Coarse-grained description of cosmic structure from Szekeres models
NASA Astrophysics Data System (ADS)
Sussman, Roberto A.; Delgado Gaspar, I.; Hidalgo, Juan Carlos
2016-03-01
We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ``pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10-20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.
Modeling of Ultrasonic Propagation in a Coarse Grain Structure
NASA Astrophysics Data System (ADS)
Jenson, F.; Fortuna, T.; Doudet, L.
2009-03-01
The metallurgical structure of centrifugally cast stainless steel components makes it difficult to ultrasonically inspect them. The centimeter-size grains forming the macrostructure strongly affect the transmitted field and thus limit inspection capabilities. Such macrostructures can be computed using an algorithm based on the Voronoi diagrams. This mathematical tool provides good qualitative representations of equiaxed and columnar structures. By combining the Voronoi diagrams with existing CIVA functionalities such as the transmitted field computation in a heterogeneous medium using the so-called pencil method, it is shown that some important physical phenomena responsible for inspection difficulties may be reproduced. For instance, the field distortions in phase and amplitude due to the velocity fluctuations that are caused by the large grain structures of these materials are properly described thanks to this approach. These distortions represent deviations from quantities that are usually described by existing theories, such as the mean field attenuation. Comparisons of simulated results with experimental data are also presented and discussed in this paper.
Crowley, M. F.; Matthews, J.; Beckham, G.; Bomble, Y.; Hynninen, A. P.; Ciesielski, P. F.
2012-01-01
Cellulose is still a mysterious polymer in many ways: structure of microfibrils, thermodynamics of synthesis and degradation, and interactions with other plant cell wall components. Our aim is to uncover the details and mechanisms of cellulose digestion and synthesis. We report the details of the structure of cellulose 1-beta under several temperature conditions and report here the results of these studies and connections to experimental measurements and the measurement in-silico the free energy of decrystallization of several morphologies of cellulose. In spatially large modeling, we show the most recent work of mapping atomistic and coarse-grain models into tomographic images of cellulose and extreme coarse-grain modeling of interactions of large cellulase complexes with microfibrils. We discuss the difficulties of modeling cellulose and suggest future work both experimental and theoretical to increase our understanding of cellulose and our ability to use it as a raw material for fuels and materials.
Predicting RNA 3D structure using a coarse-grain helix-centered model
Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.
2015-01-01
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133
Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics
Parker, David; Bryant, Zev; Delp, Scott L.
2010-01-01
Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469
Protein secondary-structure description with a coarse-grained model.
Kneller, Gerald R; Hinsen, Konrad
2015-07-01
A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
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.
2015-06-21
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.
Tetrahedrality and structural order for hydrophobic interactions in a coarse-grained water model
NASA Astrophysics Data System (ADS)
Chaimovich, Aviel; Shell, M. Scott
2014-02-01
The hydrophobic interaction manifests two separate regimes in terms of size: Small nonpolar bodies exhibit a weak oscillatory force (versus distance) while large nonpolar surfaces exhibit a strong monotonic one. This crossover in hydrophobic behavior is typically explained in terms of water's tetrahedral structure: Its tetrahedrality is enhanced near small solutes and diminished near large planar ones. Here, we demonstrate that water's tetrahedral correlations signal this switch even in a highly simplified, isotropic, "core-softened" water model. For this task, we introduce measures of tetrahedrality based on the angular distribution of water's nearest neighbors. On a quantitative basis, the coarse-grained model of course is only approximate: (1) While greater than simple Lennard-Jones liquids, its bulk tetrahedrality remains lower than that of fully atomic models; and (2) the decay length of the large-scale hydrophobic interaction is less than has been found in experiments. Even so, the qualitative behavior of the model is surprisingly rich and exhibits numerous waterlike hydrophobic behaviors, despite its simplicity. We offer several arguments for the manner in which it should be able to (at least partially) reproduce tetrahedral correlations underlying these effects.
Coarse-grained modelling of supercoiled RNA
NASA Astrophysics Data System (ADS)
Matek, Christian; Šulc, Petr; Randisi, Ferdinando; Doye, Jonathan P. K.; Louis, Ard A.
2015-12-01
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
Probing the structural dynamics of the SNARE recycling machine based on coarse-grained modeling.
Zheng, Wenjun
2016-08-01
Membrane fusion in eukaryotes is driven by the formation of a four-helix bundle by three SNARE proteins. To recycle the SNARE proteins, they must be disassembled by the ATPase NSF and four SNAP proteins which together form a 20S supercomplex. Recently, the first high-resolution structures of the NSF (in both ATP and ADP state) and 20S (in four distinct states termed I, II, IIIa, and IIIb) were solved by cryo-electron microscopy (cryo-EM), which have paved the way for structure-driven studies of the SNARE recycling mechanism. To probe the structural dynamics of SNARE disassembly at amino-acid level of details, a systematic coarse-grained modeling based on an elastic network model and related analyses were performed. Our normal mode analysis of NSF, SNARE, and 20S predicted key modes of collective motions that partially account for the observed structural changes, and illuminated how the SNARE complex can be effectively destabilized by untwisting and bending motions of the SNARE complex driven by the amino-terminal domains of NSF in state II. Our flexibility analysis identified regions with high/low flexibility that coincide with key functional sites (such as the NSF-SNAPs-SNARE binding sites). A subset of hotspot residues that control the above collective motions, which will make promising targets for future mutagenesis studies were also identified. Finally, the conformational changes in 20S as induced by the transition of NSF from ATP to ADP state were modeled, and a concerted untwisting motion of SNARE/SNAPs and a sideway flip of two amino-terminal domains were observed. In sum, the findings have offered new structural and dynamic details relevant to the SNARE disassembly mechanism, and will guide future functional studies of the SNARE recycling machinery. Proteins 2016; 84:1055-1066. © 2016 Wiley Periodicals, Inc. PMID:27090373
NASA Astrophysics Data System (ADS)
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
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.
Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo
2015-12-15
Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to
Dunn, Nicholas J. H.; Noid, W. G.
2015-12-28
The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.
Hadley, Kevin R.; McCabe, Clare
2010-01-01
Developing accurate models of water for use in computer simulations is important for the study of many chemical and biological systems, including lipid bilayer self-assembly. The large temporal and spatial scales needed to study such self-assembly have led to the development and application of coarse-grained models for the lipid-lipid, lipid-solvent and solvent-solvent interactions. Unfortunately, popular center-of-mass-based coarse-graining techniques are limited to modeling water with one-water per bead. In this work, we have utilized the K-means algorithm to determine the optimal clustering of waters to allow the mapping of multiple waters to single coarse-grained beads. Through the study of a simple mixture between water and an amphiphilic solute (1-pentanol), we find a 4-water bead model has the optimal balance between computational efficiency and accurate solvation and structural properties when compared to water models ranging from 1 to 9 waters per bead. The 4-water model was subsequently utilized in studies of the solvation of hexadecanoic acid and the structure, as measured via radial distribution functions, for the hydrophobic tails and the bulk water phase were found to agree well with experimental data and their atomistic targets. PMID:20230012
Coarse-grained modeling of DNA curvature
NASA Astrophysics Data System (ADS)
Freeman, Gordon S.; Hinckley, Daniel M.; Lequieu, Joshua P.; Whitmer, Jonathan K.; de Pablo, Juan J.
2014-10-01
The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.
Shi, Ya-Zhou; Wang, Feng-Hua; Wu, Yuan-Yan; Tan, Zhi-Jie
2014-09-14
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.
Coarse-grained models for biological simulations
NASA Astrophysics Data System (ADS)
Wu, Zhe; Cui, Qiang; Yethiraj, Arun
2011-03-01
The large timescales and length-scales of interest in biophysics preclude atomistic study of many systems and processes. One appealing approach is to use coarse-grained (CG) models where several atoms are grouped into a single CG site. In this work we describe a new CG force field for lipids, surfactants, and amino acids. The topology of CG sites is the same as in the MARTINI force field, but the new model is compatible with a recently developed CG electrostatic water (Big Multiple Water, BMW) model. The model not only gives correct structural, elastic properties and phase behavior for lipid and surfactants, but also reproduces electrostatic properties at water-membrane interface that agree with experiment and atomistic simulations, including the potential of mean force for charged amino acid residuals at membrane. Consequently, the model predicts stable attachment of cationic peptides (i.e., poly-Arg) on lipid bilayer surface, which is not shown in previous models with non-electrostatic water.
Bayesian parametrization of coarse-grain dissipative dynamics models
NASA Astrophysics Data System (ADS)
Dequidt, Alain; Solano Canchaya, Jose G.
2015-08-01
We introduce a new bottom-up method for the optimization of dissipative coarse-grain models. The method is based on Bayesian optimization of the likelihood to reproduce a coarse-grained reference trajectory obtained from analysis of a higher resolution molecular dynamics trajectory. This new method is related to force matching techniques, but using the total force on each grain averaged on a coarse time step instead of instantaneous forces. It has the advantage of not being limited to pairwise short-range interactions in the coarse-grain model and also yields an estimation of the friction parameter controlling the dynamics. The theory supporting the method is exposed in a practical perspective, with an analytical solution for the optimal set of parameters. The method was first validated by using it on a system with a known optimum. The new method was then tested on a simple system: n-pentane. The local molecular structure of the optimized model is in excellent agreement with the reference system. An extension of the method allows to get also an excellent agreement for the equilibrium density. As for the dynamic properties, they are also very satisfactory, but more sensitive to the choice of the coarse-grain representation. The quality of the final force field depends on the definition of the coarse grain degrees of freedom and interactions. We consider this method as a serious alternative to other methods like iterative Boltzmann inversion, force matching, and Green-Kubo formulae.
Coarse-grained modelling of surface nanobubbles
NASA Astrophysics Data System (ADS)
Grosfils, Patrick
2013-05-01
Surface nanobubbles are nanoscale gaseous objects that form on hydrophobic surfaces in contact with water. Understanding nanobubble formation and stability remains challenging due to the lack of appropriate theoretical framework and adequate modelling. Here we present a non-equilibrium coarse-grained model for nanobubbles at hydrophobic surfaces. The model is based on a lattice-gas model that has been proposed to understand the hydrophobic effect to which dynamical properties are added. The results presented demonstrate the ability of the model to reproduce the basic features of stable surface nanobubbles, which, thereby, supports the dynamical origin of these objects.
Coarse-grained dynamics of alignment in animal group models
NASA Astrophysics Data System (ADS)
Moon, Sung Joon; Levin, Simon; Kevrekidis, Yannis
2006-03-01
Coordinated motion in animal groups, such as bird flocks and fish schools, and their models gives rise to remarkable coherent structures. Using equation-free computational tools we explore the coarse-grained dynamics of a model for the orientational movement decision in animal groups, consisting of a small number of informed "leaders" and a large number of uninformed, nonidentical ``followers.'' The direction in which each group member is headed is characterized by a phase angle of a limit-cycle oscillator, whose dynamics are nonlinearly coupled with those of all the other group members. We identify a small number of proper coarse-grained variables (using uncertainty quantification methods) that describe the collective dynamics, and perform coarse projective integration and equation-free bifurcation analysis of the coarse-grained model behavior in these variables.
A Transferable Coarse-Grained Model for Hydrogen Bonding Liquids
Golubkov, Pavel A.; Wu, Johnny C.; Ren, Pengyu
2008-01-01
We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effectivepotential based approaches. The previous center-of-mass framework1 is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic .level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358
Coarse-Grain Modeling of Energetic Materials
NASA Astrophysics Data System (ADS)
Brennan, John
2015-06-01
Mechanical and thermal loading of energetic materials can incite responses over a wide range of spatial and temporal scales due to inherent nano- and microscale features. Many energy transfer processes within these materials are atomistically governed, yet the material response is manifested at the micro- and mesoscale. The existing state-of-the-art computational methods include continuum level approaches that rely on idealized field-based formulations that are empirically based. Our goal is to bridge the spatial and temporal modeling regimes while ensuring multiscale consistency. However, significant technical challenges exist, including that the multiscale methods linking the atomistic and microscales for molecular crystals are immature or nonexistent. To begin addressing these challenges, we have implemented a bottom-up approach for deriving microscale coarse-grain models directly from quantum mechanics-derived atomistic models. In this talk, a suite of computational tools is described for particle-based microscale simulations of the nonequilibrium response of energetic solids. Our approach builds upon recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics that includes chemical reactions.
Hinckley, Daniel M; Freeman, Gordon S; Whitmer, Jonathan K; de Pablo, Juan J
2013-10-14
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642
Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.; de Pablo, Juan J.
2013-01-01
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642
A nucleotide-level coarse-grained model of RNA
Šulc, Petr; Ouldridge, Thomas E.; Louis, Ard A.; Romano, Flavio; Doye, Jonathan P. K.
2014-06-21
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
A nucleotide-level coarse-grained model of RNA
NASA Astrophysics Data System (ADS)
Šulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.
2014-06-01
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
Szklarczyk, Oliwia; Staroń, Krzysztof; Cieplak, Marek
2009-11-01
A coarse grained molecular dynamics model with an implicit solvent is used to elucidate properties of the human topoisomerase I. The model is defined through the native structure and it allows covering significantly longer time scales than in all atom simulations. Single residue and double residue motional characteristics are studied. The results are consistent with all atom simulations reported in the literature indicating usefulness of the model in further studies of this protein. Novel findings include broadening of the description of the dynamic behavior of the lip and hinge regions and a characterization of the motional properties of the RRM binding site of the enzyme. We also consider mechanical stretching of the protein and identify sources of the force peaks. The elastic properties of topoisomerase I are predicted to be average in comparison to other proteins, yielding a maximum force of resistance to pulling which should be of order 120 pN. The contact unraveling pattern is consistent with the understanding of the structure and function of the protein. We find supporting evidence for the hypothesis that the C-terminal domain acquires an ordered structure upon binding with the core enzyme even though it forms a molten globule when in isolation. PMID:19452556
Coarse-graining of proteins based on elastic network models
NASA Astrophysics Data System (ADS)
Sinitskiy, Anton V.; Voth, Gregory A.
2013-08-01
To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.
Moving Beyond Watson-Crick Models of Coarse Grained DNA
NASA Astrophysics Data System (ADS)
Dorfman, Kevin; Linak, Margaret; Tourdot, Richard
2012-02-01
DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.
Zheng, Wenjun
2012-04-21
This study aims to model a minimal dynein motor domain capable of motor function, which consists of the linker domain, six AAA+ modules (AAA1-AAA6), coiled coil stalk, and C-terminus domain. To this end, we have used the newly solved X-ray structures of dynein motor domain to perform a coarse-grained modeling of dynein's post- and pre-powerstroke conformation and the conformational transition between them. First, we have used normal mode analysis to identify a single normal mode that captures the coupled motions of AAA1-AAA2 closing and linker domain rotation, which enables the ATP-driven recovery stroke of dynein. Second, based on the post-powerstroke conformation solved crystallographically, we have modeled dynein's pre-powerstroke conformation by computationally inducing AAA1-AAA2 closing and sliding of coiled coil stalk, and the resulting model features a linker domain near the pre-powerstroke position and a slightly tilted stalk. Third, we have modeled the conformational transition from pre- to post-powerstroke conformation, which predicts a clear sequence of structural events that couple microtubule binding, powerstroke and product release, and supports a signaling path from stalk to AAA1 via AAA3 and AAA4. Finally, we have found that a closed AAA3-AAA4 interface (compatible with nucleotide binding) is essential to the mechano-chemical coupling in dynein. Our modeling not only offers unprecedented structural insights to the motor function of dynein as described by past single-molecule, fluorescence resonance energy transfer, and electron microscopy studies, but also provides new predictions for future experiments to test. PMID:22519354
Insights on protein-DNA recognition by coarse grain modelling
Poulain, Pierre; Saladin, Adrien; Hartmann, Brigitte; Prévost, Chantal
2008-01-01
Coarse grain modelling of macromolecules is a new approach potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein–DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein–DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acids side chains strengthen the binding. Overall, this work demonstrates that coarse grain modelling can reveal itself a precious auxiliary for a general and complete description and understanding of protein–DNA association mechanisms. PMID:18478582
NASA Astrophysics Data System (ADS)
Ortiz, Carlos Pompeyo
Rigidity emerges in a broad class of soft matter systems, relevant to many industrial and biological processes. In our experiments, we study a model soft matter system, hard-sphere Brownian suspensions of submicron particles. Brownian suspensions lack rigidity in the absence of external driving, but form flow-stabilized solid-like microsphere heaps under the influence of hydrodynamic forces. The overarching question driving my dissertation is "What is the nature of the rigidity of these microsphere heaps?" Does the rigidity of the heaps follow from mechanical stability driven by a sufficiently interconnected network of particle contacts? Or, does the rigidity of the heaps follow from a kinetic glass transition characterized by a diverging resistance to flow such that the time necessary to observe rearrangements grows prohibitively large? We expect that insights into the mechanism of rigidity of Brownian microsphere heaps are applicable to a wide class of soft matter systems. In this thesis,we have overcome the limitations of previous experimental approaches. Namely, we show that the rigidity of our heaps does not emerge from the effects of gravity, inertia, static friction, or van der Waals sticking. In Chapter 1 of thesis, we review the background literature. In Chapter 2, we present the experimental, analytical, and computational methods used in the remainder of the thesis. In Chapter 3, we investigate the onset of rigidity by characterizing the steady-state size of the heap versus the imposed flow conditions. We show that thermal fluctuations and repulsive interparticle interactions, the dominant forces at the single-particle scale, suppress the development of a rigid phase. These conditions imply that the onset of rigidity in involves many-body collective interactions. In Chapter 4, we measure the response of the heap to external perturbations, which allows us to measure their elastic modulus and compare our results to hard sphere theoretical expectations. We
Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.
