A.
2004-12-01
Using a recently developed method of noise level estimation that makes use of properties of the coarse-grained entropy, we have analyzed the noise level for the Dow Jones index and a few stocks from the New York Stock Exchange. We have found that the noise level ranges from 40% to 80% of the signal variance. The condition of a minimal noise level has been applied to construct optimal portfolios from selected shares. We show that the implementation of a corresponding threshold investment strategy leads to positive returns for historical data.
DEFF Research Database (Denmark)
Kato, Yuki; Gorodkin, Jan; Havgaard, Jakob Hull
2017-01-01
. Methods: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level. This allows us to perform an all-against-all scan of all window pairs from two genomes...... without alignment. Results: Our computational experiments with simulated data and real chromosomes demonstrate that the presented method has good sensitivity. Conclusions: DotcodeR can be useful as a pre-filter in a genomic comparative scan for structured RNAs....
Krzysztof Urbanowicz; Janusz A. Holyst
2004-01-01
Using a recently developed method of noise level estimation that makes use of properties of the coarse grained-entropy we have analyzed the noise level for the Dow Jones index and a few stocks from the New York Stock Exchange. We have found that the noise level ranges from 40 to 80 percent of the signal variance. The condition of a minimal noise level has been applied to construct optimal portfolios from selected shares. We show that implementation of a corresponding threshold investment stra...
de la Cruz, Roberto; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás
2017-12-01
The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction-diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction-diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of
International Nuclear Information System (INIS)
Cruz, Roberto de la; Guerrero, Pilar; Calvo, Juan; Alarcón, Tomás
2017-01-01
The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction–diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction–diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge
Hagita, Katsumi; Murashima, Takahiro; Takano, Hiroshi; Kawakatsu, Toshihiro
2017-12-01
We proposed a thinning approximation (TA) for estimation of the two-dimensional (2D) wide-angle scattering patterns from Kremer-Grest polymer melts under shear. In the TA, extra particles are inserted at the middle of bonds for fine-graining of the coarse-grained polymers. For the case without the TA, spots corresponding to the orientation of bonds at a high shear rate are difficult to observe because the bond length of successive particles is comparable to the distance between neighboring particles. With the insertion of the extra particles, a ring pattern originating from the neighboring particles can be moved to a wide-angle region. Thus, we can observe the spots at high shear rates. We also examined the relationship between 2D scattering patterns and the Weissenberg number, which is defined as the product of the shear rate and the longest relaxation time. It is confirmed that the relationship for coarse-grained polymers with the TA is consistent with that of the all-atomistic model of polyethylene.
Truccolo, Wilson
2016-11-01
This review presents a perspective on capturing collective dynamics in recorded neuronal ensembles based on multivariate point process models, inference of low-dimensional dynamics and coarse graining of spatiotemporal measurements. A general probabilistic framework for continuous time point processes reviewed, with an emphasis on multivariate nonlinear Hawkes processes with exogenous inputs. A point process generalized linear model (PP-GLM) framework for the estimation of discrete time multivariate nonlinear Hawkes processes is described. The approach is illustrated with the modeling of collective dynamics in neocortical neuronal ensembles recorded in human and non-human primates, and prediction of single-neuron spiking. A complementary approach to capture collective dynamics based on low-dimensional dynamics ("order parameters") inferred via latent state-space models with point process observations is presented. The approach is illustrated by inferring and decoding low-dimensional dynamics in primate motor cortex during naturalistic reach and grasp movements. Finally, we briefly review hypothesis tests based on conditional inference and spatiotemporal coarse graining for assessing collective dynamics in recorded neuronal ensembles. Published by Elsevier Ltd.
International Nuclear Information System (INIS)
Graham, I.J.; Korsch, R.J.
1985-01-01
The Coffs Harbour Block, eastern Australia, includes a sequence of turbidity-current-deposited greywackes and argillites dominated by quartz-poor to quartz-intermediate, volcanic-lithic and feldspathic types. The rocks have a common provenance consisting of dacite with minor andesite and rhyolite, derived from a continental margin volcanic arc. Rb-Sr whole-rock dating of coarse-grained greywackes and argillites suggests that low-grade regional metamorphism (prehnite-pumpellyite to lowest greenschist facies) has completely equilibrated sediments of all grain sizes, giving an age of 318 +- 8 Ma. A subsequent metamorphism which produced thermal biotite on a regional scale over the southern part of the area, re-equilibrated only the fine-grained sediments 238 +- 5 Ma ago; the coarse-grained sediments were unaffected isotopically and still lie on the older isochron. The wide variations in sandstone petrographic modes imply that the older isochron represents neither the age of volcanism in the magmatic arc nor the age of sedimentation at the deposition site, but rather dates the time of earlier metamorphism. (orig.)
Directory of Open Access Journals (Sweden)
Li Weijuan
2016-09-01
Full Text Available In the present work, specimens prepared from coarse grained low carbon steel with different prestrains were baked and then, their bake hardening (BH property and internal friction were determined. TEM was used to characterize the dislocation structure in BH treated samples. The measurements of internal friction in prestrained samples and baked samples were carried out using a multifunctional internal friction apparatus. The results indicate that, in coarse grained low carbon steel, the bake hardening properties (BH values were negative, which were increased by increasing the prestrain from 2 to 5%, and then were decreased by increasing the prestrain from 5 to 10%. In the specimen with prestrain 5%, the BH value reached the maximum value and the height of Snoek-Köster peak was observed to be the maximum alike. With increasing the prestrain, both of the BH value and Snoek-Köster peak heights are similarly varied. It is concluded that Snoek-Köster and dislocation-enhanced Snoek peaks, caused by the interactions between interstitial solute carbon atoms and dislocations, can be used in further development of the bake hardening steels.
GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.
Boudard, Mélanie; Barth, Dominique; Bernauer, Julie; Denise, Alain; Cohen, Johanne
2017-08-15
Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule. We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods. GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/. melanie.boudard@lri.fr or johanne.cohen@lri.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Pandey, Ras; Farmer, Barry
2013-03-01
Quality of solvent plays a critical role in modulating the structure of a protein along with the temperature. Using a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV) we examine the structure and dynamics of a histone (H3.1). The empty lattice sites constitute the effective solvent medium in which the protein is embedded. Residue-solvent characteristic interaction is based on the hydropathy index while the residue-residue interaction is used from the knowledge-based contact matrices derived from ensembles of protein structures in the protein data bank. Large scale simulations are performed to analyze the structure of protein for a range of residue-solvent interaction strength, a measure of the solvent quality with each potential. Unlike the monotonic thermal response, the radius of gyration of the protein exhibits non-monotonic dependence of the solvent strength. Quantitative comparison of the structure and dynamics emerging from three knowledge-based potentials will be presented in this talk. This work is supported by Air Force Research Laboratory.
Dunn, Nicholas J H; Noid, W G
2016-05-28
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.
Energy Technology Data Exchange (ETDEWEB)
Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)
2016-05-28
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.
McCarty, J; Clark, A J; Copperman, J; Guenza, M G
2014-05-28
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.
Pizzirusso, Antonio; Brasiello, Antonio; De Nicola, Antonio; Marangoni, Alejandro G.; Milano, Giuseppe
2015-12-01
The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined.
International Nuclear Information System (INIS)
Pizzirusso, Antonio; De Nicola, Antonio; Milano, Giuseppe; Brasiello, Antonio; Marangoni, Alejandro G
2015-01-01
The first simulation study of the crystallisation of a binary mixture of triglycerides using molecular dynamics simulations is reported. Coarse-grained models of tristearin (SSS) and tripalmitin (PPP) molecules have been considered. The models have been preliminarily tested in the crystallisation of pure SSS and PPP systems. Two different quenching procedures have been tested and their performances have been analysed. The structures obtained from the crystallisation procedures show a high orientation order and a high content of molecules in the tuning fork conformation, comparable with the crystalline α phase. The behaviour of melting temperatures for the α phase of the mixture SSS/PPP obtained from the simulations is in qualitative agreement with the behaviour that was experimentally determined. (paper)
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.
Directory of Open Access Journals (Sweden)
Farics Éva
2017-10-01
Full Text Available The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity. The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes.
A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution
Directory of Open Access Journals (Sweden)
Roghayeh Abedi Karjiban
2013-01-01
Full Text Available The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC, dilauroylphosphatidylcholine (DLPC, dimyristoylphosphatidylcholine (DMPC, and distearoylphosphatidylcholine (DSPC in water were investigated using a coarse-grained molecular dynamics (CG-MD simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.
Fu, Yankai; Yan, Tingxuan; Xu, Xia
2017-09-28
Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.
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.
DEFF Research Database (Denmark)
Koivuniemi, A.; Vuorela, T.; Kovanen, P. T.
2012-01-01
molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained models whose results were consistent with each other. We found CETP to bind to the surface of high density lipoprotein (HDL) -like lipid droplets......Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed...... evidence that helix X acts as a lid which conducts lipid exchange by alternating the open and closed states. The findings have potential for the design of novel molecular agents to inhibit the activity of CETP....
Directory of Open Access Journals (Sweden)
Vakser Ilya A
2011-07-01
Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of
Theory of Wavelet-Based Coarse-Graining Hierarchies for Molecular Dynamics
2017-04-01
Ismail25,26. In particular, the earlier work employed Monte Carlo and did not cap - ture dynamical information. The work here develops an approach suitable...assessed by the `1- norm of the correlation matrices, about 28 versus about 21 for water, and about 315 versus about 168 for alanine dipeptide. 18...indication of the appropriateness of the diffusion wavelet DoFs, is the `1- norm of structures and forces in a given representation basis. The `1- norm is
Stresses in non-equilibrium fluids: Exact formulation and coarse-grained theory
Krüger, Matthias; Solon, Alexandre; Démery, Vincent; Rohwer, Christian M.; Dean, David S.
2018-02-01
Starting from the stochastic equation for the density operator, we formulate the exact (instantaneous) stress tensor for interacting Brownian particles and show that its average value agrees with expressions derived previously. We analyze the relation between the stress tensor and forces due to external potentials and observe that, out of equilibrium, particle currents give rise to extra forces. Next, we derive the stress tensor for a Landau-Ginzburg theory in generic, non-equilibrium situations, finding an expression analogous to that of the exact microscopic stress tensor, and discuss the computation of out-of-equilibrium (classical) Casimir forces. Subsequently, we give a general form for the stress tensor which is valid for a large variety of energy functionals and which reproduces the two mentioned cases. We then use these relations to study the spatio-temporal correlations of the stress tensor in a Brownian fluid, which we compute to leading order in the interaction potential strength. We observe that, after integration over time, the spatial correlations generally decay as power laws in space. These are expected to be of importance for driven confined systems. We also show that divergence-free parts of the stress tensor do not contribute to the Green-Kubo relation for the viscosity.
International Nuclear Information System (INIS)
He, Rui; Fan, Hong-yi
2014-01-01
Based on the solution to the master equation of the density operator describing the amplitude dissipative channel, we derive the time evolution law of the coarse-graining-smoothed Wigner operator in this channel, which demonstrates how an initial pure state evolves into a mixed state, exhibiting decoherence
Eivani, A.R.; Zhou, J.
2017-01-01
In this research, hot compression test is used to simulate the metallurgical phenomena occurring in the peripheral part of AA7020 aluminum alloy extrudates during hot extrusion and leading to the formation of the peripheral coarse grain (PCG) structure. The temperature profiles at a tracking
Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun
2008-01-01
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 of 13C atoms of
Lang, Joerg; Brandes, Christian; Winsemann, Jutta
2017-04-01
The facies distribution and architecture of submarine fans can be strongly impacted by erosion and deposition by supercritical density flows. We present field examples from the Sandino Forearc Basin (southern Central America), where cyclic-step and antidune deposits represent important sedimentary facies of coarse-grained channel-levée complexes. These bedforms occur in all sub-environments of the depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. Large-scale scours (18 to 29 m deep, 18 to 25 m wide, 60 to >120 m long) with an amalgamated infill, comprising massive, normally coarse-tail graded or spaced subhorizontally stratified conglomerates and pebbly sandstones, are interpreted as deposits of the hydraulic-jump zone of cyclic steps. These cyclic steps probably formed during avulsion, when high-density flows were routed into the evolving channel. The large-scale scour fills can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump deposits. Channel fills include repetitive successions deposited by cyclic steps with superimposed antidunes. The hydraulic-jump zone of cyclic-step deposits comprises regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m wide), which are infilled by intraclast-rich conglomerates or pebbly sandstones and display normal coarse-tail grading or backsets. Laterally and vertically these deposits are associated with subhorizontally stratified, low-angle cross-stratified or sinusoidal stratified pebbly sandstones and sandstones (wavelength 0.5 to 18 m), interpreted as representing antidune deposits formed on the stoss-side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called crudely or spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation
Directory of Open Access Journals (Sweden)
John G Koland
2014-01-01
Full Text Available Upon the ligand-dependent dimerization of the epidermal growth factor receptor (EGFR, the intrinsic protein tyrosine kinase (PTK activity of one receptor monomer is activated, and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites (P-sites in either of the two C-terminal (CT domains. While the structures of the extracellular ligand binding and intracellular PTK domains are known, that of the ∼225-amino acid CT domain is not, presumably because it is disordered. Receptor phosphorylation on CT domain P-sites is critical in signaling because of the binding of specific signaling effector molecules to individual phosphorylated P-sites. To investigate how the combination of conventional substrate recognition and the unique topological factors involved in the CT domain self-phosphorylation reaction lead to selectivity in P-site phosphorylation, we performed coarse-grained molecular simulations of the P-site/catalytic site binding reactions that precede EGFR self-phosphorylation events. Our results indicate that self-phosphorylation of the dimeric EGFR, although generally believed to occur in trans, may well occur with a similar efficiency in cis, with the P-sites of both receptor monomers being phosphorylated to a similar extent. An exception was the case of the most kinase-proximal P-site-992, the catalytic site binding of which occurred exclusively in cis via an intramolecular reaction. We discovered that the in cis interaction of P-site-992 with the catalytic site was facilitated by a cleft between the N-terminal and C-terminal lobes of the PTK domain that allows the short CT domain sequence tethering P-site-992 to the PTK core to reach the catalytic site. Our work provides several new mechanistic insights into the EGFR self-phosphorylation reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for investigating the complexities of self-phosphorylation in
Physical Modelling of Large Diameter Piles in Coarse-Grained Soil
DEFF Research Database (Denmark)
Brødbæk, K. T.; Augustesen, Anders Hust; Møller, M.
2011-01-01
of increasing the effective stresses. The test setup is thoroughly described in the paper. Two non-slender aluminium pipe piles subjected to lateral loads have been tested in the laboratory. The piles are heavily instrumented with strain gauges in order to obtain p-y curves, displacement and bending moment......Monopiles are an often-used foundation concept for offshore wind turbine converters. These piles are highly subjected to lateral loads and overturning bending moments due to wind and wave forces. To ensure enough stiffness of the foundation and an acceptable pile-head deflection, monopiles...... with diameters of 4 to 6 m are typically employed. In current practice these piles are traditionally designed by means of the p-y curve method although the method is developed and verified for slender piles in sand with diameters up to approximately 2 m. One of the limitations of the p-y curves used in current...
Misra, R D K; Nune, C; Pesacreta, T C; Somani, M C; Karjalainen, L P
2013-01-01
The rapid adsorption of proteins is the starting and primary biological response that occurs when a biomedical device is implanted in the physiological system. The biological response, however, depends on the surface characteristics of the device. Considering the significant interest in nano-/ultrafine surfaces and nanostructured coatings, we describe here, the interplay between grain structure and protein adsorption (bovine serum albumin: BSA) on osteoblasts functions by comparing nanograined/ultrafine-grained (NG/UFG) and coarse-grained (CG: grain size in the micrometer range) substrates by investigating cell-substrate interactions. The protein adsorption on NG/UFG surface was beneficial in favorably modulating biological functions including cell attachment, proliferation, and viability, whereas the effect was less pronounced on protein adsorbed CG surface. Additionally, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on protein adsorbed NG/UFG surface. The functional response followed the sequence: NG/UFG(BSA) > NG/UFG > CG(BSA) > CG. The differences in the cellular response on bare and protein adsorbed NG/UFG and CG surfaces are attributed to cumulative contribution of grain structure and degree of hydrophilicity. The study underscores the potential advantages of protein adsorption on artificial biomedical devices to enhance the bioactivity and regulate biological functions. Copyright © 2012 Wiley Periodicals, Inc.
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.
2018-04-01
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt
Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.