2008-01-01
The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325
Coarse-graining the structure of polycyclic aromatic hydrocarbons clusters.
Hernández-Rojas, J; Calvo, F; Wales, D J
2016-05-18
Clusters of polycyclic aromatic hydrocarbons (PAHs) are essential components of soot and may concentrate a significant fraction of carbon matter in the interstellar medium. In this contribution, coarse-grained potentials are parameterized using all-atom reference data to model PAH molecules, such as coronene (C24H12) or circumcoronene (C54H18), and their aggregates. Low-energy structures of pure coronene or circumcoronene clusters obtained using basin-hopping global optimization are found to agree with atomistic results, and consist of finite 1D columnar motifs, sometimes juxtaposed in larger clusters. The structures are only weakly perturbed when quadrupolar interactions are included. π-Stacking also dominates in binary coronene/circumcoronene aggregates, although intriguing motifs are predicted in which one or more molecules are sandwiched between the other PAH species. The coarse-grained model is also extended to account for interaction with a flat graphitic substrate. In this case, binding is stronger with the substrate than with other molecules, and the PAHs are predicted to arrange into a flat triangular monolayer. PMID:27055581
Molecular Dynamics Trajectory Compression with a Coarse-Grained Model
Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael
2012-01-01
Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759
Unconstrained Structure Formation in Coarse-Grained Protein Simulations
NASA Astrophysics Data System (ADS)
Bereau, Tristan
The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid
STOCK: Structure mapper and online coarse-graining kit for molecular simulations
Bevc, Staš; Junghans, Christoph; Praprotnik, Matej
2015-03-15
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.
STOCK: Structure mapper and online coarse-graining kit for molecular simulations
Bevc, Staš; Junghans, Christoph; Praprotnik, Matej
2015-03-15
We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be providedmore » by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.« less
COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS*
DENG, MINGGE
2014-01-01
We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the Cα coordinates of the protein backbone. Specifically, to mimic the unfolding process, i.e., to simulate the process of overcoming the local energy barrier on the free energy landscape with force loading, the noncovalent protein network bonds (i.e., hydrogen bonds, salt bridges, hydrophobic contacts, etc.) are broken one-by-one with a certain probability, while the strong covalent bonds along the backbone (i.e., peptide bonds, disulfide bonds, etc.) are kept intact. The jumping event from local energy minima (bonds breaking rate) are chosen according to Kramer’s theory and the Bell model. Moreover, we exploit the self-similar structure of proteins at different scales to design an effective coarse-graining procedure for DENM with optimal parameter selection. The robustness of DENM is validated by coarse-grained molecular dynamics (MD) simulation against atomistic MD simulation of force-extension processes of the Fibrinogen and Titin Immunoglobulin proteins. We observe that the native structure of the proteins determines the total unfolding dynamics (including large deviations) and not just the fluctuations around the native state. PMID:25400515
A coarse-grained model of microtubule self-assembly
NASA Astrophysics Data System (ADS)
Regmi, Chola; Cheng, Shengfeng
Microtubules play critical roles in cell structures and functions. They also serve as a model system to stimulate the next-generation smart, dynamic materials. A deep understanding of their self-assembly process and biomechanical properties will not only help elucidate how microtubules perform biological functions, but also lead to exciting insight on how microtubule dynamics can be altered or even controlled for specific purposes such as suppressing the division of cancer cells. Combining all-atom molecular dynamics (MD) simulations and the essential dynamics coarse-graining method, we construct a coarse-grained (CG) model of the tubulin protein, which is the building block of microtubules. In the CG model a tubulin dimer is represented as an elastic network of CG sites, the locations of which are determined by examining the protein dynamics of the tubulin and identifying the essential dynamic domains. Atomistic MD modeling is employed to directly compute the tubulin bond energies in the surface lattice of a microtubule, which are used to parameterize the interactions between CG building blocks. The CG model is then used to study the self-assembly pathways, kinetics, dynamics, and nanomechanics of microtubules.
Investigating the impact of representation upon coarse-grained models
NASA Astrophysics Data System (ADS)
Foley, Thomas; Shell, M. Scott; Noid, William
The first step in building a coarse-grained (CG) model is choosing a representation or `mapping' of the original system at a reduced resolution. In practice, the mapping is often chosen on the basis of `physical intuition.' Consequently this crucial step would greatly benefit from the development of systematic and principled methodologies. Accordingly, we have studied the relationship between the mapping and the resulting CG model. As a starting point, we have analytically derived, as a function of the CG mapping, the exact many-body potential of mean force (PMF) for the simple Gaussian Network Model (GNM) of protein fluctuations. We use this as a simple model for investigating the effect of the CG mapping upon the information loss and quality of the CG model. Moreover, by considering the GNM's for different proteins, we investigate the significance of high resolution structural features for the quality of the CG model. We acknowledge support from the NSF, Alfred P. Sloan Foundation, and KITP.
Coarse-Grained Modeling of Mucus Barrier Properties
Gniewek, Pawel; Kolinski, Andrzej
2012-01-01
We designed a simple coarse-grained model of the glycocalyx layer, or adhesive mucus layer (AML), covered by mucus gel (luminal mucus layer) using a polymer lattice model and stochastic sampling (replica exchange Monte Carlo) for canonical ensemble simulations. We assumed that mucin MUC16 is responsible for the structural properties of the AML. Other mucins that are much smaller in size and less relevant for layer structure formation were not included. We further assumed that the system was in quasi-equilibrium. For systems with surface coverage and concentrations of model mucins mimicking physiological conditions, we determined the equilibrium distribution of inert nanoparticles within the mucus layers using an efficient replica exchange Monte Carlo sampling procedure. The results show that the two mucus layers penetrate each other only marginally, and the bilayer imposes a strong barrier for nanoparticles, with the AML layer playing a crucial role in the mucus barrier. PMID:22339855
A Coarse-Grained Model for Simulating Chitosan Hydrogels
NASA Astrophysics Data System (ADS)
Xu, Hongcheng; Matysiak, Silvina
Hydrogels are biologically-derived materials composed of water-filled cross-linking polymer chains. It has widely been used as biodegradable material and has many applications in medical devices. The chitosan hydrogel is stimuli-responsive for undergoing pH-sensitive self-assembly process, allowing programmable tuning of the chitosan deposition through electric pulse. To explore the self-assembly mechanism of chitosan hydroge, we have developed an explicit-solvent coarse-grained chitosan model that has roots in the MARTINI force field, and the pH change is modeled by protonating chitosan chains using the Henderson-Hasselbalch equation. The mechanism of hydrogel network formation will be presented. The self-assembled polymer network qualitatively reproduce many experimental observables such as the pH-dependent strain-stress curve, bulk moduli, and structure factor. Our model is also capable of simulating other similar polyelectrolyte polymer systems.
YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.
Tan, Robert K Z; Petrov, Anton S; Harvey, Stephen C
2006-05-01
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily. PMID:22844233
Ambia Garrido, Joaquin; Vainrub, Arnold; Pettitt, Bernard M.
2010-12-01
New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6–8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with allatom simulations for the case of dense systems.
Ambia-Garrido, J.; Vainrub, Arnold; Pettitt, B. Montgomery
2010-01-01
New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6–8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems. PMID:20957064
NASA Astrophysics Data System (ADS)
Ambia-Garrido, J.; Vainrub, Arnold; Pettitt, B. Montgomery
2010-12-01
New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all-atom simulations. Our average tilt results are also in agreement with all-atom simulations for the case of dense systems.
Coarse-grained theory of a realistic tetrahedral liquid model
NASA Astrophysics Data System (ADS)
Procaccia, I.; Regev, I.
2012-02-01
Tetrahedral liquids such as water and silica-melt show unusual thermodynamic behavior such as a density maximum and an increase in specific heat when cooled to low temperatures. Previous work had shown that Monte Carlo and mean-field solutions of a lattice model can exhibit these anomalous properties with or without a phase transition, depending on the values of the different terms in the Hamiltonian. Here we use a somewhat different approach, where we start from a very popular empirical model of tetrahedral liquids —the Stillinger-Weber model— and construct a coarse-grained theory which directly quantifies the local structure of the liquid as a function of volume and temperature. We compare the theory to molecular-dynamics simulations and show that the theory can rationalize the simulation results and the anomalous behavior.
Coarse-Grained and Atomistic Modeling of Polyimides
NASA Technical Reports Server (NTRS)
Clancy, Thomas C.; Hinkley, Jeffrey A.
2004-01-01
A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.
NASA Astrophysics Data System (ADS)
Farrell, Kathryn; Oden, J. Tinsley
2014-07-01
methods through applications to representative atomic structures and we discuss extensions to the validation process for molecular models of polymer structures encountered in certain semiconductor nanomanufacturing processes. The powerful method of model plausibility as a means for selecting interaction potentials for coarse-grained models is discussed in connection with a coarse-grained hexane molecule. Discussions of how all-atom information is used to construct priors are contained in an appendix.
Coarse-grained, foldable, physical model of the polypeptide chain
Chakraborty, Promita; Zuckermann, Ronald N.
2013-01-01
Although nonflexible, scaled molecular models like Pauling–Corey’s and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to φ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human–computer interface. PMID:23898168
Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.
Mereghetti, Paolo; Maccari, Giuseppe; Spampinato, Giulia Lia Beatrice; Tozzini, Valentina
2016-08-25
The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course. PMID:27150459
Coarse-Grained Model of SNARE-Mediated Docking
Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand
2015-01-01
Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4–6 SNAREs actually increases the equilibrium distance. PMID:25954883
Coarse-Grained Model of SNARE-Mediated Docking.
Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand
2015-05-01
Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼ 3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4-6 SNAREs actually increases the equilibrium distance. PMID:25954883
Generic Coarse-Grained Model for Protein Folding and Aggregation
NASA Astrophysics Data System (ADS)
Bereau, Tristan; Deserno, Markus
2009-03-01
The complexity involved in protein structure is not only due to the rich variety of amino acids, but also the inherent weak interactions, comparable to thermal energy, and important cooperative phenomena. This presents a challenge in atomistic simulations, as it is associated with high-dimensionality and ruggedness of the energy landscape as well as long equilibration times. We have recently developed a coarse-grained (CG) implicit solvent peptide model which has been designed to reproduce key consequences of the abovementioned weak interactions. Its intermediate level of resolution, four beads per amino acid, allows for accurate sampling of local conformations by designing a force field that relies on simple interactions. A realistic ratio of α-helix to β-sheet content is achieved by mimicking a nearest-neighbor dipole interaction. We tune the model in order to fold helical proteins while systematically comparing the structure with NMR data. Very good agreement is achieved for proteins that have simple tertiary structures. We further probe the effects of cooperativity between amino acids by looking at peptide aggregation, where hydrophobic peptide fragments cooperatively form large-scale β-sheet structures. The model is able to reproduce features from atomistic simulations on a qualitative basis.
Coarse-grained models for aqueous polyethylene glycol solutions.
Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun
2014-01-01
A new coarse-grained force field is developed for polyethylene glycol (PEG) in water. The force field is based on the MARTINI model but with the big multipole water (BMW) model for the solvent. The polymer force field is reparameterized using the MARTINI protocol. The new force field removes the ring-like conformations seen in simulations of short chains with the MARTINI force field; these conformations are not observed in atomistic simulations. We also investigate the effect of using parameters for the end-group that are different from those for the repeat units, with the MARTINI and BMW/MARTINI models. We find that the new BMW/MARTINI force field removes the ring-like conformations seen in the MARTINI models and has more accurate predictions for the density of neat PEG. However, solvent-separated-pairs between chain ends and slow dynamics of the PEG reflect its own artifacts. We also carry out fine-grained simulations of PEG with bundled water clusters and show that the water bundling can lead to ring-like conformations of the polymer molecules. The simulations emphasize the pitfalls of coarse-graining several molecules into one site and suggest that polymer-solvent systems might be a stringent test for coarse-grained force fields. PMID:24350686
Anisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials
2015-01-01
Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10–200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide–peptide, peptide–water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927
Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study
NASA Astrophysics Data System (ADS)
Yang, Delian; Wang, Qiang
2015-02-01
We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of Nm monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < Nm.
Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study
Yang, Delian; Wang, Qiang
2015-02-07
We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N{sub 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{sub m}.
Coarse-Grained Models for Protein-Cell Membrane Interactions
Bradley, Ryan; Radhakrishnan, Ravi
2015-01-01
The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047
Iig, Patrick
2011-01-01
Complex fluids, such as polymers, colloids, liquid-crystals etc., show intriguing viscoelastic properties, due to the complicated interplay between flow-induced structure formation and dynamical behavior. Starting from microscopic models of complex fluids, a systematic coarse-graining method is presented that allows us to derive closed-form and thermodynamically consistent constitutive equations for such fluids. Essential ingredients of the proposed approach are thermodynamically guided simulations within a consistent coarse-graining scheme. In addition to this new type of multiscale simulations, we reconstruct the building blocks that constitute the thermodynamically consistent coarse-grained model. We illustrate the method for low-molecular polymer melts, which are subject to different imposed flow fields like planar shear and different elongational flows. The constitutive equation for general flow conditions we obtain shows rheological behavior including shear thinning, normal stress differences, and elongational viscosities in good agreement with reference results. PMID:21678766
Na, Hyuntae; Jernigan, Robert L.; Song, Guang
2015-01-01
Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491
A transferable coarse-grained model for hydrogen-bonding liquids.
Golubkov, Pavel A; Wu, Johnny C; Ren, Pengyu
2008-04-21
We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358
A quantitative coarse-grain model for lipid bilayers.
Orsi, Mario; Haubertin, David Y; Sanderson, Wendy E; Essex, Jonathan W
2008-01-24
A simplified particle-based computer model for hydrated phospholipid bilayers has been developed and applied to quantitatively predict the major physical features of fluid-phase biomembranes. Compared with available coarse-grain methods, three novel aspects are introduced. First, the main electrostatic features of the system are incorporated explicitly via charges and dipoles. Second, water is accurately (yet efficiently) described, on an individual level, by the soft sticky dipole model. Third, hydrocarbon tails are modeled using the anisotropic Gay-Berne potential. Simulations are conducted by rigid-body molecular dynamics. Our technique proves 2 orders of magnitude less demanding of computational resources than traditional atomic-level methodology. Self-assembled bilayers quantitatively reproduce experimental observables such as electron density, compressibility moduli, dipole potential, lipid diffusion, and water permeability. The lateral pressure profile has been calculated, along with the elastic curvature constants of the Helfrich expression for the membrane bending energy; results are consistent with experimental estimates and atomic-level simulation data. Several of the results presented have been obtained for the first time using a coarse-grain method. Our model is also directly compatible with atomic-level force fields, allowing mixed systems to be simulated in a multiscale fashion. PMID:18085766
An exactly solvable coarse-grained model for species diversity
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Dunn, Nicholas J. H.; Noid, W. G.
2016-05-01
This work investigates the promise of a "bottom-up" extended ensemble framework for developing coarse-grained (CG) models that provide predictive accuracy and transferability for describing both structural and thermodynamic properties. We employ a force-matching variational principle to determine system-independent, i.e., transferable, interaction potentials that optimally model the interactions in five distinct heptane-toluene mixtures. Similarly, we employ a self-consistent pressure-matching approach to determine a system-specific pressure correction for each mixture. The resulting CG potentials accurately reproduce the site-site rdfs, the volume fluctuations, and the pressure equations of state that are determined by all-atom (AA) models for the five mixtures. Furthermore, we demonstrate that these CG potentials provide similar accuracy for additional heptane-toluene mixtures that were not included their parameterization. Surprisingly, the extended ensemble approach improves not only the transferability but also the accuracy of the calculated potentials. Additionally, we observe that the required pressure corrections strongly correlate with the intermolecular cohesion of the system-specific CG potentials. Moreover, this cohesion correlates with the relative "structure" within the corresponding mapped AA ensemble. Finally, the appendix demonstrates that the self-consistent pressure-matching approach corresponds to minimizing an appropriate relative entropy.
Liao, Ming-Liang; Ju, Shin-Pon; Chang, Chun-Yi; Huang, Wei-Lin
2012-06-01
Size and chain length effects on structural behaviors of liquid crystal nanoclusters were examined by a coarse-grained model and the configurational-bias Monte Carlo (CBMC) simulation. The nanoclusters investigated in this study are composed of the biphenylcyclohexane-based BCH5H liquid crystal molecule and its derivatives. Results of the study show that the average energy decreases (i.e., more negative) as the cluster size (i.e., the number of molecules) increases. With the increasing cluster size, the equilibrium conformation of the nanocluster changes gradually from a pipe-like structure (for the smaller systems) to a ball-like cluster (for the larger systems). The order parameter of the system reduces with the transition of the equilibrium conformation. Regarding the chain length effect, the pipe-like equilibrium conformation (for the smaller systems) was observed more close to a pipe as the length of the tail alkyl chain of the derivatives extended. However, due to the flexibility of the tail alkyl chain, the pipe conformation of the system deflects slightly about its cyclohexyl group as the tail extends further. PMID:21975541
Insights into DNA-mediated interparticle interactions from a coarse-grained model.
Ding, Yajun; Mittal, Jeetain
2014-11-14
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions. PMID:25399156
Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.
Janner, A
2016-05-01
Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109
Polysaccharide-Protein Complexes in a Coarse-Grained Model.
Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek
2015-09-10
We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4-α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al. PMID:26291477
Coarse grained modeling of transport properties in monoclonal antibody solution
NASA Astrophysics Data System (ADS)
Swan, James; Wang, Gang
Monoclonal antibodies and their derivatives represent the fastest growing segment of the bio pharmaceutical industry. For many applications such as novel cancer therapies, high concentration, sub-cutaneous injections of these protein solutions are desired. However, depending on the peptide sequence within the antibody, such high concentration formulations can be too viscous to inject via human derived force alone. Understanding how heterogenous charge distribution and hydrophobicity within the antibodies leads to high viscosities is crucial to their future application. In this talk, we explore a coarse grained computational model of therapeutically relevant monoclonal antibodies that accounts for electrostatic, dispersion and hydrodynamic interactions between suspended antibodies to predict assembly and transport properties in concentrated antibody solutions. We explain the high viscosities observed in many experimental studies of the same biologics.
Coarse-grained cosmological perturbation theory: Stirring up the dust model
NASA Astrophysics Data System (ADS)
Uhlemann, Cora; Kopp, Michael
2015-04-01
We study the effect of coarse graining the dynamics of a pressureless self-gravitating fluid (coarse-grained dust) in the context of cosmological perturbation theory, in both the Eulerian and Lagrangian frameworks. We obtain recursion relations for the Eulerian perturbation kernels of the coarse-grained dust model by relating them to those of the standard pressureless fluid model. The effect of the coarse graining is illustrated by means of power and cross spectra for the density and velocity, which are computed up to one-loop order. In particular, the large-scale vorticity power spectrum that arises naturally from a mass-weighted velocity is derived from first principles. We find qualitatively good agreement for the magnitude, shape, and spectral index of the vorticity power spectrum with recent measurements from N -body simulations and results from the effective field theory of large-scale structure. To lay the ground for applications in the context of Lagrangian perturbation theory, we finally describe how the kernels obtained in Eulerian space can be mapped to Lagrangian ones.
Perez Sirkin, Yamila A; Factorovich, Matías H; Molinero, Valeria; Scherlis, Damian A
2016-06-14
The vapor pressure of water is a key property in a large class of applications from the design of membranes for fuel cells and separations to the prediction of the mixing state of atmospheric aerosols. Molecular simulations have been used to compute vapor pressures, and a few studies on liquid mixtures and solutions have been reported on the basis of the Gibbs Ensemble Monte Carlo method in combination with atomistic force fields. These simulations are costly, making them impractical for the prediction of the vapor pressure of complex materials. The goal of the present work is twofold: (1) to demonstrate the use of the grand canonical screening approach ( Factorovich , M. H. J. Chem. Phys. 2014 , 140 , 064111 ) to compute the vapor pressure of solutions and to extend the methodology for the treatment of systems without a liquid-vapor interface and (2) to investigate the ability of computationally efficient high-resolution coarse-grained models based on the mW monatomic water potential and ions described exclusively with short-range interactions to reproduce the relative vapor pressure of aqueous solutions. We find that coarse-grained models of LiCl and NaCl solutions faithfully reproduce the experimental relative pressures up to high salt concentrations, despite the inability of these models to predict cohesive energies of the solutions or the salts. A thermodynamic analysis reveals that the coarse-grained models achieve the experimental activity coefficients of water in solution through a compensation of severely underestimated hydration and vaporization free energies of the salts. Our results suggest that coarse-grained models developed to replicate the hydration structure and the effective ion-ion attraction in solution may lead to this compensation. Moreover, they suggest an avenue for the design of coarse-grained models that accurately reproduce the activity coefficients of solutions. PMID:27196963
NASA Astrophysics Data System (ADS)
Vögele, Martin; Holm, Christian; Smiatek, Jens
2015-12-01
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.
Vögele, Martin; Holm, Christian; Smiatek, Jens
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.
Fused coarse-grained model of aromatic ionic liquids and their behaviour at electrodes.
Li, Bin; Ma, Ke; Wang, Yong-Lei; Turesson, Martin; Woodward, Clifford E; Forsman, Jan
2016-03-01
A fused coarse-grained model of aromatic ionic liquids 1-alkyl-3-methylimidazoliums tetrafluoroborate ([CnMIM(+)][BF4(-)]) has been constructed. Structural and dynamical properties calculated from our model are compared with experimental data as well as with corresponding results from simulations of other suggested models. Specifically, we adopt a fused-sphere coarse-grained model for cations and anions. This model is utilized to study structure and differential capacitance in models of flat and porous carbon electrodes. We find that the capacitance varies with pore size, in a manner that is related to the packing of ions inside the pore. For very narrow pores, diffusion is slow and the establishment of thermodynamic equilibrium may exceed the practical limits for our molecular dynamics simulations. PMID:26928079
Moving beyond Watson-Crick models of coarse grained DNA dynamics
NASA Astrophysics Data System (ADS)
Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.
2011-11-01
DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.
Perspective: Coarse-grained models for biomolecular systems
NASA Astrophysics Data System (ADS)
Noid, W. G.
2013-09-01
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
Coarse-Grained Molecular Models of Water: A Review
Hadley, Kevin R.; McCabe, Clare
2012-01-01
Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601
Coarse-Grained Model for Water Involving a Virtual Site.
Deng, Mingsen; Shen, Hujun
2016-02-01
In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones. PMID:26747089
Entrainment of coarse grains using a discrete particle model
Valyrakis, Manousos; Arnold, Roger B. Jr.
2014-10-06
Conventional bedload transport models and incipient motion theories relying on a time-averaged boundary shear stress are incapable of accounting for the effects of fluctuating near-bed velocity in turbulent flow and are therefore prone to significant errors. Impulse, the product of an instantaneous force magnitude and its duration, has been recently proposed as an appropriate criterion for quantifying the effects of flow turbulence in removing coarse grains from the bed surface. Here, a discrete particle model (DPM) is used to examine the effects of impulse, representing a single idealized turbulent event, on particle entrainment. The results are classified according to the degree of grain movement into the following categories: motion prior to entrainment, initial dislodgement, and energetic displacement. The results indicate that in all three cases the degree of particle motion depends on both the force magnitude and the duration of its application and suggest that the effects of turbulence must be adequately accounted for in order to develop a more accurate method of determining incipient motion. DPM is capable of simulating the dynamics of grain entrainment and is an appropriate tool for further study of the fundamental mechanisms of sediment transport.
Capturing mechanical properties of biological cells using coarse-grained modeling
NASA Astrophysics Data System (ADS)
Mao, Wenbin; Chang, Monique; Alexeev, Alexander
2013-11-01
Understanding cell mechanics is important for a variety of biomedical applications. Our goal is to develop a coarse-grained computational model that can properly capture the micromechanics of biological cells. The coarse-grained cell model includes an elastic shell enclosing a cross-linked polymer network and a viscous fluid representing, respectively, cell membrane, cytoskeleton, and cytoplasm. We use this model to investigate the mechanical response of cells to external forces and compare the results with the experimental AFM measurements. We systematically vary the properties and structure of the internal polymer network and the outer membrane to assess their influence on the cell mechanical responses. This model not only reveals interesting insights into the cell mechanics, but also provides a promising tool for investigation of motile and multicellular systems. Acknowledge financial support from NSF under Award No. 0932510.
Folding of small knotted proteins: Insights from a mean field coarse-grained model
Najafi, Saeed; Potestio, Raffaello
2015-12-28
A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.
Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan
2014-05-14
A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented. PMID:24718295
A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models
Srivastava, Anand; Voth, Gregory A.
2012-01-01
We present a systematic methodology to develop highly coarse-grained (CG) lipid models for large scale bio-membrane simulations, in which we derive CG interactions using a powerful combination of the multiscale coarse-graining (MS-CG) method, and an analytical form of the CG potential to model interactions at short range. The resulting hybrid coarse-graining (HCG) methodology is used to develop a three-site solvent-free model for 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and a 1:1 mixture of 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and DOPC. In addition, we developed a four-site model of DOPC, demonstrating the capability of the HCG methodology in designing model lipid systems of a desired resolution. We carried out microsecond-scale molecular dynamics (MD) simulations of large vesicles, highlighting the ability of the model to study systems at mesoscopic length and time scales. The models of DLPC, DOPC and DOPC-DOPS have elastic properties consistent with experiment and structural properties such as the radial distribution functions (RDF), bond and angle distributions, and the z-density distributions that compare well with reference all-atom systems. PMID:25100925
Coarse-grained DNA modeling: Hybridization and ionic effects
NASA Astrophysics Data System (ADS)
Hinckley, Daniel M.
Deoxyribonucleic acid (DNA) is a biopolymer of enormous significance in living systems. The utility of DNA in such systems is derived from the programmable nature of DNA and its unique mechanical properties. Recently, material scientists have harnessed these properties in order to create systems that spontaneous self-assemble on the nanoscale. Both biologists and material scientists are hindered by an incomplete understanding of the physical interactions that together govern DNA's behavior. Computer simulations, especially those at the coarse-grained (CG) level, can potentially complete this understanding by resolving details indiscernible with current experimental techniques. In this thesis, we advance the state-of-the-art of DNA CG simulations by first reviewing the relevant theory and the evolution of CG DNA models since their inception. Then we present 3SPN.2, an improved CG model for DNA that should provide new insights into biological and nanotechnological systems which incorporate DNA. We perform forward flux sampling simulations in order to examine the effect of sequence, oligomer length, and ionic strength on DNA oligomer hybridization. Due to the limitations inherent in continuum treatments of electrostatic interactions in biological systems, we generate a CG model of biological ions for use with 3SPN.2 and other CG models. Lastly, we illustrate the potential of 3SPN.2 and CG ions by using the models in simulations of viral capsid packaging experiments. The models and results described in this thesis will be useful in future modeling efforts that seek to identify the fundamental physics that govern behavior such as nucleosome positioning, DNA hybridization, and DNA nanoassembly.
Development and application of coarse-grained models for lipids
NASA Astrophysics Data System (ADS)
Cui, Qiang
2013-03-01
I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recent studies of Wong and co-workers, we compare the self-assembly behaviors of lipids with cationic peptides that include either Arg residues or a combination of Lys and hydrophobic residues; in particular, we attempt to reveal factors that stabilize the cubic ``double diamond'' Pn3m phase over the inverted hexagonal HII phase. For example, to explicitly test the importance of the bidentate hydrogen-bonding capability of Arg to the stabilization of negative Gaussian curvature, we also compare results using variants of the BMW-MARTINI model that treat the side chain of Arg with different levels of details. Collectively, the results suggest that both the bidentate feature of Arg and the overall electrostatic properties of cationic peptides are important to the self-assembly behavior of these peptides with lipids. The results are expected to have general implications to the mechanism of peptides and proteins that stimulate pore formation in biomembranes. Work in collaboration with Zhe Wu, Leili Zhang
Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
2015-01-01
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop accurate coarse-grained simulation models that can reach these time scales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0 and 40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudobond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the “angle-corrected model”) slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other
A coarse-grained model for amorphous and crystalline fatty acids
NASA Astrophysics Data System (ADS)
Hadley, K. R.; McCabe, C.
2010-04-01
Fatty acids constitute one of the main components of the lipid lamellae in the top layer of the skin, known as the stratum corneum, which acts as a barrier to foreign substances entering the body and to water leaving the body. To better understand the mechanics of the skin, a molecular-level understanding of the structure of the lamellae needs to be investigated. As a first step toward this goal, the current work involves the development of a coarse-grained model for fatty acids in an amorphous and a crystalline state. In order to retain the structural details of the atomistic molecules, radial distribution functions have been used to provide target data against which the coarse-grained force field is optimized. The optimization was achieved using the method developed by Reith, Pütz, and Müller-Plathe with a damping factor introduced into the updating scheme to facilitate the convergence against the crystalline radial distribution functions. Using this approach, a transferable force field has been developed for both crystalline and amorphous systems that can be used to describe fatty acids of different chain lengths. We are unaware of any other coarse-grained model in the literature that has been developed to study solid phases. Additionally, the amorphous force field has been shown to accurately model mixtures of different free fatty acids based on the potentials derived from pure lipid systems.
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.
2015-06-28
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties.
Shen, Hujun; Li, Yan; Ren, Pengyu; Zhang, Dinglin; Li, Guohui
2014-02-10
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927
Properties of Coarse-Grained Polymer Models: Statics, Dynamics, and Crystallinity
NASA Astrophysics Data System (ADS)
Grest, Gary; Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora
2015-03-01
To capture large length and time scales, coarse-grained (CG) models that combine multiple atoms into one bead have been developed to model polymer melts. In the process microscopic detail is discarded in exchange for computational efficiency. However it is not well-understood how the scale of coarse-graining affects the polymer structure and dynamics. We compare results of atomistic simulations with CG models in which each CG bead represents three, four, or six methylene groups for C96H194, C480H962,andC960H1922. The CG potential is developed at 500K by iterative Boltzmann inversion. While static properties such as end-to-end distance and radius of gyration are captured by all CG models, the entanglement length deviates from experimental results with increased CG scale. The mean squared displacement of CG models is used to determine scale factors between the atomistic and CG models. During cooling to low temperature, the three and four-carbon models form a semi-crystalline structure while the six-carbon model and a four-carbon model based on the MARTINI force field remain amorphous at all temperatures. These findings show that the level of coarse-graining and CG interactions can strongly affect model temperature transferability. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.
Moritsugu, Kei; Smith, Jeremy C
2008-08-01
Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations. PMID:18469078
Systematic coarse-graining of the wormlike chain model for dynamic simulations
NASA Astrophysics Data System (ADS)
Koslover, Elena; Spakowitz, Andrew
2014-03-01
One of the key goals of macromolecular modeling is to elucidate how macroscale physical properties arise from the microscale behavior of the polymer constituents. For many biological and industrial applications, a direct simulation approach is impractical due to to the wide range of length and time scales that must be spanned by the model, necessitating physically sound and practically relevant procedures for coarse-graining polymer systems. We present a highly general systematic coarse-graining procedure that maps any detailed polymer model onto effective elastic-chain models at intermediate and large length scales, and we specifically focus on the wormlike chain model of semiflexible polymers. Our approach defines a continuous flow of coarse-grained models starting from the wormlike chain model, proceeding through an intermediate-scale stretchable, shearable wormlike chain, and finally resolving to a Gaussian chain at the longest lengths. Using Brownian dynamic simulations of our coarse grained polymer, we show that this approach to coarse graining the wormlike chain model captures analytical predictions for stress relaxation in a semiflexible polymer. Since we can arbitrarily coarse grain the polymer in these dynamic simulations, our approach greatly accelerates simulations.
Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.
2015-04-21
Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that
Distributions of experimental protein structures on coarse-grained free energy landscapes
NASA Astrophysics Data System (ADS)
Sankar, Kannan; Liu, Jie; Wang, Yuan; Jernigan, Robert L.
2015-12-01
Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments
Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.
2016-01-01
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior. PMID:26971574
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments
NASA Astrophysics Data System (ADS)
Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.
2016-03-01
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.
Coarse-grained model for the interconversion between different crystalline cellulose allomorphs
Langan, Paul
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.
Necessity of high-resolution for coarse-grained modeling of flexible proteins.
Jia, Zhiguang; Chen, Jianhan
2016-07-01
The popular MARTINI coarse-grained (CG) force field requires the protein structure to be fixed, and is unsuitable for simulating dynamic processes such as protein folding. Here, we examine the feasibility of developing a flexible protein model within the MARTINI framework. The results demonstrate that the MARTINI CG scheme does not properly describe the volume and packing of protein backbone and side chains and leads to excessive collapse without structural restraints in explicit CG water. Combining atomistic protein representation with the MARTINI CG solvent, such as in the PACE model, dramatically improves description of flexible protein conformations. Yet, the CG solvent is insufficient to capture the conformational dependence of protein-solvent interactions, and PACE is unable to properly model context dependent conformational transitions. Taken together, high physical resolution at or near the atomistic level is likely necessary for flexible protein models with explicit, microscopic solvents, and the coarse-graining needs to focus on possible simplification in interaction potentials. © 2016 Wiley Periodicals, Inc. PMID:27130454
A Coarse-Grained Protein Model in a Water-like Solvent
NASA Astrophysics Data System (ADS)
Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene
2013-05-01
Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.
On the representability problem and the physical meaning of coarse-grained models.
Wagner, Jacob W; Dama, James F; Durumeric, Aleksander E P; Voth, Gregory A
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. PMID:27475349
Parameterizing the Morse potential for coarse-grained modeling of blood plasma
Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan
2014-01-15
Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.
Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma
Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan
2014-01-01
Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately. PMID:24910470
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. PMID:25353565
NASA Astrophysics Data System (ADS)
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 N2-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N2 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.
Shen, Lin; Yang, Weitao
2016-04-12
We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer. PMID:26930454
Coarse Grained Approach to First Principles Modeling of Radiation Cascade in Large Fe Supercells
NASA Astrophysics Data System (ADS)
Odbadrakh, Kh; Nicholson, D. M.; Rusanu, A.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X.-G.; Stocks, G. M.