2018-03-01
Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.
Energy Technology Data Exchange (ETDEWEB)
Zeidman, Benjamin D. [Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401 (United States); Lu, Ning [Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401 (United States); Wu, David T., E-mail: dwu@mines.edu [Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401 (United States); Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401 (United States)
2016-05-07
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.
Lyu, Justin; Andrianarijaona, V. M.
2016-05-01
The causes of the misfolding of prion protein -i.e. the transformation of PrPC to PrPSc - have not been clearly elucidated. Many studies have focused on identifying possible chemical conditions, such as pH, temperature and chemical denaturation, that may trigger the pathological transformation of prion proteins (Weiwei Tao, Gwonchan Yoon, Penghui Cao, `` β-sheet-like formation during the mechanical unfolding of prion protein'', The Journal of Chemical Physics, 2015, 143, 125101). Here, we attempt to calculate the ionization energies of the prion protein, which will be able to shed light onto the possible causes of the misfolding. We plan on using the coarse-grain method which allows for a more feasible calculation time by means of approximation. We believe that by being able to approximate the ionization potential, particularly that of the regions known to form stable β-strands of the PrPSc form, the possible sources of denaturation, be it chemical or mechanical, may be narrowed down.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M
2016-04-20
RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
A Snapshot of Present Research at AAU and DTU on Large-Diameter Piles in Coarse-Grained Materials
DEFF Research Database (Denmark)
Leth, C. T.; Sørensen, Søren Peder Hyldal; Klinkvort, Rasmus Tofte
2012-01-01
are developed for piles with diameters up to approximately 2.0 m and are based on a very limited number of tests. Hence, the method has not been validated for piles with diameters of 4 to 6 m. During the last six years extensive studies on non-slender large-diameter piles in coarse-grained material have been...... conducted at Aalborg University (AAU) and at the Technical University of Denmark (DTU). The piles have been investigated by means of physical and numerical modelling. The former consists of both centrifuge tests and tests in a so-called pressure tank (1G tests but with an applied overburden pressure......). The goal of the work has been to investigate the general behaviour of monopiles for nowadays offshore wind turbines and to revise the p-y curves for piles in sand in order to account for diameter on the response of monopiles subjected to both static and cyclic loads. The paper summarizes and compares...
Ghobadi, Ahmadreza F; Jayaraman, Arthi
2016-02-28
In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.
International Nuclear Information System (INIS)
Knott, Michael; Best, Robert B.
2014-01-01
Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD
Kapoor, Abhijeet; Travesset, Alex
2014-03-01
We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.
Farics, Éva; Farics, Dávid; Kovács, József; Haas, János
2017-10-01
The main aim of this paper is to determine the depositional environments of an Upper-Eocene coarse-grained clastic succession in the Buda Hills, Hungary. First of all, we measured some commonly used parameters of samples (size, amount, roundness and sphericity) in a much more objective overall and faster way than with traditional measurement approaches, using the newly developed Rock Analyst application. For the multivariate data obtained, we applied Combined Cluster and Discriminant Analysis (CCDA) in order to determine homogeneous groups of the sampling locations based on the quantitative composition of the conglomerate as well as the shape parameters (roundness and sphericity). The result is the spatial pattern of these groups, which assists with the interpretation of the depositional processes. According to our concept, those sampling sites which belong to the same homogeneous groups were likely formed under similar geological circumstances and by similar geological processes. In the Buda Hills, we were able to distinguish various sedimentological environments within the area based on the results: fan, intermittent stream or marine.
Energy Technology Data Exchange (ETDEWEB)
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.
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.
International Nuclear Information System (INIS)
Kroonblawd, Matthew P.; Sewell, Thomas D.; Maillet, Jean-Bernard
2016-01-01
In this report, we characterize the kinetics and dynamics of energy exchange between intramolecular and intermolecular degrees of freedom (DoF) in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). All-atom molecular dynamics (MD) simulations are used to obtain predictions for relaxation from certain limiting initial distributions of energy between the intra- and intermolecular DoF. The results are used to parameterize a coarse-grained Dissipative Particle Dynamics at constant Energy (DPDE) model for TATB. Each TATB molecule in the DPDE model is represented as an all-atom, rigid-molecule mesoparticle, with explicit external (molecular translational and rotational) DoF and coarse-grained implicit internal (vibrational) DoF. In addition to conserving linear and angular momentum, the DPDE equations of motion conserve the total system energy provided that particles can exchange energy between their external and internal DoF. The internal temperature of a TATB molecule is calculated using an internal equation of state, which we develop here, and the temperatures of the external and internal DoF are coupled using a fluctuation-dissipation relation. The DPDE force expression requires specification of the input parameter σ that determines the rate at which energy is exchanged between external and internal DoF. We adjusted σ based on the predictions for relaxation processes obtained from MD simulations. The parameterized DPDE model was employed in large-scale simulations of shock compression of TATB. We show that the rate of energy exchange governed by σ can significantly influence the transient behavior of the system behind the shock
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.
Directory of Open Access Journals (Sweden)
José Maria Pires
2012-01-01
Full Text Available A 1µs Molecular Dynamic simulation was performed with a realistic model system of Sodium Dodecyl Sulfate (SDS micelles in aqueous solution, comprising of 360 DS-, 360 Na+ and 90000 water particles. After 300 ns three different micellar shapes and sizes 41, 68 and 95 monomers, were observed. The process led to stabilization in the total number of SDS clusters and an increase in the micellar radius to 2.23 nm, in agreement with experimental results. An important conclusion, is be aware that simulations employed in one aggregate, should be considered as a constraint. Size and shape distribution must be analyzed.
International Nuclear Information System (INIS)
Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo
2006-01-01
Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases
International Nuclear Information System (INIS)
Lan Liangyun; Qiu Chunlin; Zhao Dewen; Gao Xiuhua; Du Linxiu
2011-01-01
Highlights: → Total toughness can be separated into crack initiation energy and crack propagation energy. → Small effective grain size of lath martensite can improve the crack propagation energy. → MA constituent is mainly responsible for the low toughness of coarse bainite specimens. → High angle packet boundary in coarser bainite has few contributions to improving crack propagation energy. - Abstract: The correlation of microstructural characteristics and toughness of the simulated coarse grained heat affected zone (CGHAZ) of low carbon bainitic steel was investigated in this study. The toughness of simulated specimens was examined by using an instrumented Charpy impact tester after the simulation welding test was conducted with different cooling times. Microstructure observation and crystallographic feature analysis were conducted by means of optical microscope and scanning electron microscope equipped with electron back scattered diffraction (EBSD) system, respectively. The main microstructure of simulated specimen changes from lath martensite to coarse bainite with the increase in cooling time. The deterioration of its toughness occurs when the cooling time ranges from 10 to 50 s compared with base metal toughness, and the toughness becomes even worse when the cooling time increases to 90 s or more. The MA (martensite-austenite) constituent is primary responsible for the low toughness of simulated CGHAZ with high values of cooling time because the large MA constituent reduces the crack initiation energy significantly. For crack propagation energy, the small effective grain size of lath martensite plays an important role in improving the crack propagation energy. By contrast, high misorientation packet boundary in coarse bainite seems to have few contributions to the improvement of the toughness because cleavage fracture micromechanism of coarse bainite is mainly controlled by crack initiation.
Energy Technology Data Exchange (ETDEWEB)
Lan Liangyun, E-mail: lly.liangyun@gmail.com [State Key Laboratory of Rolling Technology and Automation, Northeastern University, Shenyang 110819 (China); Qiu Chunlin; Zhao Dewen; Gao Xiuhua; Du Linxiu [State Key Laboratory of Rolling Technology and Automation, Northeastern University, Shenyang 110819 (China)
2011-11-25
Highlights: {yields} Total toughness can be separated into crack initiation energy and crack propagation energy. {yields} Small effective grain size of lath martensite can improve the crack propagation energy. {yields} MA constituent is mainly responsible for the low toughness of coarse bainite specimens. {yields} High angle packet boundary in coarser bainite has few contributions to improving crack propagation energy. - Abstract: The correlation of microstructural characteristics and toughness of the simulated coarse grained heat affected zone (CGHAZ) of low carbon bainitic steel was investigated in this study. The toughness of simulated specimens was examined by using an instrumented Charpy impact tester after the simulation welding test was conducted with different cooling times. Microstructure observation and crystallographic feature analysis were conducted by means of optical microscope and scanning electron microscope equipped with electron back scattered diffraction (EBSD) system, respectively. The main microstructure of simulated specimen changes from lath martensite to coarse bainite with the increase in cooling time. The deterioration of its toughness occurs when the cooling time ranges from 10 to 50 s compared with base metal toughness, and the toughness becomes even worse when the cooling time increases to 90 s or more. The MA (martensite-austenite) constituent is primary responsible for the low toughness of simulated CGHAZ with high values of cooling time because the large MA constituent reduces the crack initiation energy significantly. For crack propagation energy, the small effective grain size of lath martensite plays an important role in improving the crack propagation energy. By contrast, high misorientation packet boundary in coarse bainite seems to have few contributions to the improvement of the toughness because cleavage fracture micromechanism of coarse bainite is mainly controlled by crack initiation.
Mohamad Yusoff, Mohamad Ariff; Abdul Hamid, Azzmer Azzar; Mohammad Bunori, Noraslinda; Abd Halim, Khairul Bariyyah
2018-06-01
Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP 2 ) and phosphatidylserine (PS) via its cationic patch. The hydrophobic loop at the C-terminal domain has also been shown to be important in the interaction between the VP40 and the membrane. However, details of the molecular mechanisms underpinning their interactions are not fully understood. This study aimed at investigating the effects of mutation in the cationic patch and hydrophobic loop on the interaction between the VP40 monomer and the plasma membrane using coarse-grained molecular dynamics simulation (CGMD). Our simulations revealed that the interaction between VP40 and the plasma membrane is mediated by the cationic patch residues. This led to the clustering of PIP 2 around the protein in the inner leaflet as a result of interactions between some cationic residues including R52, K127, K221, K224, K225, K256, K270, K274, K275 and K279 and PIP 2 lipids via electrostatic interactions. Mutation of the cationic patch or hydrophobic loop amino acids caused the protein to bind at the inner leaflet of the plasma membrane in a different orientation, where no significant clustering of PIP 2 was observed around the mutated protein. This study provides basic understanding of the interaction of the VP40 monomer and its mutants with the plasma membrane. Copyright © 2018 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Peter Mirau
2015-09-01
Full Text Available Despite enormous efforts, our understanding the structure and dynamics of α-synuclein (ASN, a disordered protein (that plays a key role in neurodegenerative disease is far from complete. In order to better understand sequence-structure-property relationships in α-SYNUCLEIN we have developed a coarse-grained model using knowledge-based residue-residue interactions and used it to study the structure of free ASN as a function of temperature (T with a large-scale Monte Carlo simulation. Snapshots of the simulation and contour contact maps show changes in structure formation due to self-assembly as a function of temperature. Variations in the residue mobility profiles reveal clear distinction among three segments along the protein sequence. The N-terminal (1-60 and C-terminal (96-140 regions contain the least mobile residues, which are separated by the higher mobility non-amyloid component (NAC (61-95. Our analysis of the intra-protein contact profile shows a higher frequency of residue aggregation (clumping in the N-terminal region relative to that in the C-terminal region, with little or no aggregation in the NAC region. The radius of gyration (Rg of ASN decays monotonically with decreasing the temperature, consistent with the finding of Allison et al. (JACS, 2009. Our analysis of the structure function provides an insight into the mass (N distribution of ASN, and the dimensionality (D of the structure as a function of temperature. We find that the globular structure with D ≈ 3 at low T, a random coil, D ≈ 2 at high T and in between (2 ≤ D ≤ 3 at the intermediate temperatures. The magnitudes of D are in agreement with experimental estimates (J. Biological Chem 2002.
Energy Technology Data Exchange (ETDEWEB)
Yu, Hang; Ma, Wen [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Han, Wei [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Schulten, Klaus, E-mail: kschulte@ks.uiuc.edu [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)
2015-12-28
Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.
Lichtner, D.; Christensen, K. T.; Best, J.; Blois, G.
2014-12-01
Exchange of fluid in the near-subsurface of a streambed is influenced by turbulence in the free flow, as well as by bed topography and permeability. Macro-roughness elements such as bedforms are known to produce pressure gradients that drive fluid into the streambed on their stoss sides and out of the bed on their lee sides. To study the modification of the near-bed flow field by self-forming permeable bedforms, laboratory experiments were conducted in a 5 mm wide flume filled with 1.3 mm glass beads. The narrow width of the flume permitted detailed examination of the fluid exiting the bed immediately downstream of a bedform. Dense 2-D velocity field measurements were gathered using particle image velocimetry (PIV). In up to 8% of instantaneous PIV realizations, the flow at the near-bed presented a component perpendicular to the streambed, indicating flow across the interface. At the downstream side of the bedform, such flow disrupted the mean recirculation pattern that is typically observed in finer sediment beds. It is hypothesized that the coarse grain size and the resulting high bed permeability promote such near-surface jet events. A qualitative analysis of raw image frames indicated that an in-place jostling of sediment is associated with these jets thus suggesting that subsurface flow may be characterized by impulsive events. These observations are relevant to hyporheic exchange rates in coarse sediments and can have strong morphodynamic implications as they can explain the lack of ripples and characteristics of dunes in high permeability gravels. Overall, further study of the flow structure over highly permeable streambeds is needed to understand subsurface exchange and bedform initiation.
Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids.
Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek
2017-10-25
We study the mechanical response of cellulose and β-amyloid microfibrils to three types of deformation: tensile, indentational, and shear. The cellulose microfibrils correspond to the allomorphs Iα or Iβ whereas the β-amyloid microfibrils correspond to the polymorphs of either two- or three-fold symmetry. This response can be characterized by three elastic moduli, namely, Y L , Y T , and S. We use a structure-based coarse-grained model to analyze the deformations in a unified manner. We find that each of the moduli is almost the same for the two allomorphs of cellulose but Y L is about 20 times larger than Y T (140 GPa vs. 7 GPa), indicating the existence of significant anisotropy. For cellulose we note that the anisotropy results from the involvement of covalent bonds in stretching. For β-amyloid, the sense of anisotropy is opposite to that of cellulose. In the three-fold symmetry case, Y L is about half of Y T (3 vs. 7) whereas for two-fold symmetry the anisotropy is much larger (1.6 vs. 21 GPa). The S modulus is derived to be 1.2 GPa for three-fold symmetry and one half of it for the other symmetry and 3.0 GPa for cellulose. The values of the moduli reflect deformations in the hydrogen-bond network. Unlike in our theoretical approach, no experiment can measure all three elastic moduli with the same apparatus. However, our theoretical results are consistent with various measured values: typical Y L for cellulose Iβ ranges from 133 to 155 GPa, Y T from 2 to 25 GPa, and S from 1.8 to 3.8 GPa. For β-amyloid, the experimental values of S and Y T are about 0.3 GPa and 3.3 GPa respectively, while the value of Y L has not been reported.
International Nuclear Information System (INIS)
You, Yang; Shang, Chengjia; Chen, Liang; Subramanian, Sundaresa
2013-01-01
Highlights: ► Area of reverted austenite is traced out by crystallographic information. ► Bainite and martensite regions were confirmed within it. ► The martensite region is considered as the blocky MA particles. ► Martensite region has high deformation to initiate fracture. ► More uniform transformation of the reverted austenite is good for toughness. -- Abstract: In present study the intercritically reheated coarse grained heat affected zone (ICCGHAZ) showing the worst impact toughness in the heat affected zone of multi-pass welding was simulated by Gleeble-1500, and its microstructure was investigated in detail by means of scanning electron microscope (SEM) and electron backscattering diffraction (EBSD). With the crystallographic information from EBSD scanning the area of a single reverted austenite grain which formed during the thermal cycles of second pass simulation was traced out. Within it two regions with different characteristic both in morphology and crystallography were found out, showing an un-uniform transformation of the reverted austenite. The region I is a bainitic region containing larger bainitic ferrite grains, while the region II is made up of several clusters containing tiny grains. Based on the crystallographic information each cluster was determined as martensite island thereby should be considered as blocky Martensite/Austenite constituent (M/A), which is hard phase and harmful for toughness. Analysis on the level of deformation shows that the region II is much higher deformed than the region I, indicating there is high stress concentration within the region II. The possible influence of the region I and the region II on fracture is discussed under the early proposed M/A’s fracture-initiating mechanisms. It suggests that the main cause of the toughness reduction is the un-uniform transformation of the reverted austenite, and the toughness performance of the ICCGHAZ could be improved if the transformation of the reverted
Hu, Mingyang; de Jong, Djurre H; Marrink, Siewert J; Deserno, Markus
2013-01-01
We calculate the Gaussian curvature modulus kappa of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We find the value kappa/kappa = -1.04 +/- 0.03 for the elastic ratio between the Gaussian and the mean curvature modulus and deduce kappa(m)/kappa(m) = -0.98 +/- 0.09 for the monolayer elastic ratio, where the latter is based on plausible assumptions for the distance z0 of the monolayer neutral surface from the bilayer midplane and the spontaneous lipid curvature K(0m). By also analyzing the lateral stress profile sigma0(z) of our system, two other lipid types and pertinent data from the literature, we show that determining K(0m) and kappa through the first and second moment of sigma0(z) gives rise to physically implausible values for these observables. This discrepancy, which we previously observed for a much simpler CG model, suggests that the moment conditions derived from simple continuum assumptions miss the effect of physically important correlations in the lipid bilayer.
Li, Zhen; Lee, Hee Sun; Darve, Eric; Karniadakis, George Em
2017-01-01
Memory effects are often introduced during coarse-graining of a complex dynamical system. In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system arises in the context of Mori-Zwanzig formalism. Upon a pairwise decomposition, GLE can be reformulated into its pairwise version, i.e., non-Markovian dissipative particle dynamics (DPD). GLE models the dynamics of a single coarse particle, while DPD considers the dynamics of many interacting CG particles, with both CG systems governed by non-Markovian interactions. We compare two different methods for the practical implementation of the non-Markovian interactions in GLE and DPD systems. More specifically, a direct evaluation of the non-Markovian (NM) terms is performed in LE-NM and DPD-NM models, which requires the storage of historical information that significantly increases computational complexity. Alternatively, we use a few auxiliary variables in LE-AUX and DPD-AUX models to replace the non-Markovian dynamics with a Markovian dynamics in a higher dimensional space, leading to a much reduced memory footprint and computational cost. In our numerical benchmarks, the GLE and non-Markovian DPD models are constructed from molecular dynamics (MD) simulations of star-polymer melts. Results show that a Markovian dynamics with auxiliary variables successfully generates equivalent non-Markovian dynamics consistent with the reference MD system, while maintaining a tractable computational cost. Also, transient subdiffusion of the star-polymers observed in the MD system can be reproduced by the coarse-grained models. The non-interacting particle models, LE-NM/AUX, are computationally much cheaper than the interacting particle models, DPD-NM/AUX. However, the pairwise models with momentum conservation are more appropriate for correctly reproducing the long-time hydrodynamics characterised by an algebraic decay in the velocity autocorrelation function.
International Nuclear Information System (INIS)
Litak, Grzegorz; Taccani, Rodolfo; Radu, Robert; Urbanowicz, Krzysztof; HoIyst, Janusz A.; Wendeker, MirosIaw; Giadrossi, Alessandro
2005-01-01
We report our results on non-periodic experimental time series of pressure in a single cylinder spark ignition engine. The experiments were performed for different levels of loading. We estimate the noise level in internal pressure calculating the coarse-grained entropy from variations of maximal pressures in successive cycles. The results show that the dynamics of the combustion is a non-linear multidimensional process mediated by noise. Our results show that so defined level of noise in internal pressure is not monotonous function of loading
Pandey, Ras; Kuang, Zhifeng; Farmer, Barry; Kim, Sang; Naik, Rajesh
2012-02-01
Recently, Kim et al. [1] have found that peptides P1: HSSYWYAFNNKT and P2: EPLQLKM bind selectively to graphene surfaces and edges respectively which are critical in modulating both the mechanical as well as electronic transport properties of graphene. Such distinctions in binding sites (edge versus surface) observed in electron micrographs were verified by computer simulation by an all-atomic model that captures the pi-pi bonding. We propose a hierarchical approach that involves input from the all-atom Molecular Dynamics (MD) study (with atomistic detail) into a coarse-grained Monte Carlo simulation to extend this study further to a larger scale. The binding energy of a free amino acid with the graphene sheet from all-atom simulation is used in the interaction parameter for the coarse-grained approach. Peptide chain executes its stochastic motion with the Metropolis algorithm. We investigate a number of local and global physical quantities and find that peptide P1 is likely to bind more strongly to graphene sheet than P2 and that it is anchored by three residues ^4Y^5W^6Y. [1] S.N. Kim et al J. Am. Chem. Soc. 133, 14480 (2011).
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LI Jing
2016-08-01
Full Text Available Coarse grain heat affected zone (HAZ of F460 steel was simulated by a Gleeble 3800 thermo-mechanical simulator. The microstructure, critical event of the HAZ formed at various heat inputs (E were characterized and determined by optical microscopy (OM and scanning electronic microscopy (SEM, and cleavage fracture stress σf was also calculated by ABAQUS software. Based on above systematic analysis, the intrinsic mechanism of ductile-brittle transition for F460 steel heat affected zones with different heat inputs were revealed. The results indicate that:with the improvement of heat input, the microstructures in sequence are a minority of lath martensite and massive fine lath bainite, more lath bainite with less granular bainite, more granular bainite with less lath bainite, bulky of granular bainite; and the maximum size of the original austenite grain and bainite packet becomes bigger with the improvement of heat input. The size of bainite packet is critical event of the cleavage fracture for coarse grain heat affected zone specimens with various heat inputs by comparing the relationships among residual crack length, original austenite grain size and bainite packet size. With the decreasing of the bainitic packet, the ductile to brittle transition temperature decreases. In addition, cleavage fracture stress σf is also calculated by ABAQUS software, σf gradually decreases with the increase of the heat input, which can explain the intrinsic mechanism of ductile to brittle transition temperature Tk with the change of the heat input.
Vimalan, G.; Muthupandi, V.; Ravichandran, G.
2018-05-01
A continuous cooling transformation diagram is constructed for simulated coarse grain heat affected zone (CGHAZ) of SA106 grade B carbon steel. Samples are heated to a peak temperature of 1200°C in the Gleeble thermo mechanical simulator and then cooled at different cooling rates varying from 0.1°C/s to 100°C/s. Microstructure of the specimens simulated at different cooling rates were characterised by optical microscopy and hardness was assessed by Vicker's hardness test and micro-hardness test. Transformation temperatures and the corresponding phase fields were identified from dilatometric curves and the same could be confirmed by correlating with the microstructures at room temperature. These data were used to construct the CCT diagram. Phase fields were found to have ferrite, pearlite, bainite and martensite or their combinations. With the help of this CCT diagram it is possible to predict the microstructure and hardness of coarse grain HAZ experiencing different cooling rates. The constructed CCT diagram becomes an important tool in evaluating the weldability of SA106 grade B carbon steel.
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Alireza Abdollahi
2014-12-01
Full Text Available In this study, ultrafine grained 2024 Al alloy based B4C particles reinforced composite was produced by mechanical milling and hot extrusion. Mechanical milling was used to synthesize the nanostructured Al2024 in attrition mill under argon atmosphere up to 50h. A similar process was used to produce Al2024-5%wt. B4C composite powder. To produce trimodal composites, milled powders were combined with coarse grained aluminum in 30 and 50 wt% and then were exposed to hot extrusion at 570°C. The microstructure of hot extruded samples were studied by optical microscope, Transmission electron microscope (TEM and scanning electron microscope (SEM equipped with EDS spectroscopy. The mechanical properties of samples were compared by using tensile, compression and hardness tests. The results showed that the strength, after 50 h milling and addition of 5wt% B4C, increased from 340 to 582 MPa and the hardness increased from 87 HBN to 173 HBN, but the elongation decreased from 14 to 0.5%. By adding the coarse-grained aluminum powder, the strength and hardness decreased slightly, but the increases in return. Ductility increase is the result of increase in dislocation movements and strength increase is the result of restriction in plastic deformation by nanostructured regions. Furthermore, the strength and hardness of trimodal composites were higher, but their ductility was lower.
Richter, Martin; Fingerhut, Benjamin P.
2017-06-01
The description of non-Markovian effects imposed by low frequency bath modes poses a persistent challenge for path integral based approaches like the iterative quasi-adiabatic propagator path integral (iQUAPI) method. We present a novel approximate method, termed mask assisted coarse graining of influence coefficients (MACGIC)-iQUAPI, that offers appealing computational savings due to substantial reduction of considered path segments for propagation. The method relies on an efficient path segment merging procedure via an intermediate coarse grained representation of Feynman-Vernon influence coefficients that exploits physical properties of system decoherence. The MACGIC-iQUAPI method allows us to access the regime of biological significant long-time bath memory on the order of hundred propagation time steps while retaining convergence to iQUAPI results. Numerical performance is demonstrated for a set of benchmark problems that cover bath assisted long range electron transfer, the transition from coherent to incoherent dynamics in a prototypical molecular dimer and excitation energy transfer in a 24-state model of the Fenna-Matthews-Olson trimer complex where in all cases excellent agreement with numerically exact reference data is obtained.
Vangaveti, S; Travesset, A
2014-12-28
We present here a method to separate the Stern and diffuse layer in general systems into two regions that can be analyzed separately. The Stern layer can be described in terms of Bjerrum pairing and the diffuse layer in terms of Poisson-Boltzmann theory (monovalent) or strong coupling theory plus a slowly decaying tail (divalent). We consider three anionic phospholipids: phosphatidyl serine, phosphatidic acid, and phosphatidylinositol(4,5)bisphosphate (PIP2), which we describe within a minimal coarse-grained model as a function of ionic concentration. The case of mixed lipid systems is also considered, which shows a high level of binding cooperativity as a function of PIP2 localization. Implications for existing experimental systems of lipid heterogeneities are also discussed.
International Nuclear Information System (INIS)
Zhang, Y.Q.; Zhang, H.Q.; Liu, W.M.; Hou, H.
2009-01-01
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, 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
Simonucci, S.; Strinati, G. C.
2014-02-01
We derive a nonlinear differential equation for the gap parameter of a superfluid Fermi system by performing a suitable coarse graining of the Bogoliubov-de Gennes (BdG) equations throughout the BCS-BEC crossover, with the aim of replacing the time-consuming solution of the original BdG equations by the simpler solution of this novel equation. We perform a favorable numerical test on the validity of this new equation over most of the temperature-coupling phase diagram, by an explicit comparison with the full solution of the original BdG equations for an isolated vortex. We also show that the new equation reduces both to the Ginzburg-Landau equation for Cooper pairs in weak coupling close to the critical temperature and to the Gross-Pitaevskii equation for composite bosons in strong coupling at low temperature.
Frusawa, Hiroshi
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 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.
International Nuclear Information System (INIS)
Frusawa, Hiroshi
2014-01-01
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 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 c and the jamming limit in the car parking problem.
Flinner, Nadine; Schleiff, Enrico
2015-01-01
Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo) or unsaturated lipids (liquid-disordered character, Ld) were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.
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Nadine Flinner
Full Text Available Membranes are central for cells as borders to the environment or intracellular organelle definition. They are composed of and harbor different molecules like various lipid species and sterols, and they are generally crowded with proteins. The membrane system is very dynamic and components show lateral, rotational and translational diffusion. The consequence of the latter is that phase separation can occur in membranes in vivo and in vitro. It was documented that molecular dynamics simulations of an idealized plasma membrane model result in formation of membrane areas where either saturated lipids and cholesterol (liquid-ordered character, Lo or unsaturated lipids (liquid-disordered character, Ld were enriched. Furthermore, current discussions favor the idea that proteins are sorted into the liquid-disordered phase of model membranes, but experimental support for the behavior of isolated proteins in native membranes is sparse. To gain insight into the protein behavior we built a model of the red blood cell membrane with integrated glycophorin A dimer. The sorting and the dynamics of the dimer were subsequently explored by coarse-grained molecular dynamics simulations. In addition, we inspected the impact of lipid head groups and the presence of cholesterol within the membrane on the dynamics of the dimer within the membrane. We observed that cholesterol is important for the formation of membrane areas with Lo and Ld character. Moreover, it is an important factor for the reproduction of the dynamic behavior of the protein found in its native environment. The protein dimer was exclusively sorted into the domain of Ld character in the model red blood cell plasma membrane. Therefore, we present structural information on the glycophorin A dimer distribution in the plasma membrane in the absence of other factors like e.g. lipid anchors in a coarse grain resolution.
Martini, William R.
1989-01-01
A FORTRAN computer code is described that could be used to design and optimize a free-displacer, free-piston Stirling engine similar to the RE-1000 engine made by Sunpower. The code contains options for specifying displacer and power piston motion or for allowing these motions to be calculated by a force balance. The engine load may be a dashpot, inertial compressor, hydraulic pump or linear alternator. Cycle analysis may be done by isothermal analysis or adiabatic analysis. Adiabatic analysis may be done using the Martini moving gas node analysis or the Rios second-order Runge-Kutta analysis. Flow loss and heat loss equations are included. Graphical display of engine motions and pressures and temperatures are included. Programming for optimizing up to 15 independent dimensions is included. Sample performance results are shown for both specified and unconstrained piston motions; these results are shown as generated by each of the two Martini analyses. Two sample optimization searches are shown using specified piston motion isothermal analysis. One is for three adjustable input and one is for four. Also, two optimization searches for calculated piston motion are presented for three and for four adjustable inputs. The effect of leakage is evaluated. Suggestions for further work are given.
Arai, Naoki; Furuta, Tadaomi; Sakurai, Minoru
2017-01-01
Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.
Romans, B.W.; Normark, W.R.; McGann, M.M.; Covault, J.A.; Graham, S.A.
2009-01-01
Utilizing accumulations of coarse-grained terrigenous sediment from deep-marine basins to evaluate the relative contributions of and history of controls on sediment flux through a source-to-sink system has been difficult as a result of limited knowledge of event timing. In this study, six new radiocarbon (14C) dates are integrated with five previously published dates that have been recalibrated from a 12.5-m-thick turbidite section from Ocean Drilling Program (ODP) Site 1015 in Santa Monica Basin, offshore California. This borehole is tied to high-resolution seismic-reflection profiles that cover an 1100 km2 area of the middle and lower Hueneme submarine fan and most of the basin plain. The resulting stratigraphic framework provides the highest temporal resolution for a thick-bedded Holocene turbidite succession to date, permitting an evaluation of source-to-sink controls at millennial (1000 yr) scales. The depositional history from 7 ka to present indicates that the recurrence interval for large turbidity-current events is relatively constant (300-360 yr), but the volume of sediment deposited on the fan and in the basin plain has increased by a factor of 2 over this period. Moreover, the amount of sand per event on the basin plain during the same interval has increased by a factor of 7. Maps of sediment distribution derived from correlation of seismic-reflection profiles indicate that this trend cannot be attributed exclusively to autogenic processes (e.g., progradation of depocenters). The observed variability in sediment accumulation rates is thus largely controlled by allogenic factors, including: (1) increased discharge of Santa Clara River as a result of increased magnitude and frequency of El Ni??o-Southern Oscillation (ENSO) events from ca. 2 ka to present, (2) an apparent change in routing of coarse-grained sediment within the staging area at ca. 3 ka (i.e., from direct river input to indirect, littoral cell input into Hueneme submarine canyon), and (3
Energy Technology Data Exchange (ETDEWEB)
Bond, Stephen D.
2014-01-01
The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.
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.
Weyman, Alexander; Bier, Markus; Holm, Christian; Smiatek, Jens
2018-05-01
We study generic properties of poly(ionic liquid)s (PILs) via coarse-grained molecular dynamics simulations in bulk solution and under confinement. The influence of different side chain lengths on the spatial properties of the PIL systems and on the ionic transport mechanism is investigated in detail. Our results reveal the formation of apolar and polar nanodomains with increasing side chain length in good agreement with previous results for molecular ionic liquids. The ion transport numbers are unaffected by the occurrence of these domains, and the corresponding values highlight the potential role of PILs as single-ion conductors in electrochemical devices. In contrast to bulk behavior, a pronounced formation of ion conductivity channels in confined systems is initiated in close vicinity to the boundaries. We observe higher ion conductivities in these channels for increasing PIL side chain lengths in comparison with bulk values and provide an explanation for this effect. The appearance of these domains points to an improved application of PILs in modern polymer electrolyte batteries.
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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.