2012-12-01
Classical Molecular Dynamics (MD) simulations characterizing dislocations and radiation damage typically treat 105-107 atoms. First principles techniques employed to understand systems at an atomistic level are not practical for such large systems consisting of millions of atoms. We present an efficient coarse grained (CG) approach to calculate local electronic and magnetic properties of large MD-generated structures from the first principles. Local atomic magnetic moments in crystalline Fe are perturbed by the presence of radiation generated vacancies and interstitials. The effects are most pronounced near the defect cores and decay slowly as the strain field of the defects decrease with distance. We develop the CG technique based on the Locally Self-consistent Multiple Scattering (LSMS) method that exploits the near-sightedness of the electron Green function. The atomic positions were determined by MD with an embedded atom force field. The local moments in the neighborhood of the defect cores are calculated with first-principles based on full local structure information. Atoms in the rest of the system are modeled by representative atoms with approximated properties. The calculations result in local moments near the defect centers with first-principles accuracy, while capturing coarse-grained details of local moments at greater length scales. This CG approach makes these large scale structures amenable to first principles study.
Bathe, Mark; Rutledge, Gregory C.; Grodzinsky, Alan J.; Tidor, Bruce
2005-01-01
A coarse-grained molecular model is presented for the study of the equilibrium conformation and titration behavior of chondroitin (CH), chondroitin sulfate (CS), and hyaluronic acid (HA)—glycosaminoglycans (GAGs) that play a central role in determining the structure and biomechanical properties of the extracellular matrix of articular cartilage. Systematic coarse-graining from an all-atom description of the disaccharide building blocks retains the polyelectrolytes' specific chemical properties while enabling the simulation of high molecular weight chains that are inaccessible to all-atom representations. Results are presented for the characteristic ratio, the ionic strength-dependent persistence length, the pH-dependent expansion factor for the end-to-end distance, and the titration behavior of the GAGs. Although 4-sulfation of the N-acetyl-D-galactosamine residue is found to increase significantly the intrinsic stiffness of CH with respect to 6-sulfation, only small differences in the titration behavior of the two sulfated forms of CH are found. Persistence length expressions are presented for each type of GAG using a macroscopic (wormlike chain-based) and a microscopic (bond vector correlation-based) definition. Model predictions agree quantitatively with experimental conformation and titration measurements, which support use of the model in the investigation of equilibrium solution properties of GAGs. PMID:15805173
NASA Astrophysics Data System (ADS)
Keten, Sinan; Xia, Wenjie; Hsu, David
2015-03-01
We present a systematic, two-bead per monomer coarse graining strategy that simulates the thermomechanical behavior of polymers several hundred times faster than all-atom MD (Hsu et al. JCTC, 2014). The predictive capability of the technique is illustrated here for 5 different methacrylate monomers and polystyrene stereoisomers. The approach involves optimization of analytical bonded potentials from atomistic bonded distributions to emulate local structure, as validated by chain end-to-end length and the radius of gyration comparisons with experiments and random coil theory. Nonbonded Lennard-Jones potentials are tuned to reproduce the elastic modulus (E) and glass transition temperature (Tg) at a single thermodynamic state. Density-corrected parameters capture temperature-modulus dependence in the 150-600 K range. Flory-Fox constants of the CG models are commensurate with all atomistic and experimental results, even though all calibrations are done at a single molecular weight. Finally, we further demonstrate the predictive capabilities of the models by examining thin film nanoconfinement effects for different polymers, film thicknesses, interfacial energies, and molecular weights. Our technique, called thermomechanically consistent coarse graining (TCCG), is demonstrated, using polystyrene and poly(methylmethacrylate) as universal benchmarks, to be a robust and effective technique to understand the thermomechanical behavior of polymers thin films and nanocomposites.
NASA Astrophysics Data System (ADS)
Zimmermann, Eva; Seifert, Udo
2015-02-01
Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F1-ATPase and the kinesin motor.
A coarse-grained model of the 10-23 DNAzyme
NASA Astrophysics Data System (ADS)
Dorfman, Kevin; Kenward, Martin
2010-03-01
DNAzymes are single-stranded DNA that catalyze nucleic acid biochemistry. We have adopted a simple bead-spring model that captures, in a coarse-grained manner, the diffusive motion and self-interactions of single-stranded DNA. We used this model to investigate the structure and dynamics of the RNA cleaving 10-23 DNAzyme over long time scales via Brownian dynamics simulations. We start from an unfolded state where the DNAzyme is bound to its substrate and allow the system to relax. The structural data thus obtained agree well with FRET measurements and provide a connection between the proposed structure of the DNAzyme and chemical rate data appearing in the literature. We have also investigated the changes in the structure of the DNAzyme/substrate complex following the cleavage of the substrate. In agreement with single-molecule FRET data, we find that the DNAzyme rapidly unwinds into an extended structure.
Bottom-up coarse-graining of a simple graphene model: the blob picture.
Kauzlarić, David; Meier, Julia T; Español, Pep; Succi, Sauro; Greiner, Andreas; Korvink, Jan G
2011-02-14
The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined. PMID:21322660
A polarizable coarse-grained protein model for dissipative particle dynamics.
Peter, Emanuel K; Lykov, Kirill; Pivkin, Igor V
2015-10-01
We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece. PMID:26339692
Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes
NASA Astrophysics Data System (ADS)
Almutairi, Amani; Luettmer-Strathmann, Jutta
The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules
Grünberger, Alexander; Lai, Pin-Kuang; Blanco, Marco A; Roberts, Christopher J
2013-01-24
A series of coarse-grained models, with different levels of structural resolution, were tested to calculate the steric contributions to protein osmotic second virial coefficients (B(22,S)) for proteins ranging from small single-domain molecules to large multidomain molecules, using the recently developed Mayer sampling method. B(22,S) was compared for different levels of coarse-graining: four-beads-per-amino-acid (4bAA), one-bead-per-amino-acid (1bAA), one-sphere-per-domain (1sD), and one-sphere-per-protein (1sP). Values for the 1bAA and 4bAA models were quantitatively indistinguishable for both spherical and nonspherical proteins, and the agreement with values from all-atom models improved with increasing protein size, making the CG approach attractive for large proteins of biotechnological interest. Interestingly, in the absence of detailed structural information, the hydrodynamic radius (R(h)) along with a simple 1sP approximation provided reasonably accurate values for B(22,S) for both globular and highly asymmetric protein structures, while other 1sP approximations gave poorer agreement; this helps to justify the currently empirical practice of estimating B(22,S) from R(h) for large proteins such as antibodies. The results also indicate that either 1bAA or 4bAA CG models may be good starting points for incorporating short-range attractions. Comparison of gD-crystallin B(22) values including both sterics and short-range attractions shows that 1bAA and 4bAA models give equivalent results when properly scaled to account for differences in the number of surface beads in the two CG descriptions. This provides a basis for future work that will also incorporate long-ranged electrostatic attractions and repulsions. PMID:23245189
Coarse grain modeling of imperfect networks and gels
NASA Astrophysics Data System (ADS)
Sliozberg, Yelena; Chantawansri, Tanya; Sirk, Timothy; Andzelm, Jan; Mrozek, Randy; Lenhart, Joseph
2013-03-01
There is a strong interest in chemically and physically cross-linked entangled polymer networks and gels due to their tailorability in respect to both mechanical and structural properties. Even so, these properties are sensitive to imperfections in the polymer networks, such as dangling ends and loops. Computational modeling is a viable tool to understand the effects of these imperfections on properties in a controlled environment, in which specific defects can be systematically created and varied. In this study, we have employed generic bead-spring models of flexible chains to study a chemically and physically cross-linked network. Our results will show the importance defects, such as dangling ends and loops, on the mechanical and structural properties of these networks. We will also discuss the effects of these defects on the time-dependent elastic modulus. The simulation results qualitatively agree with experimental results and the other theoretical predictions.
Bridging scales: from atoms to coarse-grained models for soft matter systems
NASA Astrophysics Data System (ADS)
Peter, Christine
2015-03-01
Molecular simulation has extended to increasingly complex soft matter systems, and time-scale and system-size requirements have instigated the use of simulation models on multiple levels of resolution. On the classical particle-based level, a large variety of methods to develop coarse grained (CG) simulation models has emerged, an important subgroup being those scale-bridging methods where the CG model is derived from and systematically linked to an underlying atomistic description. In my talk, I will introduce a few of these methods, address the underlying concepts as well as some of the ongoing challenges that are inherent to coarse graining. A natural consequence of reducing the level of resolution in a simulation model is a loss of transferability, i.e. a decreasing ability to correctly describe a system at several thermodynamic state points. Intimately linked to this is a loss of the ability to correctly represent all structural, thermodynamic and dynamic properties of the system. Examples for these limitations are easily found in all CG simulations of multicomponent or multiphase soft matter systems - ranging from liquid crystals, biomolecular aggregates, biomaterials to hard/soft nanocomposites. A correct representation of phase transitions, phase coexistence, environment-induced conformational transitions, or effects due to surfaces and interfaces is a severe challenge for bottom-up CG models. Addressing this challenge requires both a method of generating CG potentials as well as finding and rationalizing an appropriate reference state point to start out from. I will illustrate several of these aspects using examples from the biomolecular and (biomimetic-) materials world.
Coarse-grained variables for particle-based models: diffusion maps and animal swarming simulations
NASA Astrophysics Data System (ADS)
Liu, Ping; Safford, Hannah R.; Couzin, Iain D.; Kevrekidis, Ioannis G.
2014-12-01
As microscopic (e.g. atomistic, stochastic, agent-based, particle-based) simulations become increasingly prevalent in the modeling of complex systems, so does the need to systematically coarse-grain the information they provide. Before even starting to formulate relevant coarse-grained equations, we need to determine the right macroscopic observables—the right variables in terms of which emergent behavior will be described. This paper illustrates the use of data mining (and, in particular, diffusion maps, a nonlinear manifold learning technique) in coarse-graining the dynamics of a particle-based model of animal swarming. Our computational data-driven coarse-graining approach extracts two coarse (collective) variables from the detailed particle-based simulations, and helps formulate a low-dimensional stochastic differential equation in terms of these two collective variables; this allows the efficient quantification of the interplay of "informed" and "naive" individuals in the collective swarm dynamics. We also present a brief exploration of swarm breakup and use data-mining in an attempt to identify useful predictors for it. In our discussion of the scope and limitations of the approach we focus on the key step of selecting an informative metric, allowing us to usefully compare different particle swarm configurations.
Model reduction for agent-based social simulation: coarse-graining a civil violence model.
Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G
2012-06-01
Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20). PMID:23005161
Model reduction for agent-based social simulation: Coarse-graining a civil violence model
NASA Astrophysics Data System (ADS)
Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.
2012-06-01
Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).
Heterogeneous lamella structure unites ultrafine-grain strength with coarse-grain ductility
Wu, Xiaolei; Yang, Muxin; Yuan, Fuping; Wu, Guilin; Wei, Yujie; Huang, Xiaoxu; Zhu, Yuntian
2015-01-01
Grain refinement can make conventional metals several times stronger, but this comes at dramatic loss of ductility. Here we report a heterogeneous lamella structure in Ti produced by asymmetric rolling and partial recrystallization that can produce an unprecedented property combination: as strong as ultrafine-grained metal and at the same time as ductile as conventional coarse-grained metal. It also has higher strain hardening than coarse-grained Ti, which was hitherto believed impossible. The heterogeneous lamella structure is characterized with soft micrograined lamellae embedded in hard ultrafine-grained lamella matrix. The unusual high strength is obtained with the assistance of high back stress developed from heterogeneous yielding, whereas the high ductility is attributed to back-stress hardening and dislocation hardening. The process discovered here is amenable to large-scale industrial production at low cost, and might be applicable to other metal systems. PMID:26554017
Heterogeneous lamella structure unites ultrafine-grain strength with coarse-grain ductility.
Wu, Xiaolei; Yang, Muxin; Yuan, Fuping; Wu, Guilin; Wei, Yujie; Huang, Xiaoxu; Zhu, Yuntian
2015-11-24
Grain refinement can make conventional metals several times stronger, but this comes at dramatic loss of ductility. Here we report a heterogeneous lamella structure in Ti produced by asymmetric rolling and partial recrystallization that can produce an unprecedented property combination: as strong as ultrafine-grained metal and at the same time as ductile as conventional coarse-grained metal. It also has higher strain hardening than coarse-grained Ti, which was hitherto believed impossible. The heterogeneous lamella structure is characterized with soft micrograined lamellae embedded in hard ultrafine-grained lamella matrix. The unusual high strength is obtained with the assistance of high back stress developed from heterogeneous yielding, whereas the high ductility is attributed to back-stress hardening and dislocation hardening. The process discovered here is amenable to large-scale industrial production at low cost, and might be applicable to other metal systems. PMID:26554017
Yang, Lee-Wei; Chng, Choon-Peng
2008-01-01
In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764
Messer, Benjamin M.; Roca, Maite; Chu, Zhen T.; Vicatos, Spyridon; Kilshtain, Alexandra Vardi; Warshel, Arieh
2009-01-01
Evaluating the free energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al, Theor Chem Acc (1999) 103:77-80) uses the CG model as a reference potential for free energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. This application includes: evaluation of changes of folding energy upon mutations, calculations of transition states binding free energies (which are crucial for rational enzyme design), evaluation of catalytic landscape and simulation of the time dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. PMID:20052756
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
NASA Astrophysics Data System (ADS)
Wei, Zonghui; Luijten, Erik
2015-12-01
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Wei, Zonghui; Luijten, Erik
2015-12-28
All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
NASA Astrophysics Data System (ADS)
Lin, Yen Ting; Doering, Charles R.
2016-02-01
We present a theoretical framework to analyze the dynamics of gene expression with stochastic bursts. Beginning with an individual-based model which fully accounts for the messenger RNA (mRNA) and protein populations, we propose an expansion of the master equation for the joint process. The resulting coarse-grained model reduces the dimensionality of the system, describing only the protein population while fully accounting for the effects of discrete and fluctuating mRNA population. Closed form expressions for the stationary distribution of the protein population and mean first-passage times of the coarse-grained model are derived and large-scale Monte Carlo simulations show that the analysis accurately describes the individual-based process accounting for mRNA population, in contrast to the failure of commonly proposed diffusion-type models.
Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei
2016-02-01
In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419
A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature
NASA Astrophysics Data System (ADS)
Huang, Wenjun; Larson, Ronald
Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.
A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.
Genheden, Samuel; Essex, Jonathan W
2015-10-13
We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264
Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik
2016-01-01
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general. PMID:27578633
Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling.
Zacharias, Martin
2013-01-01
A hybrid coarse-grained (CG) and atomistic (AT) model for protein simulations and rapid searching and refinement of peptide-protein complexes has been developed. In contrast to other hybrid models that typically represent spatially separate parts of a protein by either a CG or an AT force field model, the present approach simultaneously represents the protein by an AT (united atom) and a CG model. The interactions of the protein main chain are described based on the united atom force field allowing a realistic representation of protein secondary structures. In addition, the AT description of all other bonded interactions keeps the protein compatible with a realistic bonded geometry. Nonbonded interactions between side chains and side chains and main chain are calculated at the level of a CG model using a knowledge-based potential. Unrestrained molecular dynamics simulations on several test proteins resulted in trajectories in reasonable agreement with the corresponding experimental structures. Applications to the refinement of docked peptide-protein complexes resulted in improved complex structures. Application to the rapid refinement of docked protein-protein complex is also possible but requires further optimization of force field parameters. PMID:22911567
Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
Schreck, John S; Romano, Flavio; Zimmer, Matthew H; Louis, Ard A; Doye, Jonathan P K
2016-04-26
We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology. PMID:27010928
Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine
2013-12-21
One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.
Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet
2013-12-21
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. PMID:24359360
NASA Astrophysics Data System (ADS)
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.
Generalized coarse-grained model based on point multipole and Gay-Berne potentials
NASA Astrophysics Data System (ADS)
Golubkov, Pavel A.; Ren, Pengyu
2006-08-01
This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers.
Generalized coarse-grained model based on point multipole and Gay-Berne potentials.
Golubkov, Pavel A; Ren, Pengyu
2006-08-14
This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers. PMID:16942269
Coarse-Grain Model Simulations of Nonequilibrium Dynamics in Heterogeneous Materials.