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Tekpinar Mustafa
2009-07-01
Full Text Available Abstract Backgrounds It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means. Results We have performed a large-scale evaluation of the predictions of dynamically important residues by a variety of computational protocols including three based on the perturbation and correlation analysis of a coarse-grained elastic model. This study is performed for two lists of test cases with >500 pairs of protein structures. The dynamically important residues predicted by the perturbation and correlation analysis are found to be strongly or moderately conserved in >67% of test cases. They form a sparse network of residues which are clustered both in 3D space and along protein sequence. Their overall conservation is attributed to their dynamic role rather than ligand binding or high network connectivity. Conclusion By modeling how the protein structural fluctuations respond to residue-position-specific perturbations, our highly efficient perturbation and correlation analysis can be used to dissect the functional conformational changes in various proteins with a residue level of detail. The predictions of dynamically important residues serve as promising targets for mutational and functional studies.
Cutolo, Pasquale; Basdevant, Nathalie; Bernadat, Guillaume; Bachelerie, Françoise; Ha-Duong, Tâp
2017-02-01
Despite the recent resolutions of the crystal structure of the chemokine receptor CXCR4 in complex with small antagonists or viral chemokine, a description at the molecular level of the interactions between the full-length CXCR4 and its endogenous ligand, the chemokine CXCL12, in relationship with the receptor recognition and activation, is not yet completely elucidated. Moreover, since CXCR4 is able to form dimers, the question of whether the CXCR4-CXCL12 complex has a 1:1 or 2:1 preferential stoichiometry is still an open question. We present here results of coarse-grained protein-protein docking and molecular dynamics simulations of CXCL12 in association with CXCR4 in monomeric and dimeric states. Our proposed models for the 1:1 and 2:1 CXCR4-CXCL12 quaternary structures are consistent with recognition and activation motifs of both partners provided by the available site-directed mutagenesis data. Notably, we observed that in the 2:1 complex, the chemokine N-terminus makes more steady contacts with the receptor residues critical for binding and activation than in the 1:1 structure, suggesting that the 2:1 stoichiometry would favor the receptor signaling activity with respect to the 1:1 association.
International Nuclear Information System (INIS)
Zhu, Zhixiong; Kuzmikova, Lenka; Li, Huijun; Barbaro, Frank
2014-01-01
This study investigated the influence of the inter-critical reheating temperature on the microstructure and mechanical properties of a coarse grained heat affected zone (CGHAZ) in an API 5L grade X70 pipeline steel seam weld. A Gleeble 3500 thermo-mechanical simulator was employed to duplicate particular weld thermal cycles in order to accurately assess specific regions of the weld HAZ. Detailed microstructural analysis, including investigation of the martensite–austenite (M–A) constituent, was performed using optical microscope (OM), scanning electron microscope (SEM) and selective etching techniques. It is shown that the fracture toughness of the CGHAZ is significantly reduced following exposure to a subsequent inter-critical thermal cycle. Fracture toughness gradually improves as the inter-critical temperature is increased, but does not return to the value of the original CGHAZ due to the presence of isolated large M–A particles and coarse microstructure. Significance of M–A particles to the HAZ fracture toughness is first related to the location of particles along prior austenite grain boundaries, followed by the size of individual M–A particles
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Miriam Fritsche
Full Text Available Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential.We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014, combination of segmental globules and elongated chains (T* = 0.016,0.017, predominantly elongated chains (T* = 0.019,0.020, as well as universal SAW conformations at high normalized temperature (T* ≥ 0.023. The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T(c* = 0.019 where a crossover occurs from a positive (stretching at T* ≤ T(c* to negative (contraction at T* ≥ T(c* thermal response on increasing T*.
Multiaxial creep of fine grained 0.5Cr-0.5Mo-0.25V and coarse grained 1Cr-0.5Mo steels
International Nuclear Information System (INIS)
Browne, R.J.; Flewitt, P.E.J.; Lonsdale, D.
1991-01-01
To explore the multiaxial creep response of materials used for electrical power generating plant, two steels, a fine grained 0.5Cr-0.5Mo-0.25V steel in a normalised and tempered condition with high creep ductility and a coarse grained 1Cr-0.5Mo steel in a quenched and tempered condition with low uniaxial creep ductility, have been selected. A range of multiaxial stress testing techniques which span the stress states that would allow identification of any technique dependent variables has been used. The deformation and failure of the normalised and tempered 0.5Cr-0.5Mo-0.25V steel for a range of multiaxial test techniques and, therefore, stress states may be described by an equivalent stress criterion. The results from the multiaxial tests carried out on the fully bainitic 1Cr-0.5Mo steel show that the multiaxial stress rupture criterion (MSRC) varies with stress state; at high triaxiality (notch), it is controlled by the maximum principal stress, whereas at low triaxiality (shear) it is dependent on both maximum principal stress and equivalent stress. Furthermore, a simple description of stress state based on maximum principal and equivalent stress does not define this uniquely, since the MSRC derived from uniaxial and torsion testing does not describe the failure of notch, tube, or double shear tests. (author)
Deformation Behavior of a Coarse-Grained Mg-8Al-1.5Ca-0.2Sr Magnesium Alloy at Elevated Temperatures
Lou, Yan; Liu, Xiao
2018-02-01
The compression tests were carried out on a coarse-grained Mg-8Al-1.5Ca-0.2Sr magnesium alloy samples at temperatures from 300 to 450 °C and strain rates from 0.001 to 10 s-1. The flow stress curves were analyzed using the double-differentiation method, and double minima were detected on the flow curves. The first set of minima is shown to identify the critical strain for twinning, while the second set indicates the critical strain for the initiation of dynamic recrystallization (DRX). Twin variant selection was numerically identified by comprehensive analysis of the Schmid factors for different deformation modes and the accommodation strains imposed on neighboring grains. It was found that twinning is initiated before DRX. Dynamic recrystallization volume increases with strain rate at a given deformation temperature. At high strain rate, various twin variants are activated to accommodate deformation, leading to the formation of twin intersections and high DRX volume. Fully dynamic recrystallized structure can be obtained at both high and low strain rates due to the high mobility of the grain and twin boundaries at the temperature of 400 °C.
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.
Cleaves, E.T.
1993-01-01
The possible impact of periglacial climates on the rate of chemical weathering of a coarse-grained plagioclase-muscovite-quartz schist has been determined for a small watershed near Baltimore, Maryland. The isovolumetric chemical weathering model formulated from the geochemical mass balance study of the watershed shows that the weathering front advances at a velocity of 9.1 m/m.y., if the modern environmental parameters remain the same back through time. However, recent surficial geological mapping demonstrates that periglacial climates have impacted the area. Such an impact significantly affects two key chemical weathering parameters, the concentration of CO2 in the soil and groundwater moving past the weathering front. Depending upon the assumptions used in the model, the rate of saprolitization varies from 2.2 to 5.3 m/m.y. The possible impact of periglacial processes suggested by the chemical weathering rates indicates a need to reconsider theories of landscape evolution as they apply to the northern Piedmont Province of the mid-Atlantic states. I suggest that from the Late Miocene to the present that the major rivers have become incised in their present locations; this incision has enhanced groundwater circulation and chemical weathering such that crystalline rocks beneath interfluvial areas remain mantled by saprolite; and the saprolite mantle has been partially stripped as periglacial conditions alternate with humid-temperate conditions. ?? 1993.
Coarse Grained Exponential Variational Autoencoders
Sun, Ke; Zhang, Xiangliang
2017-01-01
Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually
Curvature function and coarse graining
International Nuclear Information System (INIS)
Diaz-Marin, Homero; Zapata, Jose A.
2010-01-01
A classic theorem in the theory of connections on principal fiber bundles states that the evaluation of all holonomy functions gives enough information to characterize the bundle structure (among those sharing the same structure group and base manifold) and the connection up to a bundle equivalence map. This result and other important properties of holonomy functions have encouraged their use as the primary ingredient for the construction of families of quantum gauge theories. However, in these applications often the set of holonomy functions used is a discrete proper subset of the set of holonomy functions needed for the characterization theorem to hold. We show that the evaluation of a discrete set of holonomy functions does not characterize the bundle and does not constrain the connection modulo gauge appropriately. We exhibit a discrete set of functions of the connection and prove that in the abelian case their evaluation characterizes the bundle structure (up to equivalence), and constrains the connection modulo gauge up to ''local details'' ignored when working at a given scale. The main ingredient is the Lie algebra valued curvature function F S (A) defined below. It covers the holonomy function in the sense that expF S (A)=Hol(l=∂S,A).
Coarse Grained Exponential Variational Autoencoders
Sun, Ke
2017-02-25
Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is usually much more sophisticated. To break this limitation and apply arbitrary parametric distribution during inference, this paper derives a \\\\emph{semi-continuous} latent representation, which approximates a continuous density up to a prescribed precision, and is much easier to analyze than its continuous counterpart because it is fundamentally discrete. We showcase the proposition by applying polynomial exponential family distributions as the posterior, which are universal probability density function generators. Our experimental results show consistent improvements over commonly used VAE models.
Directory of Open Access Journals (Sweden)
Yanping Fan
Full Text Available In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs. The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+, divalent (Mg(2+ or trivalent (Co(NH(3(6 (3+ cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+, to partial aggregation with Mg(2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.
Directory of Open Access Journals (Sweden)
Vincent Frappier
2014-04-01
Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
Pandey, R. B.; Farmer, B. L.
2014-11-01
Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ˜ 3) at low temperature to a ramified fibrous network (D ˜ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ˜ 1.6) of fibrous Glu- and Thr-chain configurations.
Energy Technology Data Exchange (ETDEWEB)
Lee, Kyongwoon [Corporate R& D Institute, Doosan Heavy Industries & Construction,Gwigok-dong, Gyeongsangnam-do Seongsan-gu, Changwon-si 642-792 (Korea, Republic of); Lee, Seonghyeong; Na, Hyesung [School of Materials Science and Engineering, Pusan National University, San 30 Jangjeon-dong, Geumjeong-gu, Busan 609-735 (Korea, Republic of); Kang, Chungyun, E-mail: kangcy@pusan.ac.kr [School of Materials Science and Engineering, Pusan National University, San 30 Jangjeon-dong, Geumjeong-gu, Busan 609-735 (Korea, Republic of)
2016-11-15
Microstructural characteristics of the CGHAZ (coarse grained heat affected zone) made of the 2.25Cr-1Mo-V-Ti material for the thermal power plant boiler tube were discussed using the technique of tint etching. To conduct the micro structural characterization, the sample on which CGHAZ was produced by using a high temperature thermal cycle simulator, Gleeble 3500 equipment was used for comparative analyses using the existing Nital etching (ASTM E407-74) and the alkaline etching (ASTM E40785). The latter was used to observe a specific phase. For the microstructure on which the alkaline etching was experimented, the shape of a black strip (Ghost microstructure) in a few microns was observed, which was not observed from the Nital etching. It was found from the phase identifications based EPMA, EBSD and TEM experiments that the image of the black strip in a few microns represented the alpha phase in which C, Cr and Mo became segregated. In addition, it was verified that austenite and M{sub 23}C{sub 6} phase were present around the segregated zone. Based on such results, the mechanism by which the image of the black strip in a few microns was formed at the CGHAZ. In this study, we have investigated the mechanism of the appeared black strip in the CGHAZ. - Highlights: •Ghost microstructure was observed which was not observed from the nital etching. •Ghost microstructure has high concentrations of carbon and molybdenum than matrix. •Schematic illustration proposed of why Ghost microstructure was generated. •Ghost microstructure caused by partial dissolution of M{sub 23}C{sub 6} precipitation.
Tadmor, Arbel
2009-03-01
In this work a biophysical model of Escherichia coli is presented that predicts growth rate and an effective cellular composition from an effective, coarse-grained representation of its genome. We assume that E. coli is in a state of balanced exponential steady-state growth, growing in a temporally and spatially constant environment, rich in resources. We apply this model to a series of past measurements, where the growth rate and rRNA-to-protein ratio have been measured for seven E. coli strains with an rRNA operon copy number ranging from one to seven (the wild-type copy number). These experiments show that growth rate markedly decreases for strains with fewer than six copies. Using the model, we were able to reproduce these measurements. We show that the model that best fits these data suggests that the volume fraction of macromolecules inside E. coli is not fixed when the rRNA operon copy number is varied. Moreover, the model predicts that increasing the copy number beyond seven results in a cytoplasm densely packed with ribosomes and proteins. Assuming that under such overcrowded conditions prolonged diffusion times tend to weaken binding affinities, the model predicts that growth rate will not increase substantially beyond the wild-type growth rate, as indicated by other experiments. Our model therefore suggests that changing the rRNA operon copy number of wild-type E. coli cells growing in a constant rich environment does not substantially increase their growth rate. Other observations regarding strains with an altered rRNA operon copy number, such as nucleoid compaction and the rRNA operon feedback response, appear to be qualitatively consistent with this model. In addition, we discuss possible design principles suggested by the model and propose further experiments to test its validity.
Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H
2014-11-10
cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Directory of Open Access Journals (Sweden)
R. B. Pandey
2015-09-01
Full Text Available The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues with different numbers of protein chains, Nc = 1,5,10, and 15 (concentration 0.004 – 0.063 is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1 is ultra-slow (quasi-static at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a systematic transition from a globular structure (at low T to a random coil (high T conformation when the proteins are isolated. The crossover from globular to random coil becomes sharper upon increasing the protein concentration (i.e. with Nc = 5,10, with larger Rg at higher temperatures and concentration; Rg becomes smaller on adding more protein chains (e.g. Nc = 15 a non-monotonic response to protein concentration. Analysis of the structure factor (S(q provides an estimate of the effective dimension (D ≥ 3, globular conformation at low temperature, and D ∼ 1.7, random coil, at high temperatures of the isolated protein. With many interacting proteins, the morphology of the self-assembly varies with scale, i.e. at the low temperature (T = 0.015, D ∼ 2.9 on the scale comparable to the radius of gyration of the protein, and D ∼ 2.3 at the large scale over the entire sample. The global network of fibrils appears at high temperature (T = 0.021 with D ∼ 1.7 (i.e. a random coil morphology at large scale involving tenuous distribution of micro-globules (at small scales.
Condon, Joshua E; Jayaraman, Arthi
2017-10-04
Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.
2017-08-10
simulation program27 (version c41b1) was applied using the utilities and programming libraries of the Multiscale Modeling Tools for Structural...compactness of the generated conformations. As a noted benchmark , the prefolded peptide conformation shows a Rg ~ 10 Å in the multimeric complex. A
Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
Zavadlav, J.; Podgornik, R.; Melo, M.n.; Marrink, S.j.; Praprotnik, M.
2016-01-01
We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR- TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell
Energy Technology Data Exchange (ETDEWEB)
Challa, V.S.A. [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Misra, R.D.K., E-mail: dmisra2@utep.edu [Laboratory for Excellence in Advanced Steel Research, Department of Metallurgical, Materials Engineering, and Biomedical Engineering, University of Texas at El Paso, El Paso, TX 79968 (United States); Somani, M.C. [Center for Advanced Steels Research, The University of Oulu, P.O. Box 4200, 90014 Oulu (Finland); Wang, Z.D. [State Key Laboratory for Rolling and Automation, Northeastern University, 3-11 Wenhua Road, Shenyang 110819 (China)
2016-04-20
Nanograined/ultrafine-grained (NG/UFG) materials characterized by high strength-high ductility combination are excellent vehicles to obtain an unambiguous understanding of deformation mechanisms vis-à-vis their coarse-grained counterparts. In this context, the innovative concept of phase reversion-induced NG/UFG structure enabled achieving high strength besides comparable ductility, for instance, in metastable austenitic stainless steels. In the phase reversion process, severe deformation of austenite at room temperature (typically ~60–80%) transforms face-centered cubic austenite (γ) to body centered cubic martensite (α′). Upon annealing, martensite reverts to austenite leading to extensive grain refinement. The objective of the present study to fundamentally understand the deformation mechanisms in NG/UFG structure in relation to that of the coarse-grained (CG) structure was accomplished by combining depth-sensing nanoscale experiments on an Fe-16Cr-10Ni model austenitic alloy conducted at different strain rates, followed by the study of structural evolution in the deformed zone using transmission electron microscopy (TEM). In the high strength NG/UFG steel (YS~585 MPa), stacking faults and nanotwins contributed to the enhanced ductility (El~35%), while in the case of low strength (YS~260 MPa) coarse-grained (CG) counterpart, ductility was also high (El~40%), but chiefly due to strain-induced martensite, which points to a clear case of grain size effect (and the corresponding level of strength). The distinct change in the deformation mechanism from stacking faults and twinning-induced plasticity (TWIP) in the NG structure to transformation-induced plasticity (TRIP) in the CG structure is elucidated in terms of austenite stability-strain energy relationship. The insights on the relationship between grain structure (and strength) and deformation mechanisms are envisaged to be important in providing a new direction for the futuristic design of high strength
MARTINI: An event generator for relativistic heavy-ion collisions
International Nuclear Information System (INIS)
Schenke, Bjoern; Gale, Charles; Jeon, Sangyong
2009-01-01
We introduce the modular algorithm for relativistic treatment of heavy ion interactions (MARTINI), a comprehensive event generator for the hard and penetrating probes in high-energy nucleus-nucleus collisions. Its main components are a time-evolution model for the soft background, PYTHIA 8.1, and the McGill-Arnold, Moore, and Yaffe (AMY) parton-evolution scheme, including radiative as well as elastic processes. This allows us to generate full event configurations in the high p T region that take into account thermal quantum chromodynamic (QCD) and quantum electrodynamic (QED) effects as well as effects of the evolving medium. We present results for the neutral pion nuclear modification factor in Au+Au collisions at the BNL Relativistic Heavy Ion Collider as a function of p T for different centralities and also as a function of the angle with respect to the reaction plane for noncentral collisions. Furthermore, we study the production of high-transverse-momentum photons, incorporating a complete set of photon-production channels.