Brennan, John K; Lísal, Martin; Moore, Joshua D; Izvekov, Sergei; Schweigert, Igor V; Larentzos, James P
2014-06-19
A suite of computational tools is described for particle-based mesoscale simulations of the nonequilibrium dynamics of energetic solids, including mechanical deformation, phase transitions, and chemical reactivity triggered by shock or thermal loading. The method builds upon our recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics (DPD) that includes chemical reactions. To describe chemical reactivity, a coarse-grain particle equation-of-state was introduced into the constant-energy DPD variant that rigorously treats complex chemical reactions and the associated chemical energy release. As illustration of these developments, we present simulations of shock compression of an RDX crystal and its thermal decomposition under high temperatures. We also discuss our current efforts toward a highly scalable domain-decomposition implementation that extends applicability to micrometer-size simulations. With appropriate parametrization, the method is applicable to other materials whose dynamic response is driven by microstructural heterogeneities. PMID:26270506
Global- and local-scale characterisation of bed surface structure in coarse-grained alluvial rivers
NASA Astrophysics Data System (ADS)
Powell, Mark; Ockelford, Annie; Nguyen, Thao; Wood, Jo; Rice, Steve; Reid, Ian; Tate, Nick
2013-04-01
It is widely recognised that adjustments in bed surface grain size (texture) and grain arrangement (structure) exert significant controls on the stability of coarse-grained alluvial rivers. Modifications to bed surface texture and structure occur during active sediment transport and are mediated by the process of mobile armouring which concentrates coarser-than-average particles on the surface and organises them into a variety of grain- and bedform-scale configurations. Textural aspects of surface armouring are well understood to the extent that sediment transport models can be used to predict the size distribution of armours that develop under different sediment supply regimes and shear stresses. Research has also found that the adjustment of bed surface grain size is often patchy and that the development of finer-grained and coarser-grained areas of the bed has important implications for both the rate and grain size of transported sediment. The structural aspects of stream-bed armouring, however, are less well understood, largely because of the difficulty of recognising and characterising bedforms and bed-structures that have dimensions similar to their constituent particles. Moreover, bed structure is generally parameterised using global scale descriptors of the bed surface such that information on the spatial heterogeneity of the structure is lost. The aim of this poster is to characterise the structural characteristics of water-worked river gravels, paying particular attention to quantifying the spatial heterogeneity of those characteristics using local scale descriptors. Results reported from a number of flume experiments designed to simulate the spatio-temporal evolution of bed configurations (surface texture and structure) as the system adjusts to a condition of equilibrium transport are used to evaluate the spatial variability of bed surface structure and explore its significance for modelling sediment transport rates in gravel-bed rivers. Keywords: bed
Calero-Rubio, Cesar; Saluja, Atul; Roberts, Christopher J
2016-07-14
So-called "weak" protein-protein interactions are important for the control of solution properties and stability at elevated protein concentrations (c2) but are not practical to capture in atomistic simulations. This report focuses on a series of coarse-grained models for predicting second osmotic virial coefficients (B22) and high-concentration Rayleigh scattering (osmotic compressibility) as a function of c2 for monoclonal antibodies (MAbs) that are of interest in biotechnology. B22 and molecular volume along with c2-dependent osmotic compressibility were calculated for a series of models with increasing structural detail. Models were refined to include contributions from sterics, short-ranged van der Waals and hydrophobic attractions, screened electrostatics, and the flexibility of the mAb hinge region. The results highlight shortcomings for spherical models of MAbs and a useful balance between numerical accuracy and computational burden offered by models based on 6 or 12 spherical, partly overlapping domains. The results provide bounds for realistic values of effective charges on variable domains in order for MAbs to be stable in solution and more generally illustrate semiquantitative bounds for the space of model parameters that can reproduce experimental behavior and provide a basis for future development of computationally efficient and accurate CG mAb models to predict both low- and high-c2 behavior. PMID:27314827
Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models
NASA Astrophysics Data System (ADS)
D'Adamo, G.; Menichetti, R.; Pelissetto, A.; Pierleoni, C.
2015-09-01
We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density and density-dependent pair potentials. We highlight advantages and limitations of each option in reproducing the thermodynamic behavior and the large-scale structure of the underlying reference model. As a case study we consider solutions of linear homopolymers in a solvent of variable quality. Secondly, we extend the discussion to multi-component systems presenting, as a test case, results for mixtures of colloids and polymers. Specifically, we found the CG model with zero-density potentials to be unable to predict fluid-fluid demixing in a reasonable range of densities for mixtures of colloids and polymers of equal size. For larger colloids, the polymer volume fractions at which phase separation occurs are largely overestimated. CG models with density-dependent potentials are somewhat less accurate than models with zero-density potentials in reproducing the thermodynamics of the system and, although they present a phase separation, they significantly underestimate the polymer volume fractions along the binodal. Finally, we discuss a general multi-site strategy, which is thermodynamically consistent and fully transferable with the number of sites, and that allows us to overcome most of the limitations discussed for single-site models.
Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi
2014-03-01
We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. PMID:24418347
Coarse-grained models of stripe forming systems: Phase diagrams, anomalies, and scaling hypothesis
NASA Astrophysics Data System (ADS)
Mendoza-Coto, Alejandro; Stariolo, Daniel A.
2012-11-01
Two coarse-grained models which capture some universal characteristics of stripe forming systems are studied. At high temperatures, the structure factors of both models attain their maxima on a circle in reciprocal space, as a consequence of generic isotropic competing interactions. Although this is known to lead to some universal properties, we show that the phase diagrams have important differences, which are a consequence of the particular k⃗ dependence of the fluctuation spectrum in each model. The phase diagrams are computed in a mean field approximation and also after inclusion of small fluctuations, which are shown to modify drastically the mean field behavior. Observables like the modulation length and magnetization profiles are computed for the whole temperature range accessible to both models and some important differences in behavior are observed. A stripe compression modulus is computed, showing an anomalous behavior with temperature as recently reported in related models. Also, a recently proposed scaling hypothesis for modulated systems is tested and found to be valid for both models studied.
Thermodynamically Consistent Coarse-Graining of Polymers
NASA Astrophysics Data System (ADS)
Guenza, Marina
2015-03-01
Structural and dynamical properties of macromolecular liquids, melts and mixtures, bridge an extensive range of length- and time-scales. For these systems, the computational limitations of the atomistic description prevent the study of the properties of interest and coarse-grained models remain the only viable approach. In coarse-grained models, structural and thermodynamic consistency across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. This talk presents a coarse-graining approach that conserves structural and thermodynamic quantities independent of the extent of coarse-graining, and describes a model for the reconstruction of the dynamics measured in mesoscale simulations of the coarse-grained system. Some of the general challenges of preserving structural and thermodynamic consistency in coarse-grained models are discussed together with the conditions by which the problem is lessened. This material is based upon work partially supported by the National Science Foundation under Grant No. CHE-1362500.
Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
Daily, Michael D.; Olsen, Brett N.; Schlesinger, Paul H.; Ory, Daniel S.; Baker, Nathan A.
2014-03-24
In mammalian cells cholesterol is essential for membrane function, but in excess can be cytototoxic. The cellular response to acute cholesterol loading involves biophysical-based mechanisms that regulate cholesterol levels, through modulation of the “activity” or accessibility of cholesterol to extra-membrane acceptors. Experiments and united atom (UA) simulations show that at high concentrations of cholesterol, lipid bilayers thin significantly and cholesterol availability to external acceptors increases substantially. Such cholesterol activation is critical to its trafficking within cells. Here we aim to reduce the computational cost to enable simulation of large and complex systems involved in cholesterol regulation, such as those including oxysterols and cholesterol-sensing proteins. To accomplish this, we have modified the published MARTINI coarse-grained force field to improve its predictions of cholesterol-induced changes in both macroscopic and microscopic properties of membranes. Most notably, MARTINI fails to capture both the (macroscopic) area condensation and membrane thickening seen at less than 30% cholesterol and the thinning seen above 40% cholesterol. The thinning at high concentration is critical to cholesterol activation. Microscopic properties of interest include cholesterol-cholesterol radial distribution functions (RDFs), tilt angle, and accessible surface area. First, we develop an “angle-corrected” model wherein we modify the coarse-grained bond angle potentials based on atomistic simulations. This modification significantly improves prediction of macroscopic properties, most notably the thickening/thinning behavior, and also slightly improves microscopic property prediction relative to MARTINI. Second, we add to the angle correction a “volume correction” by also adjusting phospholipid bond lengths to achieve a more accurate volume per molecule. The angle + volume correction substantially further improves the quantitative
First-principles theory, coarse-grained models, and simulations of ferroelectrics.
Waghmare, Umesh V
2014-11-18
large-scale simulations while capturing the relevant microscopic interactions quantitatively. In this Account, we first summarize the insights obtained into chemical mechanisms of ferroelectricity using first-principles DFT calculations. We then discuss the principles of construction of first-principles model Hamiltonians for ferroelectric phase transitions in perovskite oxides, which involve coarse-graining in time domain by integrating out high frequency phonons. Molecular dynamics simulations of the resulting model are shown to give quantitative predictions of material-specific ferroelectric transition behavior in bulk as well as nanoscale ferroelectric structures. A free energy landscape obtained through coarse-graining in real-space provides deeper understanding of ferroelectric transitions, domains, and states with inhomogeneous order and points out the key role of microscopic coupling between phonons and strain. We conclude with a discussion of the multiscale modeling strategy elucidated here and its application to other materials such as shape memory alloys. PMID:25361389
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.
Pasi, Marco; Lavery, Richard; Ceres, Nicoletta
2013-01-01
We present a coarse-grain protein model PaLaCe (Pasi-Lavery-Ceres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes. PMID:26589071
Stretching and twisting of the DNA duplexes in coarse-grained dynamical models.
Niewieczerzał, Szymon; Cieplak, Marek
2009-11-25
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching-unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations. PMID:21832500
Stretching and twisting of the DNA duplexes in coarse-grained dynamical models
NASA Astrophysics Data System (ADS)
Niewieczerzał, Szymon; Cieplak, Marek
2009-11-01
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching—unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They all show similar behaviour, but the bigger the resolution, the more details in the force patterns. The models incorporate the effective Lennard-Jones potentials in the couplings between two strands and harmonic potentials to describe the structure of a single strand. The force patterns are shown to depend on the sequence studied. In particular, both shearing and unzipping for an all-AT sequence lead to lower forces than for an all-CG sequence. The unzipping patterns and the corresponding scenario diagrams for the contact rupture events are found to reflect the sequential information if the temperature is moderate and initial transients are discarded. The derived torque-force phase diagram is found to be qualitatively consistent with experiments and all-atom simulations.
Hammond, N. A.
2008-01-01
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 β-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 β-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. PMID:18440063
NASA Astrophysics Data System (ADS)
Song, Bin; Molinero, Valeria
2013-08-01
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 generalized-Yvon-Born-Green method for coarse-grained modeling. Advances, Challenges, and Insight
NASA Astrophysics Data System (ADS)
Rudzinski, J. F.; Noid, W. G.
2015-09-01
The Yvon-Born-Green (YBG) integral equation is a basic result of liquid state theory that relates the pair potential of a simple fluid to the resulting equilibrium two- and three-body correlation functions. Quite recently, we derived a more general form that can be applied to complex molecular systems. This generalized-YBG (g-YBG) theory provides not only an exact relation between a given potential and the resulting equilibrium correlation functions, but also a remarkably powerful framework for directly solving the statistical mechanics inverse problem of determining potentials from equilibrium structure ensembles. In the context of coarse-grained (CG) modeling, the g-YBG theory determines a variationally optimal approximation to the many-body potential of mean force directly (i.e., noniteratively) from structural correlation functions and, in particular, allows "force-matching" without forces. While our initial efforts numerically validated the g-YBG theory with relatively simple systems, our more recent efforts have considered increasingly complex systems, such as peptides and polymers. This minireview summarizes this progress and the resulting insight, as well as discusses the outstanding challenges and future directions for the g-YBG theory.
NASA Astrophysics Data System (ADS)
Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.
2016-02-01
Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.
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, c{sub 0}. A numerical solution to the PRISM integral equations is used to determine c{sub 0}, by adjusting the value of the effective hard sphere diameter, d{sub HS}, 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.
A coarse-grained transport model for neutral particles in turbulent plasmas
Mekkaoui, A.; Reiter, D.; Boerner, P.; Marandet, Y.; Genesio, P.; Rosato, J.; Capes, H.; Koubiti, M.; Godbert-Mouret, L.; Stamm, R.
2012-12-15
The transport of neutral particles in turbulent plasmas is addressed from the prospect of developing coarse-grained transport models which can be implemented in code suites like B2-EIRENE, currently used for designing the ITER divertor. The statistical properties of turbulent fluctuations are described by a multivariate Gamma distribution able to retain space and time correlations through a proper choice of covariance function. We show that in the scattering free case, relevant for molecules and impurity atoms, the average neutral particle density obeys a Boltzmann equation with an ionization rate renormalized by fluctuations. This result lends itself to a straightforward implementation in the EIRENE Monte Carlo solver for neutral particles. Special emphasis is put on the inclusion of time correlations, and in particular on the ballistic motion of coherent turbulent structures. The role of these time dependent effects is discussed for D{sub 2} molecules and beryllium atoms. The sensitivity of our results to the assumptions on the statistical properties of fluctuations is investigated.
Li, Xianfeng; Latour, Robert A.
2009-01-01
A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 102, thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications. PMID:20161121
A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.
Riniker, Sereina; van Gunsteren, Wilfred F
2011-02-28
The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models. PMID:21361530
Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation
Globisch, Christoph; Krishnamani, Venkatramanan; Deserno, Markus; Peter, Christine
2013-01-01
The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable. PMID:23613730
Coarse-graining methods for computational biology.
Saunders, Marissa G; Voth, Gregory A
2013-01-01
Connecting the molecular world to biology requires understanding how molecular-scale dynamics propagate upward in scale to define the function of biological structures. To address this challenge, multiscale approaches, including coarse-graining methods, become necessary. We discuss here the theoretical underpinnings and history of coarse-graining and summarize the state of the field, organizing key methodologies based on an emerging paradigm for multiscale theory and modeling of biomolecular systems. This framework involves an integrated, iterative approach to couple information from different scales. The primary steps, which coincide with key areas of method development, include developing first-pass coarse-grained models guided by experimental results, performing numerous large-scale coarse-grained simulations, identifying important interactions that drive emergent behaviors, and finally reconnecting to the molecular scale by performing all-atom molecular dynamics simulations guided by the coarse-grained results. The coarse-grained modeling can then be extended and refined, with the entire loop repeated iteratively if necessary. PMID:23451897
D’Adamo, Giuseppe; Pelissetto, Andrea; Pierleoni, Carlo
2014-12-28
A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach, groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to reproduce some large-scale structural properties in the zero-density limit. We show that an accurate parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained (CG) model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmann inversion scheme, taking full-monomer (FM) pair correlation functions at zero-density as targets. For a larger number n of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite accurate for q ≲ 1 (q=R{sup ^}{sub g}/R{sub c}, where R{sup ^}{sub g} is the zero-density polymer radius of gyration and R{sub c} is the colloid radius) and reasonably good also for q = 2. For q = 2, an accurate coarse-grained description is obtained by using the n = 10 blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.
Computational Study of Uniaxial Deformations in Silica Aerogel Using a Coarse-Grained Model.
Ferreiro-Rangel, Carlos A; Gelb, Lev D
2015-07-01
Simulations of a flexible coarse-grained model are used to study silica aerogels. This model, introduced in a previous study (J. Phys. Chem. C 2007, 111, 15792), consists of spherical particles which interact through weak nonbonded forces and strong interparticle bonds that may form and break during the simulations. Small-deformation simulations are used to determine the elastic moduli of a wide range of material models, and large-deformation simulations are used to probe structural evolution and plastic deformation. Uniaxial deformation at constant transverse pressure is simulated using two methods: a hybrid Monte Carlo approach combining molecular dynamics for the motion of individual particles and stochastic moves for transverse stress equilibration, and isothermal molecular dynamics simulations at fixed Poisson ratio. Reasonable agreement on elastic moduli is obtained except at very low densities. The model aerogels exhibit Poisson ratios between 0.17 and 0.24, with higher-density gels clustered around 0.20, and Young's moduli that vary with aerogel density according to a power-law dependence with an exponent near 3.0. These results are in agreement with reported experimental values. The models are shown to satisfy the expected homogeneous isotropic linear-elastic relationship between bulk and Young's moduli at higher densities, but there are systematic deviations at the lowest densities. Simulations of large compressive and tensile strains indicate that these materials display a ductile-to-brittle transition as the density is increased, and that the tensile strength varies with density according to a power law, with an exponent in reasonable agreement with experiment. Auxetic behavior is observed at large tensile strains in some models. Finally, at maximum tensile stress very few broken bonds are found in the materials, in accord with the theory that only a small fraction of the material structure is actually load-bearing. PMID:26039801
NASA Astrophysics Data System (ADS)
de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; Junghans, Christoph; Mukherji, Debashish
2016-05-01
We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion ( C -IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within C -IBI compared to IBI. To validate the robustness, we apply C -IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.
The impact of resolution upon entropy and information in coarse-grained models
Foley, Thomas T.; Shell, M. Scott; Noid, W. G.
2015-12-28
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, S{sub W}, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into S{sub W}. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, −TS{sub W} is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.
The impact of resolution upon entropy and information in coarse-grained models
NASA Astrophysics Data System (ADS)
Foley, Thomas T.; Shell, M. Scott; Noid, W. G.
2015-12-01
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, SW, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into SW. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, -TSW is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.
Coarse-grained particle model for pedestrian flow using diffusion maps
NASA Astrophysics Data System (ADS)
Marschler, Christian; Starke, Jens; Liu, Ping; Kevrekidis, Ioannis G.
2014-01-01
Interacting particle systems constitute the dynamic model of choice in a variety of application areas. A prominent example is pedestrian dynamics, where good design of escape routes for large buildings and public areas can improve evacuation in emergency situations, avoiding exit blocking and the ensuing panic. Here we employ diffusion maps to study the coarse-grained dynamics of two pedestrian crowds trying to pass through a door from opposite sides. These macroscopic variables and the associated smooth embeddings lead to a better description and a clearer understanding of the nature of the transition to oscillatory dynamics. We also compare the results to those obtained through intuitively chosen macroscopic variables.