Czech Academy of Sciences Publication Activity Database
Stadlbauer, Petr; Mazzanti, L.; Cragnolini, T.; Wales, D.J.; Derreumaux, P.; Pasquali, C.; Sponer, Jiri
2016-01-01
Roč. 12, č. 12 (2016), s. 6077-6097 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GA16-13721S Institutional support: RVO:68081707 Keywords : particle mesh ewald * amber force-field * free-energy profiles * binding dna aptamer Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016
Lang, Jörg; Brandes, Christian; Winsemann, Jutta
2017-03-01
Erosion and deposition by supercritical density flows can strongly impact the facies distribution and architecture of submarine fans. Field examples from coarse-grained channel-levée complexes from the Sandino Forearc Basin (southern Central America) show that cyclic-step and antidune deposits represent common sedimentary facies of these depositional systems and relate to the different stages of avulsion, bypass, levée construction and channel backfilling. During channel avulsion, large-scale scour-fill complexes (18 to 29 m deep, 18 to 25 m wide, 60 to > 120 m long) were incised by supercritical density flows. The multi-storey infill of the large-scale scour-fill complexes comprises amalgamated massive, normally coarse-tail graded or widely spaced subhorizontally stratified conglomerates and pebbly sandstones, interpreted as deposits of the hydraulic-jump zone of cyclic steps. The large-scale scour-fill complexes can be distinguished from small-scale channel fills based on the preservation of a steep upper margin and a coarse-grained infill comprising mainly amalgamated hydraulic-jump zone deposits. Channel fills include repeated successions deposited by cyclic steps with superimposed antidunes. The deposits of the hydraulic-jump zone of cyclic steps comprise regularly spaced scours (0.2 to 2.6 m deep, 0.8 to 23 m long) infilled by intraclast-rich conglomerates or pebbly sandstones, displaying normal coarse-tail grading or backsets. These deposits are laterally and vertically associated with subhorizontally stratified, low-angle cross-stratified or sinusoidally stratified sandstones and pebbly sandstones, which were deposited by antidunes on the stoss side of the cyclic steps during flow re-acceleration. The field examples indicate that so-called spaced stratified deposits may commonly represent antidune deposits with varying stratification styles controlled by the aggradation rate, grain-size distribution and amalgamation. The deposits of small-scale cyclic
De leyendas y pinturas áureas: Jacobo de Vorágine y Simone Martini
Directory of Open Access Journals (Sweden)
Ricardo Isidro PIÑERO MORAL
2009-08-01
Full Text Available RESUMEN: Este artículo investiga la conexión existente entre la literatura artística y el arte plástico de la Edad Media mediante el análisis de la relación entre Jacobo de Vorágine, un narrador de leyendas, y Simone Martini, un pintor de historias. Así, el objetivo principal es mostrar que, en ocasiones, narrar leyendas no es algo tan diferente del hecho de pintarlas. De hecho, en el contexto examinado en este artículo, escribir y pintar se presentan como actos imbricados en los que el hombre se muestra a sí mismo narrando historias que pretenden dar razón de este mundo, pero que terminan yendo más allá de élABSTRACT: This article delves into the connection between artistic literature and artistic production in the Middle Ages through the analysis of the links between Jacobo de Vorágine, a tale spinner, and Simore Martini, a painter of stories. The main objective is to illustrate how sometimes to narrate stories is not that different from painting them. In fact, in the context of the article, to write and to paint are presented as intimately related. Man reasons out the world through stories but those stories go well beyond man himself.
Nonequilibrium forces between atoms and dielectrics mediated by a quantum field
International Nuclear Information System (INIS)
Behunin, Ryan O.; Hu, Bei-Lok
2011-01-01
In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables--the medium, the quantum field, and the atom's internal degrees of freedom, in that order--to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom's internal degrees of freedom results in an equation of motion for the atom's center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom's motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.
How a hospital must face a massive emergency: the case of Martini Hospital, Turin
Directory of Open Access Journals (Sweden)
Antonio Morra
2008-09-01
Full Text Available The terms “disaster” or “surge capability”, referred to hospitals, are often used to define a massive casualty admission. This may be a misleading concept, because emergency may as well arise from inside hospitals, and the last years high figures related to fires in the about 2,000 italian hospitals should suggest a different point of view. In this article the authors describe their experience in hospital preparedness at Ospedale Martini in Turin. Hospital operators regularly attend basic (GOM and advanced (HDM© courses about disaster response and organization, and a specific course is dedicated to operators involved in internal safety (fire emergency. In this courses, computer simulations are widely used, associated with conventional didactic. If education is one of the two cornerstones of disaster preparedness at Ospedale Martini, well designed emergency plans and an effective disaster management are the other one. The Internal Emergency Plan (Fire and Evacuation is aimed to give a proper response to fires and other events arising from inside the hospital and potentially requiring its partial or total evacuation. The Massive Casualties Admission Emergency Plan increases the surge capability of the hospital allowing to take care of a great number of injured people, and at the same time avoiding a dramatic fall in the treatment quality. The “Hospital Disaster Management©” system, created by the authors, is an organizational scheme based on team work. Its aim is to “put order in chaos” when hospitals are facing a disaster. Properly trained physicians and nurses, assigned to key positions, act in this system as Hospital Disaster Managers: their tasks are to coordinate the teams, to manage critical resources and to use the emergency plans as powerful instruments.
Long-range force and moment calculations in multiresolution simulations of molecular systems
International Nuclear Information System (INIS)
Poursina, Mohammad; Anderson, Kurt S.
2012-01-01
Multiresolution simulations of molecular systems such as DNAs, RNAs, and proteins are implemented using models with different resolutions ranging from a fully atomistic model to coarse-grained molecules, or even to continuum level system descriptions. For such simulations, pairwise force calculation is a serious bottleneck which can impose a prohibitive amount of computational load on the simulation if not performed wisely. Herein, we approximate the resultant force due to long-range particle-body and body-body interactions applicable to multiresolution simulations. Since the resultant force does not necessarily act through the center of mass of the body, it creates a moment about the mass center. Although this potentially important torque is neglected in many coarse-grained models which only use particle dynamics to formulate the dynamics of the system, it should be calculated and used when coarse-grained simulations are performed in a multibody scheme. Herein, the approximation for this moment due to far-field particle-body and body-body interactions is also provided.
B-spline tight frame based force matching method
Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei
2018-06-01
In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.
Book review, Patologie articolari nel cane e nel gatto, Filippo Maria Martini
Directory of Open Access Journals (Sweden)
Manuel Graziani
2008-03-01
Full Text Available Con il cambiare dei tempi, sono cambiate anche le priorità nell’ambito sempre più vasto degli animali da compagnia. Se, infatti, fino allo scorso decennio chi si occupava di ortopedia veterinaria aveva a che fare esclusivamente con pazienti traumatizzati, ora l’ortopedia e la traumatologia veterinaria devono fare i conti sempre più spesso con le patologie articolari. I motivi di questa inversione di tendenza sono molti e di diverso genere, certamente i più influenti riguardano la diffusione di soggetti atleti che sviluppano specifiche patologie, l’allungamento della vita media che espone i pazienti a malattie articolari degenerative un tempo prerogativa dell’uomo e la presenza di razze canine particolarmente predisposte a tali patologie. A ciò si aggiunga l’esigenza crescente dei proprietari degli animali, di comprendere a fondo quali siano le migliori cure per i propri compagni. Per questi motivi lo specialista in Ortopedia degli animali domestici, Filippo Maria Martini, ha redatto Patologie articolari nel cane e nel gatto: un volume che non vuole essere un manuale sulle tecniche chirurgiche (nonostante al suo interno vengano comunque descritte, piuttosto un manuale pratico in grado da una parte di fornire gli strumenti necessari per comprendere, interpretare e diagnosticare le patologie articolari; dall’altra di dare le basi teoriche per impostare un protocollo terapeutico in modo corretto ed emettere una prognosi adeguata. Tutto ciò nella convinzione che un buon clinico non possa limitarsi ad eseguire una visita e ad impostare una terapia, ma debba necessariamente stilare un elenco di esami utili ai fini della definizione della diagnosi, discuterne con il proprietario e consigliare il più adeguato protocollo diagnostico e terapeutico.
Directory of Open Access Journals (Sweden)
Paolo Clini
2015-09-01
Full Text Available The subject of the military architecture was widely studied and analyzed by the architect Francesco di Giorgio Martini (1439-1501, who created important defensive works in the duchy of Montefeltro. A defensive line connects a series of medieval villages of the Marches: b Between the Martini’s fortifications, Cagli has still a fortified tower perfectly preserved and some traces of the fortress. The analysis conducted on them involves the information inferable by the essay, by historical surveys and the recent laser scanner survey. The aim of the research was to identify the generating geometry of the architecture: taking the precepts of Vitruvius, in the Renaissance period geometry was synonymous with proportion, order and symmetry. Two are subjects: the first one is the in-depth knowledge of the tower through the digital data obtained from the point cloud, the other one is the reconstruction of a global image of the complex tower-fortress.
Coarse-grained simulation of polymer-filler blends
Legters, Gregg; Kuppa, Vikram; Beaucage, Gregory; Univ of Dayton Collaboration; Univ of Cincinnati Collaboration
The practical use of polymers often relies on additives that improve the property of the mixture. Examples of such complex blends include tires, pigments, blowing agents and other reactive additives in thermoplastics, and recycled polymers. Such systems usually exhibit a complex partitioning of the components. Most prior work has either focused on fine-grained details such as molecular modeling of chains at interfaces, or on coarse, heuristic, trial-and-error approaches to compounding (eg: tire industry). Thus, there is a significant gap in our understanding of how complex hierarchical structure (across several decades in length) develops in these multicomponent systems. This research employs dissipative particle thermodynamics in conjunction with a pseudo-thermodynamic parameter derived from scattering experiments to represent polymer-filler interactions. DPD simulations will probe how filler dispersion and hierarchical morphology develops in these complex blends, and are validated against experimental (scattering) data. The outcome of our approach is a practical solution to compounding issues, based on a mutually validating experimental and simulation methodology. Support from the NSF (CMMI-1636036/1635865) is gratefully acknowledged.
Shark: Fast Data Analysis Using Coarse-grained Distributed Memory
2013-05-01
Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 7.1.1 Java Objects...often MySQL or Derby) with a namespace for tables, table metadata, and par- tition information. Table data is stored in an HDFS directory, while a...saving time and space for large data sets. This is achieved with support for custom SerDe (serialization/deserialization) java interface implementations
Coarse-grained elastodynamics of fast moving dislocations
International Nuclear Information System (INIS)
Xiong, Liming; Rigelesaiyin, Ji; Chen, Xiang; Xu, Shuozhi; McDowell, David L.; Chen, Youping
2016-01-01
The fundamental mechanism of dynamic plasticity in metallic materials subjected to shock loading remains unclear because it is difficult to obtain the precise information of individual fast moving dislocations in metals from the state-of-the-art experiments. In this work, the dynamics of sonic dislocations in anisotropic crystalline materials is explored through a concurrent atomistic-continuum modeling method. We make a first attempt to characterize the complexity of nonuniformly moving dislocations in anisotropic crystals from atomistic to microscale, including the energy intensities as well as the wavelengths of acoustic phonons emitted from sonic dislocations, and the velocity-dependent stress fluctuations around the core of nonuniformly moving dislocations. Instantaneous dislocation velocities and phonon drag effects on the dislocation motions are quantified and analyzed. Mach cones in a V-shaped pattern of the phonon wave-fronts are observed in the wake of the sonic dislocations. Analysis of simulation results based on a wavelet transform show that the faster a dislocation is moving, the longer the emitted phonon wavelength. The dislocation velocity drops dramatically with the occurrence of the interactions between dislocations and phonon waves reflected from the boundaries of specimens. The concurrent atomistic-continuum modeling framework is demonstrated to be the first multiscale method that explicitly treats the strong coupling between the long-range elastic fields away from the dislocation core, the highly nonlinear time-dependent stress field within the core, and the evolutions of the atomic-scale dislocation core structures. As such, it is shown that this method is capable in predicting elastodynamics of dislocations in the presence of inertia effects associated with sonic dislocations in micron-sized anisotropic crystalline materials from the atomic level, which is not directly accessible to the recent elastodynamic discrete dislocation model.
Coarse-grained description of cosmic structure from Szekeres models
International Nuclear Information System (INIS)
Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos
2016-01-01
We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ''pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10–20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research
7 CFR 457.113 - Coarse grains crop insurance provisions.
2010-01-01
..., including but not limited to protein and oil, will not be considered. Planted acreage—In addition to the..., Bosque, Johnson, Tarrant, Wise, Cooke Counties, Texas, and all Texas counties lying south and east..., Johnson, Tarrant, Wise, Cooke Counties, Texas, and all Texas counties lying south and east thereof to and...
Morphing methods to visualize coarse-grained protein dynamics.
Weiss, Dahlia R; Koehl, Patrice
2014-01-01
Morphing was initially developed as a cinematic effect, where one image is seamlessly transformed into another image. The technique was widely adopted by biologists to visualize the transition between protein conformational states, generating an interpolated pathway from an initial to a final protein structure. Geometric morphing seeks to create visually suggestive movies that illustrate structural changes between conformations but do not necessarily represent a biologically relevant pathway, while minimum energy path (MEP) interpolations aim at describing the true transition state between the crystal structure minima in the energy landscape.
Shear Strength of the Volcanic Coarse-Grained Soil
Gotoh, Keinosuke; Yamanaka, Minoru; Abdelhadi, Monther
1997-01-01
Japan is awarded with a total of about 144 volcanos distributed over the whole country from the south to the north. In Kyushu Island there are three main volcanos, namely Unzen, Sakurajima and Aso. The eruption of these volcanos has created the need to utilize these huge amounts of debris flow deposits as a construction material. In this paper, the physical and chemical properties of debris flow deposits of the Unzen and Sakurajima Volcanos are examined by a series of laboratory tests and the...
Vesicles and vesicle fusion: coarse-grained simulations
DEFF Research Database (Denmark)
Shillcock, Julian C.
2010-01-01
of vesicles that is crucial for this transport is their ability to fuse to target membranes and release their contents to the distal side. In industry, some personal care products contain vesicles to help transport reagents across the skin, and research on drug formulation shows that packaging active......Biological cells are highly dynamic, and continually move material around their own volume and between their interior and exterior. Much of this transport encapsulates the material inside phospholipid vesicles that shuttle to and fro, fusing with, and budding from, other membranes. A feature...
Coarse Grain Reconfigurable ASIC through Multiplexer Based Switches
2015-09-15
chip area (0.5 mm2), and from simulation their power consumption is negligible (0.002% from simulation, too small to measure in physical system...performing implementation that is also flexible. REFERENCES [1] I. Kuon and J. Rose, “ Measuring the gap between FPGAs and ASICs,” IEEE Trans...A 3GPP- LTE Example," Solid-State Circuits, IEEE Journal of , vol.47, no.3, pp.757,768, March 2012. [5] Agarwal, A.; Hassanieh, H.; Abari, O
Information-based physics, influence, and forces
International Nuclear Information System (INIS)
Walsh, James Lyons; Knuth, Kevin H.
2015-01-01
In recent works, Knuth and Bahreyni have demonstrated that the concepts of space and time are emergent in a coarse-grained model of direct particle-particle influence. In addition, Knuth demonstrated that observer-made inferences regarding the free particle, which is defined as a particle that influences others, but is not itself influenced, result in a situation identical to the Feynman checkerboard model of the Dirac equation. This suggests that the same theoretical framework that gives rise to an emergent spacetime is consistent with quantum mechanics. In this paper, we begin to explore the effect of influence on the emergent properties of a particle. This initial study suggests that when a particle is influenced, it is interpreted as accelerating in a manner consistent with special relativity implying that, at least in this situation, influence can be conceived of as a force
Rigorous force field optimization principles based on statistical distance minimization
Energy Technology Data Exchange (ETDEWEB)
Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)
2015-10-14
We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.
Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins
Dahlke, K.; Sing, C. E.
2018-02-01
Interactions between nucleoid associated proteins (NAPs) and DNA affect DNA polymer conformation, leading to phenomena such as concentration dependent force-extension behavior. These effects, in turn, also impact the local binding behavior of the protein, such as high forces causing proteins to unbind, or proteins binding favorably to locally bent DNA. We develop a coarse-grained NAP-DNA simulation model that incorporates both force- and concentration-dependent behaviors, in order to study the interplay between NAP binding and DNA conformation. This model system includes multi-state protein binding and unbinding, motivated by prior work, but is now dependent on the local structure of the DNA, which is related to external forces acting on the DNA strand. We observe the expected qualitative binding behavior, where more proteins are bound at lower forces than at higher forces. Our model also includes NAP-induced DNA bending, which affects DNA elasticity. We see semi-quantitative matching of our simulated force-extension behavior to the reported experimental data. By using a coarse-grained simulation, we are also able to look at non-equilibrium behaviors, such as dynamic extension of a DNA strand. We stretch a DNA strand at different rates and at different NAP concentrations to observe how the time scales of the system (such as pulling time and unbinding time) work in concert. When these time scales are similar, we observe measurable rate-dependent changes in the system, which include the number of proteins bound and the force required to extend the DNA molecule. This suggests that the relative time scales of different dynamic processes play an important role in the behavior of NAP-DNA systems.
Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force
Chun, Hyun-Myung; Durang, Xavier; Noh, Jae Dong
2018-03-01
We investigate the low mass limit of Langevin dynamics for a charged Brownian particle driven by a magnetic Lorentz force. In the low mass limit, velocity variables relaxing quickly are coarse-grained out to yield effective dynamics for position variables. Without the Lorentz force, the low mass limit is equivalent to the high friction limit. Both cases share the same Langevin equation that is obtained by setting the mass to zero. The equivalence breaks down in the presence of the Lorentz force. The low mass limit cannot be achieved by setting the mass to zero. The limit is also distinct from the large friction limit. We derive the effective equations of motion in the low mass limit. The resulting stochastic differential equation involves a nonwhite noise whose correlation matrix has antisymmetric components. We demonstrate the importance of the nonwhite noise by investigating the heat dissipation by a driven Brownian particle, where the emergent nonwhite noise has a physically measurable effect.
Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.
Pluhackova, Kristyna; Wassenaar, Tsjerk A; Kirsch, Sonja; Böckmann, Rainer A
2015-03-26
A molecular description of the lipid-protein interactions underlying the adsorption of proteins to membranes is crucial for understanding, for example, the specificity of adsorption or the binding strength of a protein to a bilayer, or for characterizing protein-induced changes of membrane properties. In this paper, we extend an automated in silico assay (DAFT) for binding studies and apply it to characterize the adsorption of the model fusion peptides E and K to a mixed phospholipid/cholesterol membrane using coarse-grained molecular dynamics simulations. In addition, we couple the coarse-grained protocol to reverse transformation to atomistic resolution, thereby allowing to study molecular interactions with high detail. The experimentally observed differential binding of the peptides E and K to membranes, as well as the increased binding affinity of helical over unstructered peptides, could be well reproduced using the polarizable Martini coarse-grained (CG) force field. Binding to neutral membranes is shown to be dominated by initial binding of the positively charged N-terminus to the phospholipid headgroup region, followed by membrane surface-aligned insertion of the peptide at the interface between the hydrophobic core of the membrane and its polar headgroup region. Both coarse-grained and atomistic simulations confirm a before hypothesized snorkeling of lysine side chains for the membrane-bound state of the peptide K. Cholesterol was found to be enriched in peptide vicinity, which is probably of importance for the mechanism of membrane fusion. The applied sequential multiscale method, using coarse-grained simulations for the slow adsorption process of peptides to membranes followed by backward transformation to atomistic detail and subsequent atomistic simulations of the preformed peptide-lipid complexes, is shown to be a versatile approach to study the interactions of peptides or proteins with biomembranes.
Directory of Open Access Journals (Sweden)
de Ferrater Ramoneda, Jaime
1965-04-01
Full Text Available In the construction of this set of buildings, for a wine producing firm, the strictly functional needs were naturally the paramount design criterion. All the various stages in the manufacture of the well known liqueurs and aperitif drinks marketed by this firm had to be studied in detail, to provide the best possible housing accommodation. A detailed pattern of all the requirements, including communications, sequence of operations, and possible future developments, was the initial step from which the architects proceeded, in their progressive elaboration of the final design. The interplay of volumes and planes is a direct consequence of the essential purpose of the buildings. The bottling nave consists of a series of parabolic arches and portal frames which support, by means of adjustable tie members, many of the stored materials. This is an original and highly functional design, into which a great deal of care and thought has been put.En el planeamiento y construcción de cada una de las edificaciones que componen este establecimiento enológico, se siguió un criterio preponderantemente objetivo y funcional; para cada función sucesiva —del tratamiento de vinos para la obtención de aperitivos y licores— fue estudiado y diseñado el albergue adecuado, y estudiadas sus relaciones con las otras funciones. Del organigrama dimensionado se derivó directamente la, planta general y la composición de volúmenes; y de ello surgió la variedad y dinamisma que las mismas presentan. La nave de embotellado está constituida por una serie de pórticos—arcos parabólicos—, de los que queda suspendido, mediante tensores reglables, el almacén. En resumen, el conjunto construido destaca, por su originalidad y elegante sencillez.
Force-Induced Unravelling of DNA Origami.
Engel, Megan C; Smith, David M; Jobst, Markus A; Sajfutdinow, Martin; Liedl, Tim; Romano, Flavio; Rovigatti, Lorenzo; Louis, Ard A; Doye, Jonathan P K
2018-05-31
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently-proposed origami biosensor, whose function takes advantage of origami behaviour under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inwards for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces; and what design principles can be applied to enhance stability.
Stoll, S; Roelcke, V; Raspe, H
2005-07-29
The article addresses the history of evidence-based medicine in Germany. Its aim was to reconstruct the standard of clinical-therapeutic investigation in Germany at the beginning of the 20 (th) century. By a historical investigation of five important German general medical journals for the time between 1918 and 1932 an overview of the situation of clinical investigation is given. 268 clinical trails are identified, and are analysed in view of their methodological design. Heterogeneous results are found: While few examples of sophisticated methodology exist, the design of the majority of the studies is poor. A response to the situation described can be seen in Paul Martini's book "Methodology of Therapeutic Investigation", first published in 1932. Paul Martini's biography, his criticism of the situation of clinical-therapeutic investigation of his time, the major points of his methodology and the reception of the book in Germany and abroad are described.
A theoretical study of colloidal forces near an amphiphilic polymer brush
Wu, Jianzhong
2011-03-01
Polymer-based ``non-stick'' coatings are promising as the next generation of effective, environmentally-friendly marine antifouling systems that minimize nonspecific adsorption of extracellular polymeric substances (EPS). However, design and development of such systems are impeded by the poor knowledge of polymer-mediated interactions of biomacromolecules with the protected substrate. In this work, a polymer density functional theory (DFT) is used to predict the potential of mean force between spherical biomacromolecules and amphiphilic copolymer brushes within a coarse-grained model that captures essential nonspecific interactions such as the molecular excluded volume effects and the hydrophobic energies. The relevance of theoretical results for practical control of the EPS adsorption is discussed in terms of the efficiency of different brush configurations to prevent biofouling. It is shown that the most effective antifouling surface may be accomplished by using amphiphilic brushes with a long hydrophilic backbone and a hydrophobic end at moderate grafting density.
Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.
Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael F
2012-02-14
Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.
Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam
2014-12-23
To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.
Javier Alberto Pinzón-Torres; Nelson Jovany Contreras Porras; Diego Camilo Durán García; Jairo René Martínez Morales; Elena Stashenko
2014-01-01
El uso de fertilizantes minerales en cultivos de Cymbopogon martini Roxb. (Palmarosa) con el fin de incrementar la biomasa y el rendimiento de aceite esencial (AE) es una práctica cada vez más frecuente. Este aceite es rico en geraniol y acetato de geranilo, moléculas con alto valor en las industrias de productos cosméticos y farmacéutica. Las plantas fueron obtenidas del Centro Nacional de Investigación Agroindustrial de Plantas Aromaticas y Medicinales de la Universidad Industrial de Santan...
Folding and insertion thermodynamics of the transmembrane WALP peptide
Energy Technology Data Exchange (ETDEWEB)
Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Bennett, W. F. Drew [Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada); Pfaendtner, Jim [Department of Chemical Engineering, University of Washington, Seattle, Washington 98195 (United States); Deserno, Markus [Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Karttunen, Mikko [Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, 5600 MB Eindhoven (Netherlands)
2015-12-28
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.
Folding and insertion thermodynamics of the transmembrane WALP peptide
International Nuclear Information System (INIS)
Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko
2015-01-01
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA) n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence
Liu, Jin; Jewel, Yead; Dutta, Prashanta
2017-11-01
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule to a wild-type LacY. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from microsecond simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with experiments. Our analysis suggest that the conformational changes of LacY are a cumulative consequence of inter-domain H-bonds breaking at the periplasmic side, inter-domain salt-bridge formation at the cytoplasmic side, as well as the TDG orientational changes during the transition. This work is supported by US National Science Foundation under Grant No. CBET-1604211.
Analytical equation of state with three-body forces: Application to noble gases
International Nuclear Information System (INIS)
Río, Fernando del; Díaz-Herrera, Enrique; Guzmán, Orlando; Moreno-Razo, José Antonio; Ramos, J. Eloy
2013-01-01
We developed an explicit equation of state (EOS) for small non polar molecules by means of an effective two-body potential. The average effect of three-body forces was incorporated as a perturbation, which results in rescaled values for the parameters of the two-body potential. These values replace the original ones in the EOS corresponding to the two-body interaction. We applied this procedure to the heavier noble gases and used a modified Kihara function with an effective Axilrod-Teller-Muto (ATM) term to represent the two- and three-body forces. We also performed molecular dynamics simulations with two- and three-body forces. There was good agreement between predicted, simulated, and experimental thermodynamic properties of neon, argon, krypton, and xenon, up to twice the critical density and up to five times the critical temperature. In order to achieve 1% accuracy of the pressure at liquid densities, the EOS must incorporate the effect of ATM forces. The ATM factor in the rescaled two-body energy is most important at temperatures around and lower than the critical one. Nonetheless, the rescaling of two-body diameter cannot be neglected at liquid-like densities even at high temperature. This methodology can be extended straightforwardly to deal with other two- and three-body potentials. It could also be used for other nonpolar substances where a spherical two-body potential is still a reasonable coarse-grain approximation
DEFF Research Database (Denmark)
Poursoroush, Asma; Sperotto, Maria Maddalena; Laradji, Mohamed
2017-01-01
Solid-supported lipid bilayers are utilized by experimental scientists as models for biological membranes because of their stability. However, compared to free standing bilayers, their close proximity to the substrate may affect their phase behavior. As this is still poorly understood, and few co...
Transferable coarse-grained potential for de novo protein folding and design.
Directory of Open Access Journals (Sweden)
Ivan Coluzza
Full Text Available Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. 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 require further experimental testing. For an independent set of proteins, previously used as benchmark, the correct folded structure of both the designed and the natural sequences is also demonstrated. The equilibrium folding properties are characterized by free energy calculations. The resulting free energy profiles not only are consistent among natural and designed proteins, but also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, the updated Caterpillar model is unique in the combination of its fundamental three features: its simplicity, its ability to produce natural foldable designed sequences, and its structure prediction precision. It is also remarkable that low frustration sequences can be obtained with such a simple and universal design procedure, and that the folding of natural proteins shows funnelled free energy landscapes without the need of any potentials based on the native structure.
Multi-scale coarse graining and molecular dynamics simulations of vesicle formation
Hoof, van B.
2013-01-01
The basic mechanisms of living cells have attracted an increased interest in recent years, triggered perhaps by the prospect of creating life in the laboratory through synthetic biology. This once-futuristic idea has become realistic through scientific progress in the past decade. One of the main
Microstructure-grain orientation relationship in coarse grain nickel cold-rolled to large strain
International Nuclear Information System (INIS)
Chen, H.S.; Godfrey, A.; Hansen, N.; Xie, J.X.; Liu, Q.
2008-01-01
The relationship between crystallographic orientation and the deformation microstructure formed during cold-rolling to high strains (up to ε vM = 4.5) has been investigated. The starting material was Ni (99.96% purity) with a coarse initial average grain size (approximately 500 μm). Microstructural characterization was carried out using a combination of electron channeling contrast imaging and electron back-scatter diffraction orientation mapping. An orientation dependence of the deformation microstructure was observed even at the highest strain examined. A large increase in the average boundary misorientation is found at strains above ε vM = 1.8 for regions with the {1 1 2} and {1 2 3} orientations. This increase accompanies the structural transition from a medium strain microstructure to a high strain lamellar microstructure. In contrast, the average misorientation in regions of {1 1 0} orientation increases only slowly even up to the highest strain examined
Braun, S.; Kraska, T.; Kalikmanov, V.I.
2013-01-01
Binary clusters formed by vapor-liquid nucleation are frequently nonhomogeneous objects in which components are not well mixed. The structure of a cluster plays an important role in nucleation and cluster growth. We demonstrate structuring effects by studying high-pressure nucleation and cluster
ɛ-connectedness, finite approximations, shape theory and coarse graining in hyperspaces
Alonso-Morón, Manuel; Cuchillo-Ibanez, Eduardo; Luzón, Ana
2008-12-01
We use upper semifinite hyperspaces of compacta to describe ε-connectedness and to compute homology from finite approximations. We find a new connection between ε-connectedness and the so-called Shape Theory. We construct a geodesically complete R-tree, by means of ε-components at different resolutions, whose behavior at infinite captures the topological structure of the space of components of a given compact metric space. We also construct inverse sequences of finite spaces using internal finite approximations of compact metric spaces. These sequences can be converted into inverse sequences of polyhedra and simplicial maps by means of what we call the Alexandroff-McCord correspondence. This correspondence allows us to relate upper semifinite hyperspaces of finite approximation with the Vietoris-Rips complexes of such approximations at different resolutions. Two motivating examples are included in the introduction. We propose this procedure as a different mathematical foundation for problems on data analysis. This process is intrinsically related to the methodology of shape theory. This paper reinforces Robins’s idea of using methods from shape theory to compute homology from finite approximations.
Structure optimization by heuristic algorithm in a coarse-grained off-lattice model
International Nuclear Information System (INIS)
Jing-Fa, Liu
2009-01-01
A heuristic algorithm is presented for a three-dimensional off-lattice AB model consisting of hydrophobic (A) and hydrophilic (B) residues in Fibonacci sequences. By incorporating extra energy contributions into the original potential function, we convert the constrained optimization problem of AB model into an unconstrained optimization problem which can be solved by the gradient method. After the gradient minimization leads to the basins of the local energy minima, the heuristic off-trap strategy and subsequent neighborhood search mechanism are then proposed to get out of local minima and search for the lower-energy configurations. Furthermore, in order to improve the efficiency of the proposed algorithm, we apply the improved version called the new PERM with importance sampling (nPERMis) of the chain-growth algorithm, pruned-enriched-Rosenbluth method (PERM), to face-centered-cubic (FCC)-lattice to produce the initial configurations. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we found the ground state energies are lower than the best values reported in the present literature
Role of Neutral Lipids in Tear Fluid Lipid Layer: Coarse-Grained Simulation Study
DEFF Research Database (Denmark)
Telenius, J.; Koivuniemi, A.; Kulovesi, P.
2012-01-01
Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse...
Coarse-grained molecular dynamics simulation of transport through the nuclear pore complex
Ghavami, Ali
2014-01-01
Dit proefschrift is gewijd aan het mechanisme van Nucleo - cytoplasmatisch transport openbaren door grofkorrelige moleculaire dynamica simulaties van ontvouwen eiwitten in de nucleaire porie complex (NPC) . NPC's zijn zeer selectief poorten, die alle transporten over nucleaire envelop controleren .