Coarse Grained Modeling of The Interface BetweenWater and Heterogeneous Surfaces
Willard, Adam; Chandler, David
2008-06-23
Using coarse grained models we investigate the behavior of water adjacent to an extended hydrophobic surface peppered with various fractions of hydrophilic patches of different sizes. We study the spatial dependence of the mean interface height, the solvent density fluctuations related to drying the patchy substrate, and the spatial dependence of interfacial fluctuations. We find that adding small uniform attractive interactions between the substrate and solvent cause the mean position of the interface to be very close to the substrate. Nevertheless, the interfacial fluctuations are large and spatially heterogeneous in response to the underlying patchy substrate. We discuss the implications of these findings to the assembly of heterogeneous surfaces.
Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling
MacDonald, James T.; Kelley, Lawrence A.; Freemont, Paul S.
2013-01-01
Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http
Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome.
Korolev, Nikolay; Nordenskiöld, Lars; Lyubartsev, Alexander P
2016-06-01
To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed. PMID:26956528
A coarse-grained model to study calcium activation of the cardiac thin filament
NASA Astrophysics Data System (ADS)
Zhang, Jing; Schwartz, Steven
2015-03-01
Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.
Two-Component Coarse-Grained Molecular-Dynamics Model for the Human Erythrocyte Membrane
Li, He; Lykotrafitis, George
2012-01-01
We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane. PMID:22225800
Coding coarse grained polymer model for LAMMPS and its application to polymer crystallization
NASA Astrophysics Data System (ADS)
Luo, Chuanfu; Sommer, Jens-Uwe
2009-08-01
We present a patch code for LAMMPS to implement a coarse grained (CG) model of poly(vinyl alcohol) (PVA). LAMMPS is a powerful molecular dynamics (MD) simulator developed at Sandia National Laboratories. Our patch code implements tabulated angular potential and Lennard-Jones-9-6 (LJ96) style interaction for PVA. Benefited from the excellent parallel efficiency of LAMMPS, our patch code is suitable for large-scale simulations. This CG-PVA code is used to study polymer crystallization, which is a long-standing unsolved problem in polymer physics. By using parallel computing, cooling and heating processes for long chains are simulated. The results show that chain-folded structures resembling the lamellae of polymer crystals are formed during the cooling process. The evolution of the static structure factor during the crystallization transition indicates that long-range density order appears before local crystalline packing. This is consistent with some experimental observations by small/wide angle X-ray scattering (SAXS/WAXS). During the heating process, it is found that the crystalline regions are still growing until they are fully melted, which can be confirmed by the evolution both of the static structure factor and average stem length formed by the chains. This two-stage behavior indicates that melting of polymer crystals is far from thermodynamic equilibrium. Our results concur with various experiments. It is the first time that such growth/reorganization behavior is clearly observed by MD simulations. Our code can be easily used to model other type of polymers by providing a file containing the tabulated angle potential data and a set of appropriate parameters. Program summaryProgram title: lammps-cgpva Catalogue identifier: AEDE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU's GPL No. of lines in distributed program
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
Li, Zhen; Bian, Xin; Karniadakis, George Em; Li, Xiantao
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-28
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613
Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism
NASA Astrophysics Data System (ADS)
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em
2015-12-01
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.
Virtual ultrasound sources for inspecting nuclear components of coarse-grained structure
Brizuela, J.; Katchadjian, P.; Desimone, C.; Garcia, A.
2014-02-18
This work describes an ultrasonic inspection procedure designed for verifying coarse-grained structure materials, which are commonly used on nuclear reactors. In this case, conventional phased array techniques cannot be used due to attenuating characteristics and backscattered noise from microstructures inside the material. Thus, synthetic aperture ultrasonic imaging (SAFT) is used for this approach in contact conditions. In order to increase energy transferred to the medium, synthetic transmit aperture is formed by several elements which generate a diverging wavefront equivalent to a virtual ultrasound source behind the transducer. On the other hand, the phase coherence technique has been applied to reduce more structural noise and improve the image quality. The beamforming process has been implemented over a GPU platform to reduce computing time.
The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes
Orsi, Mario; Essex, Jonathan W.
2011-01-01
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 (). 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. PMID:22194874
Coarse-graining molecular dynamics models using an extended Galerkin method
NASA Astrophysics Data System (ADS)
Li, Xiantao
2013-03-01
I will present a systematic approach to coarse-grain molecular dynamics models for solids. The coarse-grained models are derived by Galerkin projection to a sequence of Krylov subspaces. On the coarsest space, the model corresponds to a finite element discretization of the continuum elasto-dynamics model. On the other hand, the projection to the finest space yields the full molecular dynamics description. The models in between serve as a smooth transition between the two scales. We start with a molecular dynamics (MD) model, mix¨i = -∂V/∂xi . First, let Y0 be the approximation space for the continuum model. By projecting the MD model onto the subspace, we obtain a coarse-grained model, M q ¨ = F (q) . Using the Cauchy-Born approximation, this model can be shown to coincide with the finite element representation of the continuum elastodynamics model. This model has limited accuracy near lattice defects. One natural idea is to switch to the MD model in regions surround local defect. As a result, one creates an interface between the continuum and atomistic description, where coupling conditions are needed. Direct coupling methods may involve enforcing constraints or mixing the energy or forces. Such an approach may suffer from large phonon reflections at the interface, and introduce large modeling error. In order to seamlessly couple this model to MD, we successively expand the approximation space to the Krylov spaces, Kl =Y0 + AY0 + ⋯ +AlY0 . Here A is the force constant matrix, computed from the atomistic model. Due to the translational invariance, only a smaller number of such matrices need to be computed. By projecting the MD model onto this new subspace, we obtain an extended system, M q .. =F0 (q ,ξ1 , ... ,ξl) ,ξ̈1 =F1 (q ,ξ1 , ... ,ξl) , ... ... ,ξ̈l =Fl (q ,ξ1 , ... ,ξl) . The additional variables ξj represent the coefficients in the extended approximation space. Using this systematic approach, one can build a hierarchy of models with
Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea
2012-05-01
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 in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard. PMID:26593649
Coarse-graining to the meso and continuum scales with molecular-dynamics-like models
NASA Astrophysics Data System (ADS)
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.
Pandey, Harsh; Underhill, Patrick T
2015-11-01
The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large. PMID:26651689
Development of DPD coarse-grained models: From bulk to interfacial properties
NASA Astrophysics Data System (ADS)
Solano Canchaya, José G.; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice
2016-08-01
A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.
Development of DPD coarse-grained models: From bulk to interfacial properties.
Solano Canchaya, José G; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice
2016-08-01
A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve. PMID:27497539
NASA Astrophysics Data System (ADS)
Pandey, Harsh; Underhill, Patrick T.
2015-11-01
The electrophoretic mobility of molecules such as λ -DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.
Systematic coarse-graining of spectrin-level red blood cell models
Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em
2013-01-01
We present a rigorous procedure to derive coarse-grained red blood cell (RBC) models, which yield accurate mechanical response. Based on a semi-analytic theory the linear and nonlinear elastic properties of healthy and infected RBCs in malaria can be matched with those obtained in optical tweezers stretching experiments. The present analysis predicts correctly the membrane Young’s modulus in contrast to about 50% error in predictions by previous models. In addition, we develop a stress-free model which avoids a number of pitfalls of existing RBC models, such as non-smooth or poorly controlled equilibrium shape and dependence of the mechanical properties on the initial triangulation quality. Here we employ dissipative particle dynamics for the implementation but the proposed model is general and suitable for use in many existing continuum and particle-based numerical methods. PMID:24353352
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. PMID:26575407
Automated optimization of water-water interaction parameters for a coarse-grained model.
Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A
2014-02-13
We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506
Automated Optimization of Water–Water Interaction Parameters for a Coarse-Grained Model
2015-01-01
We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder–Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
Sengupta, Durba; Marrink, Siewert J.
2010-01-01
Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. PMID:20548957
Studying the Enhanced Ductility of Bimodal Nanocrystalline Copper Using a Coarse-Grained Model
NASA Astrophysics Data System (ADS)
Gao, Guo-Jie Jason; Wang, Yun-Jiang; Ogata, Shigenobu
Viewing a bimodal configuration of nanocrystalline copper as composed of soft grains containing stiff cores, we proposed a coarse-grained model with systematically tunable stiffness of grains to study the enhanced ductility of bimodal nanocrystalline copper [Y. Wang, M. Chen, F. Zhou, and E. Ma, Nature 419 (2002) 912]. Using molecular dynamics simulations, we shear our model quasistatically. Our results not only qualitatively confirms that a bimodal configuration could behave more ductile than a monomodal one but also predicts there exists a range of ratio of soft/stiff domains that best minimizes shear localization. Moreover, our model indicates that a bimodal configuration could sometimes exacerbate shear localization and therefore jeopardize ductility if the ratio of soft/stiff domains is not properly chosen. This may explain why some experimental results are hard to be reproduced.
A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.
Dannenhoffer-Lafage, Thomas; White, Andrew D; Voth, Gregory A
2016-05-10
To extract meaningful data from molecular simulations, it is necessary to incorporate new experimental observations as they become available. Recently, a new method was developed for incorporating experimental observations into molecular simulations, called experiment directed simulation (EDS), which utilizes a maximum entropy argument to bias an existing model to agree with experimental observations while changing the original model by a minimal amount. However, there is no discussion in the literature of whether or not the minimal bias systematically and generally improves the model by creating agreement with the experiment. In this work, we show that the relative entropy of the biased system with respect to an ideal target is always reduced by the application of a minimal bias, such as the one utilized by EDS. Using all-atom simulations that have been biased with EDS, one can then easily and rapidly improve a bottom-up multiscale coarse-grained (MS-CG) model without the need for a time-consuming reparametrization of the underlying atomistic force field. Furthermore, the improvement given by the many-body interactions introduced by the EDS bias can be maintained after being projected down to effective two-body MS-CG interactions. The result of this analysis is a new paradigm in coarse-grained modeling and simulation in which the "bottom-up" and "top-down" approaches are combined within a single, rigorous formalism based on statistical mechanics. The utility of building the resulting EDS-MS-CG models is demonstrated on two molecular systems: liquid methanol and ethylene carbonate. PMID:27045328
Abbott, Lauren J.; Stevens, Mark J.
2015-12-22
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.
Coarse-graining intermittent intracellular transport: Two- and three-dimensional models
NASA Astrophysics Data System (ADS)
Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.
2015-10-01
Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.
NASA Astrophysics Data System (ADS)
Abbott, Lauren J.; Stevens, Mark J.
2015-12-01
A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil-globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.
Abbott, Lauren J; Stevens, Mark J
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. PMID:26723705
Abbott, Lauren J.; Stevens, Mark J.
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.
Abbott, Lauren J.; Stevens, Mark J.
2015-12-22
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 atomisticmore » simulations.« less
NASA Astrophysics Data System (ADS)
Chan, Hue Sun; Zhang, Zhuqing; Wallin, Stefan; Liu, Zhirong
2011-05-01
Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing interactions. Many of these principles have been elucidated by native-centric models, wherein nonnative interactions may be treated perturbatively. We discuss these developments as well as recent applications of coarse-grained chain modeling to knotted proteins and to intrinsically disordered proteins.
Chan, Hue Sun; Zhang, Zhuqing; Wallin, Stefan; Liu, Zhirong
2011-01-01
Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimental discovery of two-state-like folding in the late 1960s, rather than to the problem of conformational search per se. Comparisons between theory and experiment indicate a prominent role of desolvation barriers in cooperative folding, which likely emerges generally from a coupling between local conformational preferences and nonlocal packing interactions. Many of these principles have been elucidated by native-centric models, wherein nonnative interactions may be treated perturbatively. We discuss these developments as well as recent applications of coarse-grained chain modeling to knotted proteins and to intrinsically disordered proteins. PMID:21453060
Davtyan, Aram; Schafer, Nicholas P.; Zheng, Weihua; Clementi, Cecilia; Wolynes, Peter G.; Papoian, Garegin A.
2012-01-01
The Associative memory, Water mediated, Structure and Energy Model (AWSEM) is a coarse-grained protein force field. AWSEM contains physically motivated terms, such as hydrogen bonding, as well as a bioinformatically based local structure biasing term, which efficiently takes into account many-body effects that are modulated by the local sequence. When combined with appropriate local or global alignments to choose memories, AWSEM can be used to perform de novo protein structure prediction. Herein we present structure prediction results for a particular choice of local sequence alignment method based on short residue sequences called fragments. We demonstrate the model’s structure prediction capabilities for three levels of global homology between the target sequence and those proteins used for local structure biasing, all of which assume that the structure of the target sequence is not known. When there are no homologs in the database of structures used for local structure biasing, AWSEM calculations produce structural predictions that are somewhat improved compared with prior works using related approaches. The inclusion of a small number of structures from homologous sequences improves structure prediction only marginally but when the fragment search is restricted to only homologous sequences, AWSEM can perform high resolution structure prediction and can be used for kinetics and dynamics studies. PMID:22545654
Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles
NASA Astrophysics Data System (ADS)
Lopez, Hender; Lobaskin, Vladimir
2015-12-01
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles (NPs). The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the aminoacids via a central force that depends on the nanoparticle size. The proposed methodology is used to predict the adsorption energies for six common human blood plasma proteins on hydrophobic charged or neutral nanoparticles of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the nanoparticle, which can be used for predicting the composition of the NP-protein corona. The predicted ranking is in good agreement with known experimental data for protein adsorption on surfaces.
Proteins at air-water interfaces: a coarse-grained model.
Cieplak, Marek; Allan, Daniel B; Leheny, Robert L; Reich, Daniel H
2014-11-01
We present a coarse-grained model to describe the adsorption and deformation of proteins at an air-water interface. The interface is introduced empirically in the form of a localized field that couples to a hydropathy scale of amino acids. We consider three kinds of proteins: protein G, egg-white lysozyme, and hydrophobin. We characterize the nature of the deformation and the orientation of the proteins induced by their proximity to and association with the interface. We also study protein diffusion in the layer formed at the interface and show that the diffusion slows with increasing concentration in a manner similar to that for a colloidal suspension approaching the glass transition. PMID:25310625
Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers
West, Beate; Brown, Frank L.H.; Schmid, Friederike
2009-01-01
Abstract We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; lipid-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution. The mechanisms leading to hydrophobic mismatch interactions are critically analyzed. PMID:18835907
Large-scale structural transitions in supercoiled DNA revealed by coarse-grained simulations
NASA Astrophysics Data System (ADS)
Krajina, Brad; Spakowitz, Andrew
Topological constraints, such as DNA supercoiling, play an integral role in genomic regulation and organization in living systems. However, physical understanding of the principles that underlie DNA structure and organization at biologically-relevant length-scales remains a formidable challenge. We develop a coarse-grained simulation approach for predicting equilibrium conformations of supercoiled DNA. With this approach, we study the conformational transitions that arise due to supercoiling across the full range of supercoiling densities that are commonly explored by living systems. Simulations of ring DNA molecules with lengths up to the scale of topological domains in the E. coli chromosome (~10 kilobases) reveal large-scale structural transitions elicited by supercoiling, resulting in 3 supercoiling conformational regimes: chiral coils, extended plectonemes, and branched hyper-supercoils. These results capture the non-monotonic relationship of size versus degree of supercoiling observed in experimental sedimentation studies of supercoiled DNA, and our results provide a physical explanation of the structural transitions underlying this behavior.
NASA Astrophysics Data System (ADS)
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.
Theodorakis, Panagiotis E; Dellago, Christoph; Kahl, Gerhard
2013-01-14
We discuss a coarse-grained model recently proposed by Starr and Sciortino [J. Phys.: Condens. Matter 18, L347 (2006)] for spherical particles functionalized with short single DNA strands. The model incorporates two key aspects of DNA hybridization, i.e., the specificity of binding between DNA bases and the strong directionality of hydrogen bonds. Here, we calculate the effective potential between two DNA-functionalized particles of equal size using a parallel replica protocol. We find that the transition from bonded to unbonded configurations takes place at considerably lower temperatures compared to those that were originally predicted using standard simulations in the canonical ensemble. We put particular focus on DNA-decorations of tetrahedral and octahedral symmetry, as they are promising candidates for the self-assembly into a single-component diamond structure. Increasing colloid size hinders hybridization of the DNA strands, in agreement with experimental findings. PMID:23320725
NASA Astrophysics Data System (ADS)
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.
A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding
Yap, Eng-Hui; Fawzi, Nicolas Lux; Head-Gordon, Teresa
2012-01-01
We develop a sequence based α-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize α-helices and β-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein–protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain. PMID:17879350
Coarse-grained red blood cell model with accurate mechanical properties, rheology and dynamics.
Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George E
2009-01-01
We present a coarse-grained red blood cell (RBC) model with accurate and realistic mechanical properties, rheology and dynamics. The modeled membrane is represented by a triangular mesh which incorporates shear inplane energy, bending energy, and area and volume conservation constraints. The macroscopic membrane elastic properties are imposed through semi-analytic theory, and are matched with those obtained in optical tweezers stretching experiments. Rheological measurements characterized by time-dependent complex modulus are extracted from the membrane thermal fluctuations, and compared with those obtained from the optical magnetic twisting cytometry results. The results allow us to define a meaningful characteristic time of the membrane. The dynamics of RBCs observed in shear flow suggests that a purely elastic model for the RBC membrane is not appropriate, and therefore a viscoelastic model is required. The set of proposed analyses and numerical tests can be used as a complete model testbed in order to calibrate the modeled viscoelastic membranes to accurately represent RBCs in health and disease. PMID:19965026
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
NASA Astrophysics Data System (ADS)
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V.