Controls on the size and occurrence of pools in coarse-grained forest rivers
John M. Buffington; Thomas E. Lisle; Richard D. Woodsmith; Sue Hilton
2002-01-01
Controls on pool formation are examined in gravel- and cobble-bed rivers in forest mountain drainage basins of northern California, southern Oregon, and southeastern Alaska. We demonstrate that the majority of pools at our study sites are formed by flow obstructions and that pool geometry and frequency largely depend on obstruction characteristics (size, type, and...
Shark: SQL and Analytics with Cost-Based Query Optimization on Coarse-Grained Distributed Memory
2014-01-13
RDBMS and contains a database (often MySQL or Derby) with a namespace for tables, table metadata and partition information. Table data is stored in an...serialization/deserialization) Java interface implementations with corresponding object inspectors. The Hive driver controls the processing of queries, coordinat...native API, RDD operations are invoked through a functional interface similar to DryadLINQ [32] in Scala, Java or Python. For example, the Scala code for
Coarse-grain parallel solution of few-group neutron diffusion equations
International Nuclear Information System (INIS)
Sarsour, H.N.; Turinsky, P.J.
1991-01-01
The authors present a parallel numerical algorithm for the solution of the finite difference representation of the few-group neutron diffusion equations. The targeted architectures are multiprocessor computers with shared memory like the Cray Y-MP and the IBM 3090/VF, where coarse granularity is important for minimizing overhead. Most of the work done in the past, which attempts to exploit concurrence, has concentrated on the inner iterations of the standard outer-inner iterative strategy. This produces very fine granularity. To coarsen granularity, the authors introduce parallelism at the nested outer-inner level. The problem's spatial domain was partitioned into contiguous subregions and assigned a processor to solve for each subregion independent of all other subregions, hence, processors; i.e., each subregion is treated as a reactor core with imposed boundary conditions. Since those boundary conditions on interior surfaces, referred to as internal boundary conditions (IBCs), are not known, a third iterative level, the recomposition iterations, is introduced to communicate results between subregions
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
DEFF Research Database (Denmark)
Stovgaard, Kasper; Andreetta, Christian; Ferkinghoff-Borg, Jesper
2010-01-01
, 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......DBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for use in statistical inference of protein structures from SAXS data....
Electro-Acoustic Behavior of the Mitotic Spindle: A Semi-Classical Coarse-Grained Model
Czech Academy of Sciences Publication Activity Database
Havelka, Daniel; Kučera, Ondřej; Deriu, M.A.; Cifra, Michal
2014-01-01
Roč. 9, č. 1 (2014), e86501 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP102/11/0649 Institutional support: RVO:67985882 Keywords : electric fields * tubulin * chromosomes Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 3.234, year: 2014
Dynamics in coarse-grained models for oligomer-grafted silica nanoparticles
Hong, Bingbing; Chremos, Alexandros; Panagiotopoulos, Athanassios Z.
2012-01-01
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
mineral elements content of some coarse grains used as staple food
African Journals Online (AJOL)
DR. AMINU
2014-06-01
Jun 1, 2014 ... in white and brown cowpea, the values are within the range reported ... ages of 18 - 50 years (FNB, 2013). Magnesium ... that of female adult is 320mg/day (NIH, 2013). ..... Environmental Geochemistry and Health 27, 19–. 30.
Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems
International Nuclear Information System (INIS)
Kalligiannaki, Evangelia; Katsoulakis, Markos A.; Plecháč, Petr; Vlachos, Dionisios G.
2012-01-01
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.
A fast global sum on the coarse-grained scalar parallel computer
International Nuclear Information System (INIS)
Ohta, Toshio.
1996-03-01
A new global sum subroutine, which has the same function as the prepared one on the Intel Paragon, is developed. The algorithm is simple and faster. It makes the performance 10 times faster than the original one in case of 128 nodes. The results will be shown with the characteristics, restrictions and extendability. (author)
Risselada, H. Jelger; Marrink, Siewert J.
2009-01-01
The molecular packing details of lipids in planar bilayers are well characterized. For curved bilayers, however, little data is available. In this paper we study the effect of temperature and membrane composition on the structural and dynamical properties of a liposomal membrane in the limit of high
Covering all the bases : Coarse-grained model design and application for nucleic acids
Uusitalo, Jaakko Juhani
2016-01-01
Nucleic acids play a crucial role in the storage, transportation and expression of our genetic information. They have also become an interesting tool for many applications in nanotechnology. Studying biomolecular systems containing nucleic acids using experimental and imaging techniques has its
Coarse-grained versus atomistic simulations : realistic interaction free energies for real proteins
May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton
2014-01-01
MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full
DEFF Research Database (Denmark)
Andreetta, Christian
-likelihood estimators for the form factors employed in the Debye formula, a theoretical forward model for SAXS profiles. The resulting computation compares favorably with the state of the art tool in the field, the program CRYSOL in the suite ATSAS. A faster, parallel implementation on Graphical Processor Units (GPUs......The present work describes the design and the implementation of a protocol for arbitrary precision computation of Small Angle X-ray Scattering (SAXS) profiles, and its inclusion in a probabilistic framework for protein structure determination. This protocol identifies a set of maximum...... of protein structures all fitting the experimental data. For the first time, we describe in full atomic detail a set of different conformations attainable by flexible polypeptides in solution. This method is not limited by assumptions in shape or size of the samples. It allows therefore to investigate...
An OFDM receiver implemented on the coarse-grain reconfigurable Montium processor
Rauwerda, G.K.; Heysters, P.M.; Smit, Gerardus Johannes Maria
Future mobile terminals become multimode communication systems. In order to handle different standards, we propose to perform baseband processing in heterogeneous reconfigurable hardware. OFDM is one of the techniques that exists in multimode communication systems. As an example, we present the
Coarse-grain bandwidth estimation techniques for large-scale network
Cheung, Kar-Ming; Jennings, E.
In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-and-forward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.
Designing coarse grained-and atom based-potentials for protein-protein docking
Directory of Open Access Journals (Sweden)
Tobi Dror
2010-11-01
Full Text Available Abstract Background Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results Using a linear programming (LP technique, we developed two types of potentials: (i Side chain-based and (ii Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys, based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked structure, a potential energy lower than those of any of the non-native (misdocked structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atom-based potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.
Difference in luminescence sensitivity of coarse-grained quartz from deserts of northern China
International Nuclear Information System (INIS)
Zheng, C.X.; Zhou, L.P.; Qin, J.T.
2009-01-01
The luminescence sensitivity of coarse quartz extracted from desert sands in northern China was investigated. In general, the western deserts' samples are shown to be less sensitive than samples from the eastern deserts with respect to both OSL and the 110 deg. C TL peak. However, internal scatter among different aliquots of the same sample is observed for these two signals, which have already been normalized by weight. Laboratory dosing/bleach experiments indicate that earth surface processes, such as repeated burial and transportation can cause the sensitivity change and suggest that they may be responsible for the internal scatter. An intrinsic property of quartz was explored via the luminescence response to thermal activation to a maximum temperature of 700 deg. C. The thermal activation curves obtained with quartz from western and central deserts are similar, except one sample from Gurbantungut, which follows the pattern of eastern samples. The differences in quartz luminescence sensitivity exhibited by OSL/110 deg. C TL sensitivity and response to thermal activation are in accordance with the published results of geochemical studies.
Second harmonic generation and dielectric study of the fine and coarse grain PMN-35PT ceramics
Czech Academy of Sciences Publication Activity Database
Kroupa, Jan; Bovtun, Viktor; Nuzhnyy, Dmitry; Savinov, Maxim; Vaněk, Přemysl; Kamba, Stanislav; Petzelt, Jan; Holc, J.; Kosec, M.; Amorin, H.; Alguero, M.
2008-01-01
Roč. 81, 11-12 (2008), s. 1059-1064 ISSN 0141-1594 R&D Projects: GA ČR(CZ) GA202/06/0403; GA MŠk OC 101 Institutional research plan: CEZ:AV0Z10100520 Keywords : relaxor ferroelectrics * phase transitions * PMN-PT * SHG * dielectric Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.201, year: 2008
Coarse-Grain Bandwidth Estimation Scheme for Large-Scale Network
Cheung, Kar-Ming; Jennings, Esther H.; Sergui, John S.
2013-01-01
A large-scale network that supports a large number of users can have an aggregate data rate of hundreds of Mbps at any time. High-fidelity simulation of a large-scale network might be too complicated and memory-intensive for typical commercial-off-the-shelf (COTS) tools. Unlike a large commercial wide-area-network (WAN) that shares diverse network resources among diverse users and has a complex topology that requires routing mechanism and flow control, the ground communication links of a space network operate under the assumption of a guaranteed dedicated bandwidth allocation between specific sparse endpoints in a star-like topology. This work solved the network design problem of estimating the bandwidths of a ground network architecture option that offer different service classes to meet the latency requirements of different user data types. In this work, a top-down analysis and simulation approach was created to size the bandwidths of a store-and-forward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. These techniques were used to estimate the WAN bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network. A new analytical approach, called the "leveling scheme," was developed to model the store-and-forward mechanism of the network data flow. The term "leveling" refers to the spreading of data across a longer time horizon without violating the corresponding latency requirement of the data type. Two versions of the leveling scheme were developed: 1. A straightforward version that simply spreads the data of each data type across the time horizon and doesn't take into account the interactions among data types within a pass, or between data types across overlapping passes at a network node, and is inherently sub-optimal. 2. Two-state Markov leveling scheme that takes into account the second order behavior of the store-and-forward mechanism, and the interactions among data types within a pass. The novelty of this approach lies in the modeling of the store-and-forward mechanism of each network node. The term store-and-forward refers to the data traffic regulation technique in which data is sent to an intermediate network node where they are temporarily stored and sent at a later time to the destination node or to another intermediate node. Store-and-forward can be applied to both space-based networks that have intermittent connectivity, and ground-based networks with deterministic connectivity. For groundbased networks, the store-and-forward mechanism is used to regulate the network data flow and link resource utilization such that the user data types can be delivered to their destination nodes without violating their respective latency requirements.
Coarse-Grain Bandwidth Estimation Techniques for Large-Scale Space Network
Cheung, Kar-Ming; Jennings, Esther
2013-01-01
In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-andforward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.
Archie’s saturation exponent for natural gas hydrate in coarse-grained reservoirs
Cook, Ann E.; Waite, William F.
2018-01-01
Accurately quantifying the amount of naturally occurring gas hydrate in marine and permafrost environments is important for assessing its resource potential and understanding the role of gas hydrate in the global carbon cycle. Electrical resistivity well logs are often used to calculate gas hydrate saturations, Sh, using Archie's equation. Archie's equation, in turn, relies on an empirical saturation parameter, n. Though n = 1.9 has been measured for ice‐bearing sands and is widely used within the hydrate community, it is highly questionable if this n value is appropriate for hydrate‐bearing sands. In this work, we calibrate n for hydrate‐bearing sands from the Canadian permafrost gas hydrate research well, Mallik 5L‐38, by establishing an independent downhole Sh profile based on compressional‐wave velocity log data. Using the independently determined Sh profile and colocated electrical resistivity and bulk density logs, Archie's saturation equation is solved for n, and uncertainty is tracked throughout the iterative process. In addition to the Mallik 5L‐38 well, we also apply this method to two marine, coarse‐grained reservoirs from the northern Gulf of Mexico Gas Hydrate Joint Industry Project: Walker Ridge 313‐H and Green Canyon 955‐H. All locations yield similar results, each suggesting n ≈ 2.5 ± 0.5. Thus, for the coarse‐grained hydrate bearing (Sh > 0.4) of greatest interest as potential energy resources, we suggest that n = 2.5 ± 0.5 should be applied in Archie's equation for either marine or permafrost gas hydrate settings if independent estimates of n are not available.
The role of geology in sediment supply and bedload transport patterns in coarse-grained streams
Sandra E. Ryan
2007-01-01
This paper compares gross differences in rates of bedload sediment moved at bankfull discharges in 19 channels on national forests in the Middle and Southern Rocky Mountains. Each stream has its own "bedload signal," in that the rate and size of materials transported at bankfull discharge largely reflect the nature of flow and sediment particular to that...
Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
Deplazes, Evelyne; Louhivuori, Martti; Jayatilaka, Dylan; Marrink, Siewert J.; Corry, Ben
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
International Nuclear Information System (INIS)
Kretzschmar, U.; Gomez-Cornejo, J.; Astarloa, A.; Bidarte, U.; Ser, J. Del
2016-01-01
The expansion of FPGA technology in numerous application fields is a fact. Single Event Effects (SEE) are a critical factor for the reliability of FPGA based systems. For this reason, a number of researches have been studying fault tolerance techniques to harden different elements of FPGA designs. Using Partial Reconfiguration (PR) in conjunction with Triple Modular Redundancy (TMR) is an emerging approach in recent publications dealing with the implementation of fault tolerant processors on SRAM-based FPGAs. While these works pay great attention to the repair of erroneous instances by means of reconfiguration, the essential step of synchronizing the repaired processors is insufficiently addressed. In this context, this paper poses four different synchronization approaches for soft core processors, which balance differently the trade-off between synchronization speed and hardware overhead. All approaches are assessed in practice by synchronizing TMR protected PicoBlaze processors implemented on a Virtex-5 FPGA. Nevertheless all methods are of a general nature and can be applied for different processor architectures in a straightforward fashion. - Highlights: • Four different synchronization methods for faulty processors are proposed. • The methods balance between synchronization speed and hardware overhead. • They can be applied to TMR-protected reconfigurable FPGA designs. • The proposed schemes are implemented and tested in real hardware.
Expressing Coarse-Grain Dependencies Among Tasks in Shared Memory Programs
DEFF Research Database (Denmark)
Larsen, Per; Karlsson, Sven; Madsen, Jan
2011-01-01
Designers of embedded systems face tight constraints on resources, response time and cost. The ability to analyze embedded systems is essential to timely delivery of new designs. Many analysis techniques model parallel programs as task graphs. Task graphs capture the worst-case execution times....... The overhead of verifying the correct use of the directives was measured on a set of benchmarks on two platforms. The overhead of runtime checks was found to be negligible in all instances....
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
May, A.; Pool, R.; van Dijk, E.; Bijlard, J.; Abeln, S.; Heringa, J.; Feenstra, K.A.
2014-01-01
MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full
Low Power Implementation of Non Power-of-Two FFTs on Coarse-Grain Reconfigurable Architectures
Zhang, Q.; Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Rivaton, Arnaud; Quevremont, Jérôme
2005-01-01
The DRM standard for digital radio broadcast in the AM band requires integrated devices for radio receivers at very low power. A System on Chip (SoC) call DiMITRI was developed based on a dual ARM9 RISC core architecture. Analyses showed that most computation power is used in the Coded Orthogonal
In silico modelling of drug–polymer interactions for pharmaceutical formulations
Ahmad, Samina; Johnston, Blair F.; Mackay, Simon P.; Schatzlein, Andreas G.; Gellert, Paul; Sengupta, Durba; Uchegbu, Ijeoma F.
2010-01-01
Selecting polymers for drug encapsulation in pharmaceutical formulations is usually made after extensive trial and error experiments. To speed up excipient choice procedures, we have explored coarse-grained computer simulations (dissipative particle dynamics (DPD) and coarse-grained molecular dynamics using the MARTINI force field) of polymer–drug interactions to study the encapsulation of prednisolone (log p = 1.6), paracetamol (log p = 0.3) and isoniazid (log p = −1.1) in poly(l-lactic acid) (PLA) controlled release microspheres, as well as the encapsulation of propofol (log p = 4.1) in bioavailability enhancing quaternary ammonium palmitoyl glycol chitosan (GCPQ) micelles. Simulations have been compared with experimental data. DPD simulations, in good correlation with experimental data, correctly revealed that hydrophobic drugs (prednisolone and paracetamol) could be encapsulated within PLA microspheres and predicted the experimentally observed paracetamol encapsulation levels (5–8% of the initial drug level) in 50 mg ml−1 PLA microspheres, but only when initial paracetamol levels exceeded 5 mg ml−1. However, the mesoscale technique was unable to model the hydrophilic drug (isoniazid) encapsulation (4–9% of the initial drug level) which was observed in experiments. Molecular dynamics simulations using the MARTINI force field indicated that the self-assembly of GCPQ is rapid, with propofol residing at the interface between micellar hydrophobic and hydrophilic groups, and that there is a heterogeneous distribution of propofol within the GCPQ micelle population. GCPQ–propofol experiments also revealed a population of relatively empty and drug-filled GCPQ particles. PMID:20519214
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele
2015-10-01
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.