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V
2016-01-01
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments. PMID:26747818
Vibrational solvatochromism and electrochromism: Coarse-grained models and their relationships
NASA Astrophysics Data System (ADS)
Cho, Minhaeng
2009-03-01
A theoretical description of vibrational solvatochromism and electrochromism is presented by using a coarse-grained model based on a distributed charge and multipole interaction theory. Solvatochromic frequency shift has been described by considering the interaction between distributed charges of a solute and electrostatic potential due to distributed charges of solvent molecules. Another approach was based on the expansion of the solvatochromic frequency shift in terms of solvent electric field and its gradient at distributed sites on solute. The relationship between these two approaches is elucidated and their validities are discussed. It is also shown that the distributed charge and multipole model for solvatochromism developed here can be used to describe vibrational Stark effects on frequency and transition dipole moment. The relationship between the vibrational Stark tuning rate and the parameters obtained from recent vibrational solvatochromism studies is clarified and used to determine the vibrational Stark tuning rates of a few stretching modes, which are then directly compared with experimentally measured values. We anticipate that the present theoretical model can be used to study a variety of vibrational solvatochromic and electrochromic phenomena and to extract critical information on local electrostatic environment around a small IR probe in solution or protein from linear and nonlinear IR spectroscopic studies.
A Coarse-Grained Model for Thermoresponsive Poly(N-isopropylacrylamide)
NASA Astrophysics Data System (ADS)
Abbott, Lauren J.; Stevens, Mark J.
Poly(N-isopropylacrylamide) (PNIPAM) is a thermoresponsive polymer that undergoes a phase transition at its lower critical solution temperature (LCST). Although atomistic simulations have been effective to study PNIPAM single chains in solution, they are limited in reaching longer length- and time-scales. In this work, a coarse-grained (CG) model is developed for PNIPAM that captures its thermoresponsive behavior. Nonbonded parameters are fit to experimental thermodynamic data, 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 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 and experiment. The self-assembly of PNIPAM surfactants is also explored. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
A coarse-grained model for the simulations of biomolecular interactions in cellular environments
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2014-02-07
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.
NASA Astrophysics Data System (ADS)
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.
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2013-05-15
A multiscale coarse-grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long-range solute/solvent electrostatic microscopic interactions, up to the 1-μm scale, by considering a reduced amount of computational resources. All the required parameters are assigned to reproduce available data concerning the solvation of single ions. Such a strategy makes it possible to reproduce with good accuracy the solvation properties concerning simple ion pairs in solution (in particular, the asymptotic behavior of the ion pair potentials of mean force). This new method represents an extension of the polarizable pseudoparticle solvent model, which has been recently improved to account for the main features of hydrophobic effects in liquid water (Masella et al., J. Comput. Chem. 2011, 32, 2664). This multiscale approach is well suited to be used for computing the impact of charge changes in free energy computations, in terms of both accuracy and efficiency. PMID:23382002
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. PMID:26687716
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.
2016-01-01
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. PMID:26687716
Yang, Lee-Wei; Chng, Choon-Peng
2008-01-01
In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of 'open to close' (open-->close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764
Anderson, Michael T.; Cumblidge, Stephen E.; Doctor, Steven R.
2003-12-18
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.
Mechanism of the formation of peripheral coarse grain structure in hot extrusion of Al-4.5Zn-1Mg
NASA Astrophysics Data System (ADS)
Eivani, A. R.; Zhou, J.; Duszczyk, J.
2016-04-01
Microstructural evolution leading to peripheral coarse grain (PCG) structure in hot extruded Al-4.5Zn-1Mg rods is investigated. The extent of dynamic recrystallization (DRX) in the as-extruded product falls not in line with the basis over which the existing mechanisms for interpretation of PCG formation are built. A new mechanism is therefore proposed based on partial DRX during extrusion and nucleation and abnormal growth of statically recrsystallised grains.
de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; Junghans, Christoph; Mukherji, Debashish
2016-05-03
We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion (C–IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. In addition, we observe much faster convergence within C–IBI compared to IBI. To validate the robustness, we apply C–IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.
Coarse-Grained Molecular Dynamics for Computer Modeling of Nanomechanical Systems
Rudd, R E
2003-11-02
Unique challenges for computer modeling and simulation arise in the course of the development and design of nanoscale mechanical systems. Materials often exhibit unconventional behavior at the nanoscale that can affect device operation and failure. This uncertainty poses a problem because of the limited experimental characterization at these ultra-small length scales. In this Article we give an overview of how we have used concurrent multiscale modeling techniques to address some of these issues. Of particular interest are the dynamic and temperature-dependent processes found in nanomechanical systems. We focus on the behavior of sub-micron mechanical components of Micro-Electro-Mechanical Systems (MEMS) and Nano-Electro-Mechanical Systems (NEMS), especially flexural-mode resonators. The concurrent multiscale methodology we have developed for NEMS employs an atomistic description of millions of atoms in relatively small but key regions of the system, coupled to, and run concurrently with, a generalized finite element model of the periphery. We describe two such techniques. The more precise model, Coarse-Grained Molecular Dynamics (CGMD), describes the dynamics on a mesh of elements, but the equations of motion are built up from the underlying atomistic physics to ensure a smooth coupling between regions governed by different length scales. In many cases the degrees of smoothness of the coupling provided by CGMD is not necessary. The hybrid Coupling of Length Scales (CLS) methodology, combining molecular dynamics with conventional finite element modeling, provides a suitable technique for these cases at a greatly reduced computation expense. We review these models and some of the results we have obtained regarding size effects in the elasticity and dissipation of nanomechanical systems.
Multi-scale morphology in self-assembly of peptides to proteins via a coarse-grain model
NASA Astrophysics Data System (ADS)
Pandey, Ras; Farmer, Barry
2015-03-01
Self-organizing structures of short peptides (6-7 residues) and proteins (136 residues) are studied by a coarse-grained Monte Carlo simulation. Peptides and proteins are described by coarse-grained chains of residues whose interactions are described by a knowledge-based residue-residue interaction potential that captures the compositional specificity. Large-scale computer simulations are performed to study the structural evolution e.g. aggregation, network, etc. at a range of temperatures and concentrations. A number of local and global physical quantities including structure factor are examined. We find that the residue interactions, concentration, and size of chains are very important in modulating the structure of emerging morphologies in the specified temperature range. Estimates are provided for the effective (fractal) dimension of the assembly over various length scales as a function of temperature. This work is supported by the Air Force Research Laboratory.
Coarse-Grained Model for Colloidal Protein Interactions, B22, and Protein Cluster Formation
Blanco, Marco A.; Sahin, Eric; Robinson, Anne S.; Roberts, Christopher J.
2014-01-01
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semi-quantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work, this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental values of the B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependance on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids / surface patches that form inter-protein contacts
A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry
Sharma, Satyan; Kim, Brian N.; Stansfeld, Phillip J.; Sansom, Mark S. P.; Lindau, Manfred
2015-01-01
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(4,5)bisphosphate 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. PMID:26659855
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.
Marrink, Siewert J; Risselada, Jelger; Mark, Alan E
2005-06-01
The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to 8000 lipids. The critical step in the transformation process is the nucleation of a gel cluster consisting of 20-80 lipids, spanning both monolayers. After the formation of the critical cluster, a fast growth regime is entered. Growth slows when multiple gel domains start interacting, forming a percolating network. Long-lived fluid domains remain trapped and can be metastable on a microsecond time scale. From the temperature dependence of the rate of cluster growth, the line tension of the fluid-gel interface was estimated to be 3+/-2 pN. The reverse process is observed when heating the gel phase. No evidence is found for a hexatic phase as an intermediate stage of melting. The hysteresis observed in the freezing and melting transformation is found to depend both on the system size and on the time scale of the simulation. Extrapolating to macroscopic length and time scales, the transition temperature for heating and cooling converges to 295+/-5 K, in semi-quantitative agreement with the experimental value for DPPC (315 K). The phase transformation is associated with a drop in lateral mobility of the lipids by two orders of magnitude, and an increase in the rotational correlation time of the same order of magnitude. The lipid headgroups, however, remain fluid. These observations are in agreement with experimental findings, and show that the nature of the ordered phase obtained with the CG model is indeed a gel rather than a crystalline phase. Simulations performed at different levels of hydration furthermore show that the gel phase is stabilized at low hydration. A simulation of a small DPPC vesicle reveals that curvature has the opposite effect. PMID:15921980
NASA Astrophysics Data System (ADS)
Trylska, Joanna
2010-11-01
Biopolymers are of dynamic nature and undergo functional motions spanning a large spectrum of timescales. To study the internal dynamics of nano-sized molecular complexes that exceed hundred thousands of atoms with atomic detail is computationally inefficient. Therefore, to achieve both the spatial and temporal scales of biological interest coarse-grained models of macromolecules are often used. By uniting groups of atoms into single interacting centers one decreases the resolution of the system and gets rid of the irrelevant degrees of freedom. This simplification, even though it requires parameterization, makes the studies of biomolecular dynamics computationally tractable and allows us to reach beyond the microsecond time frame. Here, I review the coarse-grained models of macromolecules composed of proteins and nucleic acids. I give examples of one-bead models that were developed to investigate the internal dynamics and focus on their applications to the ribosome—the nanoscale protein synthesis machine.
Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Garrido, J. M.; Algaba, J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.; Blas, F. J.
2016-04-01
We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with
Garrido, J M; Algaba, J; Míguez, J M; Mendiboure, B; Moreno-Ventas Bravo, A I; Piñeiro, M M; Blas, F J
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
N-Body interactions in soft-sphere coarse-grained models of star polymers.
Pelissetto, Andrea
2012-02-01
We consider the coarse-grained approach in which star polymers are mapped onto atoms located at the centers of the stars interacting by means of ultrasoft potentials. We generalize the Witten-Pincus formula to all n-body potentials: in the good-solvent regime all potentials show an ultrasoft logarithmic divergence when the relative distance of all n stars goes to zero, with coefficients that can be related to the partition-function exponents γ(f). PMID:22463232
NASA Astrophysics Data System (ADS)
Sanyal, Tanmoy; Shell, M. Scott
2016-07-01
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
Sanyal, Tanmoy; Shell, M Scott
2016-07-21
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. PMID:27448876
Richardson, Robin A; Papachristos, Konstantinos; Read, Daniel J; Harlen, Oliver G; Harrison, Michael; Paci, Emanuele; Muench, Stephen P; Harris, Sarah A
2014-12-01
Advances in structural biology, such as cryo-electron microscopy (cryo-EM) have allowed for a number of sophisticated protein complexes to be characterized. However, often only a static snapshot of a protein complex is visualized despite the fact that conformational change is frequently inherent to biological function, as is the case for molecular motors. Computer simulations provide valuable insights into the different conformations available to a particular system that are not accessible using conventional structural techniques. For larger proteins and protein complexes, where a fully atomistic description would be computationally prohibitive, coarse-grained simulation techniques such as Elastic Network Modeling (ENM) are often employed, whereby each atom or group of atoms is linked by a set of springs whose properties can be customized according to the system of interest. Here we compare ENM with a recently proposed continuum model known as Fluctuating Finite Element Analysis (FFEA), which represents the biomolecule as a viscoelastic solid subject to thermal fluctuations. These two complementary computational techniques are used to answer a critical question in the rotary ATPase family; implicit within these motors is the need for a rotor axle and proton pump to rotate freely of the motor domain and stator structures. However, current single particle cryo-EM reconstructions have shown an apparent connection between the stators and rotor axle or pump region, hindering rotation. Both modeling approaches show a possible role for this connection and how it would significantly constrain the mobility of the rotary ATPase family. PMID:25174610
NASA Astrophysics Data System (ADS)
DeMille, Robert C.; Molinero, Valeria
2009-07-01
A coarse-grained model of NaCl in water is presented where the ions are modeled without charge to avoid computationally challenging electrostatics. A monatomic model of water [V. Molinero and E. B. Moore, J. Phys. Chem. B 113, 4008 (2009)] is used as the basis for this coarse-grain approach. The ability of Na+ to disrupt the native tetrahedral arrangement of water molecules, and of Cl- to integrate within this organization, is preserved in this mW-ion model through parametrization focused on water's solvation of these ions. This model successfully reproduces the structural effect of ions on water, referenced to observations from experiments and atomistic molecular dynamics simulations, while using extremely short-ranged potentials. Without Coulomb interactions the model replicates details of the ion-water structure such as distinguishing contact and solvent-separated ion pairs and the free energy barriers between them. The approach of mimicking ionic effects with short-ranged interactions results in performance gains of two orders of magnitude compared to Ewald methods. Explored over a broad range of salt concentration, the model reproduces the solvation structure and trends of diffusion relative to atomistic simulations and experimental results. The functional form of the mW-ion model can be parametrized to represent other electrolytes. With increased computational efficiency and reliable structural fidelity, this model promises to be an asset for accessing significantly longer simulation time scales with an explicit solvent in a coarse-grained system involving, for example, polyelectrolytes such as proteins, nucleic acids, and fuel-cell membranes.
Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation.
Blanco, Marco A; Sahin, Erinc; Robinson, Anne S; Roberts, Christopher J
2013-12-19
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino
Knott, Michael; Best, Robert B.
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.
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. PMID:24811666
Molecular Dynamics Simulations of DPPC Bilayers Using “LIME,” a New Coarse-grained Model
Curtis, Emily M.
2013-01-01
A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit-solvent model was developed using a multi-scale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC resulted in the formation of a defect free bilayer in less than 4 hours. The bilayer formed quantitatively reproduces the main structural properties (e.g. area per lipid, bilayer thickness, bond order parameters) that are observed experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced. Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is observed when the temperature is increased. PMID:23521567
NASA Astrophysics Data System (ADS)
Zhang, Yang; Heermann, Dieter; Farmer, Barry; Pandey, Ras
2011-03-01
A coarse-grained model is used to study the self-assembly of active sites in a DNA (chromatin) chain. The chromosome is described by a bond-fluctuating chain of two types of nodes A (interacting) and B (non-interacting), distributed randomly with concentration C and 1 - C respectively. Active nodes interact with a Lennard-Jones (LJ) potential and execute their stochastic motion with the Metropolis algorithm. The depth of the LJ potential (f) , a measure of interaction strength and the concentration (C) of the active sites are varied. A number of local and global physical quantities are studied such as mobility (Mn) profile of each node, their local structural profile, root mean square (RMS) displacement (R) , radius of gyration (Rg) , and structure factor S (q) . We find that the chain segments assemble into microphase of blobs which requires higher concentration of active sites at weaker interaction. These findings are consistent with that of a dynamic loop model of chromatin on global (large) scale but differ at small scales. This work is supported in part by the Alexander von Humboldt foundation and AFRL.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2011-09-01
A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces. PMID:21647929
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. PMID:26233119
Ando, Tadashi; Skolnick, Jeffrey
2014-01-01
DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA. Recent experimental results and theoretical analyses revealed that the proteins show a rotation-coupled sliding along DNA helical pitch. Here, we performed Brownian dynamics simulations using newly developed coarse-grained protein and DNA models for evaluating how hydrodynamic interactions between the protein and DNA molecules, binding affinity of the protein to DNA, and DNA fluctuations affect the one dimensional diffusion of the protein on the DNA. Our results indicate that intermolecular hydrodynamic interactions reduce 1D diffusivity by 30%. On the other hand, structural fluctuations of DNA give rise to steric collisions between the CG-proteins and DNA, resulting in faster 1D sliding of the protein. Proteins with low binding affinities consistent with experimental estimates of non-specific DNA binding show hopping along the CG-DNA. This hopping significantly increases sliding speed. These simulation studies provide additional insights into the mechanism of how DNA binding proteins find their target sites on the genome. PMID:25504215
NASA Astrophysics Data System (ADS)
Baxevanis, Th.
2008-08-01
A coarse-grained mean-field model is proposed where the damage enhanced creep of heterogeneous materials is described by the theory of absolute reaction rates. The dynamics of the proposed model, below a critical load, is characterized by an intensive precursor activity in the form of avalanches of microscopic breaking events that leads to a final catastrophic cascade occurring at a finite strain. Above the critical load, failure is instantaneous. The critical load is the static (elastic) fracture strength; thus the model is consistent with its time-independent analogue. Finally, the proposed model reproduces the experimental observations on the time evolution of the creep rate.