Sun, Delin; Forsman, Jan; Woodward, Clifford E
2015-04-14
Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.
Combined use of heat and saline tracer to estimate aquifer properties in a forced gradient test
Colombani, N.; Giambastiani, B. M. S.; Mastrocicco, M.
2015-06-01
Usually electrolytic tracers are employed for subsurface characterization, but the interpretation of tracer test data collected by low cost techniques, such as electrical conductivity logging, can be biased by cation exchange reactions. To characterize the aquifer transport properties a saline and heat forced gradient test was employed. The field site, located near Ferrara (Northern Italy), is a well characterized site, which covers an area of 200 m2 and is equipped with a grid of 13 monitoring wells. A two-well (injection and pumping) system was employed to perform the forced gradient test and a straddle packer was installed in the injection well to avoid in-well artificial mixing. The contemporary continuous monitor of hydraulic head, electrical conductivity and temperature within the wells permitted to obtain a robust dataset, which was then used to accurately simulate injection conditions, to calibrate a 3D transient flow and transport model and to obtain aquifer properties at small scale. The transient groundwater flow and solute-heat transport model was built using SEAWAT. The result significance was further investigated by comparing the results with already published column experiments and a natural gradient tracer test performed in the same field. The test procedure shown here can provide a fast and low cost technique to characterize coarse grain aquifer properties, although some limitations can be highlighted, such as the small value of the dispersion coefficient compared to values obtained by natural gradient tracer test, or the fast depletion of heat signal due to high thermal diffusivity.
Directory of Open Access Journals (Sweden)
Catherine Hincker
2011-08-01
Full Text Available Narjys El Alaoui nous propose d'aborder les Idaw Martini — qui forment une entité territoriale proche et en même temps distincte du groupe des Isaffen — par le biais de leurs pratiques rituelles. Sur ce groupe, peu connu, de l'Anti-atlas marocain, aucune étude de cette ampleur n'a jusqu'à présent été réalisée. Défrichant cet espace nouveau - où seuls quelques rapports militaires, ethnographiques ou documents rédigés par des lettrés, et maintenant anciens, font mention des Idaw Martini – l'aut...
Application of Taguchi method for cutting force optimization in rock ...
Indian Academy of Sciences (India)
Mechanical properties Uniaxial compressive strength. Sawing characteristics .... texture, coarse-grained, grains between 0.08 mm and 4.80 mm, and the coarsest ..... piezoelectric ceramic of Bi0.5Na0.5TiO3 using the Taguchi method. Powder ...
Mechanisms of Plastic Deformation in Collagen Networks Induced by Cellular Forces.
Ban, Ehsan; Franklin, J Matthew; Nam, Sungmin; Smith, Lucas R; Wang, Hailong; Wells, Rebecca G; Chaudhuri, Ovijit; Liphardt, Jan T; Shenoy, Vivek B
2018-01-23
Contractile cells can reorganize fibrous extracellular matrices and form dense tracts of fibers between neighboring cells. These tracts guide the development of tubular tissue structures and provide paths for the invasion of cancer cells. Here, we studied the mechanisms of the mechanical plasticity of collagen tracts formed by contractile premalignant acinar cells and fibroblasts. Using fluorescence microscopy and second harmonic generation, we quantified the collagen densification, fiber alignment, and strains that remain within the tracts after cellular forces are abolished. We explained these observations using a theoretical fiber network model that accounts for the stretch-dependent formation of weak cross-links between nearby fibers. We tested the predictions of our model using shear rheology experiments. Both our model and rheological experiments demonstrated that increasing collagen concentration leads to substantial increases in plasticity. We also considered the effect of permanent elongation of fibers on network plasticity and derived a phase diagram that classifies the dominant mechanisms of plasticity based on the rate and magnitude of deformation and the mechanical properties of individual fibers. Plasticity is caused by the formation of new cross-links if moderate strains are applied at small rates or due to permanent fiber elongation if large strains are applied over short periods. Finally, we developed a coarse-grained model for plastic deformation of collagen networks that can be employed to simulate multicellular interactions in processes such as morphogenesis, cancer invasion, and fibrosis. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
International Nuclear Information System (INIS)
Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando
2015-01-01
We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers
Ma, Ke; Forsman, Jan; Woodward, Clifford E
2015-05-07
We explore the influence of ion pairing in room temperature ionic liquids confined by planar electrode surfaces. Using a coarse-grained model for the aromatic ionic liquid [C4MIM(+)][BF4 (-)], we account for an ion pairing component as an equilibrium associating species within a classical density functional theory. We investigated the resulting structure of the electrical double layer as well as the ensuing surface forces and differential capacitance, as a function of the degree of ion association. We found that the short-range structure adjacent to surfaces was remarkably unaffected by the degree of ion pairing, up to several molecular diameters. This was even the case for 100% of ions being paired. The physical implications of ion pairing only become apparent in equilibrium properties that depend upon the long-range screening of charges, such as the asymptotic behaviour of surface forces and the differential capacitance, especially at low surface potential. The effect of ion pairing on capacitance is consistent with their invocation as a source of the anomalous temperature dependence of the latter. This work shows that ion pairing effects on equilibrium properties are subtle and may be difficult to extract directly from simulations.
International Nuclear Information System (INIS)
Sutton, C.
1989-01-01
Inside the atom, particles interact through two forces which are never felt in the everyday world. But they may hold the key to the Universe. These ideas on subatomic forces are discussed with respect to the strong force, the electromagnetic force and the electroweak force. (author)
Energy Technology Data Exchange (ETDEWEB)
Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
2016-05-28
Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.
International Nuclear Information System (INIS)
Taborsky, J.; Tryzna, P.; Formanek, Z.; Vales, J.
1982-01-01
The conveyor belt is gripped in the chosen place with benches to form a V shape with a constant cross section independent of the immediate amount of transported coal. At this point the source and the radiation intensity monitor are placed in horizontal plane on the sides of the conveyor belt. Their connecting line is perpendicular to the direction of the movement of the conveyor belt. Thus, monitoring of the ash content of mined coal and operative control of mining according to measured values are made possible. (Ha)
Energy Technology Data Exchange (ETDEWEB)
Hu, Jun, E-mail: hujunral@163.com [The State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang 110819 (China); Du, Lin-Xiu [The State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang 110819 (China); Wang, Jian-Jun [Institute of Materials Research, School of Material and Metallurgy, Northeastern University, Shenyang 110819 (China); Xie, Hui; Gao, Cai-Ru [The State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang 110819 (China); Misra, R.D.K. [Laboratory for Excellence in Advanced Steel Research, Center for Structural and Functional Materials, University of Louisiana at Lafayette, Lafayette, LA 70504-4130 (United States)
2014-01-10
Motivated by the small lattice mismatch between ferrite and vanadium nitride (VN), we describe here the welding thermal cycle simulation that provides high toughness in the ICRCG HAZ of low carbon V–N steel. This unique behavior is attributed to the formation of ultra-fine grained ferrite along prior austenite grain boundaries generated by the first pass welding thermal cycle with high misorientation boundaries, where V(C, N) precipitates provide potential nucleation sites for ferrite, leading to extraordinary refinement of martensite/austenite (M/A) constituent. Nitrogen stimulates the precipitation behavior of V(C, N). The nucleation of high density of V(C, N) precipitates consumes carbon-content in the austenite, leading to decrease in the carbon-content in the M/A constituent, with consequent decrease in hardness. The increase in toughness is explained in terms of Griffith's crack propagation theory.
Efficiencies of joint non-local update moves in Monte Carlo simulations of coarse-grained polymers
Austin, Kieran S.; Marenz, Martin; Janke, Wolfhard
2018-03-01
In this study four update methods are compared in their performance in a Monte Carlo simulation of polymers in continuum space. The efficiencies of the update methods and combinations thereof are compared with the aid of the autocorrelation time with a fixed (optimal) acceptance ratio. Results are obtained for polymer lengths N = 14, 28 and 42 and temperatures below, at and above the collapse transition. In terms of autocorrelation, the optimal acceptance ratio is approximately 0.4. Furthermore, an overview of the step sizes of the update methods that correspond to this optimal acceptance ratio is given. This shall serve as a guide for future studies that rely on efficient computer simulations.
International Nuclear Information System (INIS)
Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; In Kim, Jae; Joon Chang, Hyun; Baek, Inchul; Na, Sungsoo; Eom, Kilho
2015-01-01
Amyloid fibrils are responsible for pathogenesis of various diseases and exhibit the structural feature of an ordered, hierarchical structure such as multi-stranded helical structure. As the multi-strandedness of amyloid fibrils has recently been found to be highly correlated with their toxicity and infectivity, it is necessary to study how the hierarchical (i.e. multi-stranded) structure of amyloid fibril is formed. Moreover, although it has recently been reported that the nanomechanics of amyloid proteins plays a key role on the amyloid-induced pathogenesis, a critical role that the multi-stranded helical structure of the fibrils plays in their nanomechanical properties has not fully characterized. In this work, we characterize the morphology and mechanical properties of multi-stranded amyloid fibrils by using equilibrium molecular dynamics simulation and elastic network model. It is shown that the helical pitch of multi-stranded amyloid fibril is linearly proportional to the number of filaments comprising the amyloid fibril, and that multi-strandedness gives rise to improving the bending rigidity of the fibril. Moreover, we have also studied the morphology and mechanical properties of a single protofilament (filament) in order to understand the effect of cross-β structure and mutation on the structures and mechanical properties of amyloid fibrils. Our study sheds light on the underlying design principles showing how the multi-stranded amyloid fibril is formed and how the structure of amyloid fibrils governs their nanomechanical properties. (paper)
Blokpoel, Mark; Grootjen, Franc; van den Broek, Egon; Hoenkamp, E.; De Cock, M.; Hoste, V.
2008-01-01
A parallel implementation of Ganter’s algorithm to calculate concept lattices for Formal Concept Analysis is presented. A benchmark was executed to experimentally determine the algorithm’s performance, including an AMD Athlon64, Intel dual Xeon, and UltraSPARC T1, with respectively 1, 4, and 24
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
Gu, Ruo-Xu; Ingólfsson, Helgi I; De Vries, Alex H.; Marrink, Siewert J.; Tieleman, D. Peter
2017-01-01
Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal
Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang
2016-01-07
Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for (60)Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with (60)Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.
International Nuclear Information System (INIS)
Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang
2016-01-01
Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for 60 Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60 Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage. (paper)
Eriksson, P. G.
A widely developed, thin, coarse-matrix conglomerate occurs within early Proterozoic lacustrine mudrocks in the Transvaal Sequence, South Africa. The poorly sorted tabular chert clasts, alternation of a planar clast fabric with disorientated zones, plus normal and inverse grading in the former rock type suggest deposition by density-modified grain-flow and high density turbidity currents. The lower fan-delta slope palæenvironment inferred for the conglomerate is consistent with the lacustrine interpretation for the enclosing mudrock facies. This intracratonic setting contrasts with the marine environment generally associated with density-modified grain-flow deposits.
International Nuclear Information System (INIS)
Becquart, C.S.; Barbu, A.; Bocquet, J.L.; Caturla, M.J.; Domain, C.; Fu, C.-C.; Golubov, S.I.; Hou, M.; Malerba, L.; Ortiz, C.J.; Souidi, A.; Stoller, R.E.
2010-01-01
Knowledge of the long-term evolution of the microstructure after introduction of primary damage is an essential ingredient in understanding mechanical property changes that occur during irradiation. Within the European integrated project 'PERFECT,' different techniques have been developed or improved to model microstructure evolution of Fe alloys under irradiation. This review paper aims to present the current state of the art of these techniques, as developed in the project, as well as the main results obtained.
Barnouin, Olivier S.; Daly, R. Terik; Cintala, Mark J.; Crawford, David A.
2018-01-01
The surfaces of many planets and asteroids contain coarsely fragmental material generated by impacts or other geologic processes. The presence of such pre-existing structures may affect subsequent impacts, particularly when the width of the shock is comparable to or smaller than the size of pre-existing structures. Reasonable theoretical predictions and low speed (<300m/s) impact experiments suggest that in such targets the cratering process should be highly dissipative, which would reduce cratering efficiencies and cause a rapid decay in ejection velocity as a function of distance from the impact point. In this study, we assess whether these results apply at higher impact speeds between 0.5 and 2.5 km s-1. This study shows little change in cratering efficiency when 3.18 mm diameter glass beads are launched into targets composed of these same beads. These impacts are very efficient, and ejection velocity decays slowly as function of distance from the impact point. This slow decay in ejection velocity probably indicates a correspondingly slow decay of the shock stresses. However, these experiments reveal that initial interactions between projectile and target strongly influence the cratering process and lead to asymmetries in crater shape and ejection angles, as well as significant variations in ejection velocity at a given launch position. Such effects of asymmetric coupling could be further enhanced by heterogeneity in the initial distribution of grains in the target and by mechanical collisions between grains. These experiments help to explain why so few craters are seen on the rubble-pile asteroid Itokawa: impacts into its coarsely fragmental surface by projectiles comparable to or smaller than the size of these fragments likely yield craters that are not easily recognizable.
Cruz, Victor L.; Ramos, Javier; Martinez-Salazar, Javier; Melo, Manuel N.
Bacteriocin AS-48 is a membrane-interacting peptide that acts as a broad-spectrum antimicrobial against Gram-positive and Gram-negative bacteria. Prior Nuclear Magnetic Resonance experiments and the high resolution crystal structure of AS-48 have suggested a mechanism for the molecular activity of
International Nuclear Information System (INIS)
Hu, Jun; Du, Lin-Xiu; Wang, Jian-Jun; Xie, Hui; Gao, Cai-Ru; Misra, R.D.K.
2014-01-01
Motivated by the small lattice mismatch between ferrite and vanadium nitride (VN), we describe here the welding thermal cycle simulation that provides high toughness in the ICRCG HAZ of low carbon V–N steel. This unique behavior is attributed to the formation of ultra-fine grained ferrite along prior austenite grain boundaries generated by the first pass welding thermal cycle with high misorientation boundaries, where V(C, N) precipitates provide potential nucleation sites for ferrite, leading to extraordinary refinement of martensite/austenite (M/A) constituent. Nitrogen stimulates the precipitation behavior of V(C, N). The nucleation of high density of V(C, N) precipitates consumes carbon-content in the austenite, leading to decrease in the carbon-content in the M/A constituent, with consequent decrease in hardness. The increase in toughness is explained in terms of Griffith's crack propagation theory
Energy Technology Data Exchange (ETDEWEB)
Wirth, Brian [Univ. of Tennessee, Knoxville, TN (United States)
2016-01-12
Exposure of metallic structural materials to irradiation environments results in significant microstructural evolution, property changes and performance degradation, which limits the extended operation of current generation light water reactors and restricts the design of advanced fission and fusion reactors [1-8]. This effect of irradiation on materials microstructure and properties is a classic example of an inherently multiscale phenomenon, as schematically illustrated in Figure 1a. Pertinent processes range from the atomic nucleus to structural component length scales, spanning more than 15 orders of magnitude. Time scales bridge more than 22 orders of magnitude, with the shortest being less than a femtosecond [1,8]. Further, the mix of radiation-induced features formed and the corresponding property degradation depend on a wide range of material and irradiation variables. This emphasizes the importance of closely integrating models with high-resolution experimental characterization of the evolving radiation- damaged microstructure, including measurements performed in-situ during irradiation. In this article, we review some recent successes through the use of closely coordinated modeling and experimental studies of the defect cluster evolution in irradiated body-centered cubic materials, followed by a discussion of outstanding challenges still to be addressed, which are necessary for the development of comprehensive models of radiation effects in structural materials.
Na, Hyuntae; Song, Guang
2015-07-01
In a recent work we developed a method for deriving accurate simplified models that capture the essentials of conventional all-atom NMA and identified two best simplified models: ssNMA and eANM, both of which have a significantly higher correlation with NMA in mean square fluctuation calculations than existing elastic network models such as ANM and ANMr2, a variant of ANM that uses the inverse of the squared separation distances as spring constants. Here, we examine closely how the performance of these elastic network models depends on various factors, namely, the presence of hydrogen atoms in the model, the quality of input structures, and the effect of crystal packing. The study reveals the strengths and limitations of these models. Our results indicate that ssNMA and eANM are the best fine-grained elastic network models but their performance is sensitive to the quality of input structures. When the quality of input structures is poor, ANMr2 is a good alternative for computing mean-square fluctuations while ANM model is a good alternative for obtaining normal modes. © 2015 Wiley Periodicals, Inc.