Sterpone, Fabio; Melchionna, Simone; Tuffery, Pierre; Pasquali, Samuela; Mousseau, Normand; Cragnolini, Tristan; Chebaro, Yassmine; Saint-Pierre, Jean-Francois; Kalimeri, Maria; Barducci, Alessandro; Laurin, Yohan; Tek, Alex; Baaden, Marc; Nguyen, Phuong Hoang; Derreumaux, Philippe
2015-01-01
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the on-going developments. PMID:24759934
2015-01-01
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
Mantha, Sriteja; Yethiraj, Arun
2015-08-27
Polymer solutions present a significant computational challenge because chemical realism on small length scales can be important, but the polymer molecules are very large. In polyelectrolyte solutions, there is often the additional complexity that the molecules consist of hydrophobic and charged groups, which makes an accurate treatment of the solvent, water, crucial. One route to achieve this balance is through coarse-grained models where several atoms on a monomer are grouped into one interaction site. In this work, we develop a coarse grained (CG) model for sodium polystyrenesulfonate (NaPSS) in water using a methodology consistent with the MARTINI coarse-graining philosophy, where four heavy atoms are grouped into one CG site. We consider two models for water: polarizable MARTINI (POL) and big multipole water (BMW). In each case, interaction parameters for the polymer sites are obtained by matching the potential of mean force between two monomers to results of atomistic simulations. The force field based on the POL water provides a more reasonable description of polymer properties than that based on the BMW water. We study the properties of single chains using the POL force field. Fully sulfonated chains are rodlike (i.e., the root-mean-square radius of gyration, Rg, scales linearly with degree of polymerization, N). When the fraction of sulfonation, f, is 0.25 or less, the chain collapses into a cylindrical globule. For f = 0.5, pearl-necklace conformations are observed when every second monomer is sulfonated. The lifetime of a counterion around a polymer is on the order of 100 ps, suggesting that there is no counterion condensation. The model is computationally feasible and should allow one to study the effect of local chemistry on the properties of polymers in aqueous solution. PMID:26047770
Lee, One-Sun; Cho, Vince; Schatz, George C
2012-09-12
We have studied the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber starting from a homogeneous mixture of PAs in water using coarse-grained molecular dynamics simulations. Nine independent 16 μs runs all show spontaneous fiber formation in which the PA molecules first form spherical micelles, and then micelles form a three-dimensional network via van der Waals interactions. As the hydrophobic core belonging to the different micelles merge, the three-dimensional network disappears and a fiber having a diameter of ∼80 Å appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to ∼15 Å away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and ∼92% of the epitope is exposed to water molecules. PMID:22924639
Coarse-grained model and light scattering of the twist-bend nematic phase
NASA Astrophysics Data System (ADS)
Shamid, Shaikh; Allender, David; Selinger, Jonathan
2015-03-01
We develop a coarse-grained version of the continuum theory for the twist-bend (TB) nematic phase of liquid crystals. In this theoretical approach, we begin with an ideal, undistorted TB phase, which has a heliconical modulation of the director field. We then calculate the elastic free energy cost of a position-dependent local rotation of the director away from the ideal state. We diagonalize this free energy density to find the eigenmodes of the system. Of these eigenmodes, the soft mode can be regarded as a smectic-like distortion of periodic planes in the TB phase; this mode has effective elastic constants for layer compression and curvature. By comparison, the hard mode involves director variations away from the optimum cone angle. This calculation leads to a prediction for light scattering from the TB nematic phase. This work was supported by NSF Grant DMR-1409658.
NASA Astrophysics Data System (ADS)
Nikoubashman, Arash; Mahynski, Nathan A.; Capone, Barbara; Panagiotopoulos, Athanassios Z.; Likos, Christos N.
2015-12-01
We study the effective interactions and phase behavior of star polymer-colloid mixtures through theory and Monte Carlo simulations. We extend previous theoretical approaches for calculating the effective star-colloid pair potential to take into account attractive contributions, which become significant at worsening solvent conditions. In order to assess the validity of our simulation and theory, we compute the effective interactions via virtual move parallel tempering Monte Carlo simulations using a microscopic bead-spring model for the star polymer and achieve excellent agreement. Finally, we perform grand canonical Monte Carlo simulations of the coarse-grained systems to study the effect of solvent quality on the phase behavior.
Ferreiro-Rangel, Carlos A; Gelb, Lev D
2013-06-13
Structural and mechanical properties of silica aerogels are studied using a flexible coarse-grained model and a variety of simulation techniques. The model, introduced in a previous study (J. Phys. Chem. C 2007, 111, 15792-15802), consists of spherical "primary" gel particles that interact through weak nonbonded forces and through microscopically motivated interparticle bonds that may break and form during the simulations. Aerogel models are prepared using a three-stage protocol consisting of separate simulations of gelation, aging, and a final relaxation during which no further bond formation is permitted. Models of varying particle size, density, and size dispersity are considered. These are characterized in terms of fractal dimensions and pore size distributions, and generally good agreement with experimental data is obtained for these metrics. The bulk moduli of these materials are studied in detail. Two different techniques for obtaining the bulk modulus are considered, fluctuation analysis and direct compression/expansion simulations. We find that the fluctuation result can be subject to systematic error due to coupling with the simulation barostat but, if performed carefully, yields results equivalent with those of compression/expansion experiments. The dependence of the bulk modulus on density follows a power law with an exponent between 3.00 and 3.15, in agreement with reported experimental results. The best correlate for the bulk modulus appears to be the volumetric bond density, on which there is also a power law dependence. Polydisperse models exhibit lower bulk moduli than comparable monodisperse models, which is due to lower bond densities in the polydisperse materials. PMID:23631801
Zhang, Peng; Gao, Chao; Zhang, Na; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
2014-01-01
We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions. PMID:25530818
NASA Astrophysics Data System (ADS)
He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.
2010-02-01
A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.
Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Mustafa, Ghulam; Nandekar, Prajwal P.; Yu, Xiaofeng; Wade, Rebecca C.
2015-12-01
An important step in the simulation of a membrane protein in a phospholipid bilayer is the correct immersion of the protein in the bilayer. Crystal structures are determined without the bilayer. Particularly for proteins with monotopic domains, it can be unclear how deeply and in which orientation the protein is being inserted in the membrane. We have previously developed a procedure combining coarse-grain (CG) with all-atom (AA) molecular dynamics (MD) simulations to insert and simulate a cytochrome P450 (CYP) possessing an N-terminal transmembrane helix connected by a flexible linker region to a globular domain that dips into the membrane. The CG simulations provide a computationally efficient means to explore different orientations and conformations of the CYP in the membrane. Converged configurations obtained in the CG simulations are then refined in AA simulations. Here, we tested different variants of the MARTINI CG model, differing in the water model, the treatment of long-range non-bonded interactions, and the implementation (GROMACS 4.5.5 vs 5.0.4), for this purpose. We examined the behavior of the models for simulating a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in water and for the immersion of CYP3A4 in a POPC bilayer, and compared the CG-MD results with the previously reported experimental and simulation results. We also tested the methodology on a set of four other CYPs. Finally, we propose an optimized protocol for modeling such protein-membrane systems that provides the most plausible configurations and is computationally efficient; this incorporates the standard non-polar water model and the GROMACS 5.0.4 implementation with a reaction field treatment of long-range interactions.
Mustafa, Ghulam E-mail: rebecca.wade@h-its.org; Nandekar, Prajwal P.; Yu, Xiaofeng; Wade, Rebecca C. E-mail: rebecca.wade@h-its.org
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.
Cragnell, Carolina; Durand, Dominique; Cabane, Bernard; Skepö, Marie
2016-06-01
Monte Carlo simulations and coarse-grained modeling have been used to analyze Histatin 5, an unstructured short cationic salivary peptide known to have anticandidical properties. The calculated scattering functions have been compared with intensity curves and the distance distribution function P(r) obtained from small angle X-ray scattering (SAXS), at both high and low salt concentrations. The aim was to achieve a molecular understanding and a physico-chemical insight of the obtained SAXS results and to gain information of the conformational changes of Histatin 5 due to altering salt content, charge distribution, and net charge. From a modeling perspective, the accuracy of the electrostatic interactions are of special interest. The used coarse-grained model was based on the primitive model in which charged hard spheres differing in charge and in size represent the ionic particles, and the solvent only enters the model through its relative permittivity. The Hamiltonian of the model comprises three different contributions: (i) excluded volumes, (ii) electrostatic, and (iii) van der Waals interactions. Even though the model can be considered as gross omitting all atomistic details, a great correspondence is obtained with the experimental results. Proteins 2016; 84:777-791. © 2016 Wiley Periodicals, Inc. PMID:26914439
Non-Markovian coarse-grained modeling of polymeric fluids based on the Mori-Zwanzig formalism
NASA Astrophysics Data System (ADS)
Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George
The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables based on the Mori-Zwanzig formalism. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons on both static and dynamic properties between the CG models with Markovian and non-Markovian approximations will be presented. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.
Khatri, Bhavin S.; Goldstein, Richard A.
2015-01-01
Speciation is fundamental to understanding the huge diversity of life on Earth. Although still controversial, empirical evidence suggests that the rate of speciation is larger for smaller populations. Here, we explore a biophysical model of speciation by developing a simple coarse-grained theory of transcription factor-DNA binding and how their co-evolution in two geographically isolated lineages leads to incompatibilities. To develop a tractable analytical theory, we derive a Smoluchowski equation for the dynamics of binding energy evolution that accounts for the fact that natural selection acts on phenotypes, but variation arises from mutations in sequences; the Smoluchowski equation includes selection due to both gradients in fitness and gradients in sequence entropy, which is the logarithm of the number of sequences that correspond to a particular binding energy. This simple consideration predicts that smaller populations develop incompatibilities more quickly in the weak mutation regime; this trend arises as sequence entropy poises smaller populations closer to incompatible regions of phenotype space. These results suggest a generic coarse-grained approach to evolutionary stochastic dynamics, allowing realistic modelling at the phenotypic level. PMID:25936759
Coarse-graining in peridynamics.
Silling, Stewart Andrew
2010-11-01
The peridynamic theory is an extension of traditional solid mechanics that treats discontinuous media, including the evolution of discontinuities due to fracture, on the same mathematical basis as classically smooth media. A recent advance in the linearized peridynamic theory permits the reduction of the number of degrees of freedom modeled within a body. Under equilibrium conditions, this coarse graining method exactly reproduces the internal forces on the coarsened degrees of freedom, including the effect of the omitted material that is no longer explicitly modeled. The method applies to heterogeneous as well as homogeneous media and accounts for defects in the material. The coarse graining procedure can be repeated over and over, resulting in a hierarchically coarsened description that, at each stage, continues to reproduce the exact internal forces present in the original, detailed model. Each coarsening step results in reduced computational cost. This talk will describe the new peridynamic coarsening method and show computational examples.
Energy-conserving coarse-graining of complex molecules.
Español, Pep; Serrano, Mar; Pagonabarraga, Ignacio; Zúñiga, Ignacio
2016-05-25
Coarse-graining (CG) of complex molecules is a method to reach time scales that would be impossible to access through brute force molecular simulations. In this paper, we formulate a coarse-grained model for complex molecules using first principles caculations that ensures energy conservation. Each molecule is described in a coarse way by a thermal blob characterized by the position and momentum of the center of mass of the molecule, together with its internal energy as an additional degree of freedom. This level of description gives rise to an entropy-based framework instead of the usual one based on the configurational free energy (i.e. potential of mean force). The resulting dynamic equations, which account for an appropriate description of heat transfer at the coarse-grained level, have the structure of the dissipative particle dynamics with energy conservation (DPDE) model but with a clear microscopic underpinning. Under suitable approximations, we provide explicit microscopic expressions for each component (entropy, mean force, friction and conductivity coefficients) appearing in the coarse-grained model. These quantities can be computed directly using MD simulations. The proposed non-isothermal coarse-grained model is thermodynamically consistent and opens up a first principles CG strategy for the study of energy transport issues that are not accessible using current isothermal models. PMID:27127809
Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang
2016-07-01
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. PMID:27394096
NASA Astrophysics Data System (ADS)
Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang
2016-07-01
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 Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences
Ruff, Kiersten M.; Khan, Siddique J.; Pappu, Rohit V.
2014-01-01
The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington’s disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation. PMID:25185558
Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models
Latek, Dorota; Kolinski, Andrzej
2008-01-01
Background Several different methods for contact prediction succeeded within the Sixth Critical Assessment of Techniques for Protein Structure Prediction (CASP6). The most relevant were non-local contact predictions for targets from the most difficult categories: fold recognition-analogy and new fold. Such contacts could provide valuable structural information in case a template structure cannot be found in the PDB. Results We described comprehensive tests of the effectiveness of contact data in various aspects of de novo modeling with CABS, an algorithm which was used successfully in CASP6 by the Kolinski-Bujnicki group. We used the predicted contacts in a simple scoring function for the post-simulation ranking of protein models and as a soft bias in the folding simulations and in the fold-refinement procedure. The latter approach turned out to be the most successful. The CABS force field used in the Replica Exchange Monte Carlo simulations cooperated with the true contacts and discriminated the false ones, which resulted in an improvement of the majority of Kolinski-Bujnicki's protein models. In the modeling we tested different sets of predicted contact data submitted to the CASP6 server. According to our results, the best performing were the contacts with the accuracy balanced with the coverage, obtained either from the best two predictors only or by a consensus from as many predictors as possible. Conclusion Our tests have shown that theoretically predicted contacts can be very beneficial for protein structure prediction. Depending on the protein modeling method, a contact data set applied should be prepared with differently balanced coverage and accuracy of predicted contacts. Namely, high coverage of contact data is important for the model ranking and high accuracy for the folding simulations. PMID:18694501
2013-01-01
Background Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins. Methods This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics. Results Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path. Conclusions The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. PMID:24564964
Li, Tong; Gu, YuanTong
2014-04-15
As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grained level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.
Eun, Changsun; Das, Jhuma; Berkowitz, Max L
2013-12-12
A lattice model is proposed to explain the restructuring of an ionic surfactant absorbed on a charged surface. When immersed in water, an ionic mica plate initially covered by a monolayer of surfactants rearranges to a surface inhomogeneously covered by patches of surfactant bilayer and bare mica. The model considers four species that can cover lattice sites of a surface. These species include (i) a surfactant molecule with its headgroup down, (ii) surfactant molecule with the headgroup up, (iii) a surfactant dimer arranged in a tail-to-tail configuration, which is a part of a bilayer, and (iv) a mica lattice site covered by water. We consider that only nearest neighbors on the lattice interact and describe the interactions by an interaction matrix. Using this model, we perform Monte Carlo simulations and study how the structure of the inhomogeneous surface depends on the interaction between water covered lattice site and its neighboring surfactant species covered sites. We observe that when this interaction is absent, the system undergoes phase separation into a bilayer phase and mica surface covered with water. When this interaction is taken into account, patches of surfactant bilayer and water are present in our system. The interaction between mica surfaces covered by patches of ionic surfactants is studied in experiments to understand the nature of long-ranged "hydrophobic" forces. PMID:23962357
Coarse graining in micromagnetics.
Grinstein, G; Koch, R H
2003-05-23
Numerical solutions of the micromagnetic Landau-Lifshitz-Gilbert equations provide valuable information at low temperatures (T), but produce egregious errors at higher T. For example, Curie temperatures are often overestimated by an order of magnitude. We show that these errors result from the use of block or coarse-grained variables, without a concomitant renormalization of the system parameters to account for the block size. Renormalization solves the problem of the Curie-point anomaly and improves the accuracy of more complicated micromagnetic simulations, even at low T. PMID:12785922
Nair, Nitish; Park, Michelle; Handgraaf, Jan-Willem; Cassiola, Flavia M
2016-09-01
In the tertiary oil recovery method known as "polymer flooding", the viscosity of the injected water is increased by dissolving partially hydrolyzed polyacrylamide so as to lower the mobility ratio and raise the vertical and areal sweep efficiencies. However, its drawbacks include the degradation of the polymer in the reservoir due to (1) shear while passing through chokes, perforations, and pore throats, (2) morphological changes induced by divalent ions, and (3) complete hydrolysis of the polymer at high temperatures. These factors adversely affect the viscosity of the polymer flood. Past experimental research showed that polymer-grafted nanoparticles (PNPs) could achieve the same viscosity enhancement at lower quantities than traditional linear polymers. The PNPs have the putative advantage of greater stability when confronted with the aforementioned reservoir conditions. In this work, we use dissipative particle dynamics (DPD) to simulate the oil-PNP-water system at the mesoscale and estimate its sensitivity to brine in ways that could serve as guidelines to experiments. We study the effect of salinity on the structure of linear and branched polyelectrolytes before extending the DPD model to PNPs at the oil-water interface. To this end, we parameterize the interactions of the polymer with the oil and water phases, and broadly map out solvent conditions that change the graft's morphology and affect the interfacial behavior of the grafted particle. We find that the equilibrium location of the grafted nanoparticle in an oil-brine system depends on its grafting density and the salinity. PMID:27513884
2015-01-01
Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg9) into a model DPPC bilayer. In the case of the Arg9 cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg9) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg9 [Huang, K.; et al. Biophys. J., 2013, 104, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg9 translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg9 translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths
NASA Astrophysics Data System (ADS)
Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo
Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.
de los Santos, Francisco; Franzese, Giancarlo
2011-12-01
We study, by Monte Carlo simulations, a coarse-grained model of a water monolayer between hydrophobic walls at partial hydration, with a wall-to-wall distance of about 0.5 nm. We analyze how the diffusion constant parallel to the walls, D(∥), changes and correlates to the phase diagram of the system. We find a locus of D(∥) maxima and a locus of D(∥) minima along isotherms, with lines of constant D(∥) resembling the melting line of bulk water. The two loci of D(∥) extrema envelope the line of temperatures of density maxima at constant P. We show how these loci are related to the anomalous volume behavior due to the hydrogen bonds. At much lower T, confined water becomes subdiffusive, and we discuss how this behavior is a consequence of the increased correlations among water molecules when the hydrogen bond network develops. Within the subdiffusive region, although translations are largely hampered, we observe that the hydrogen bond network can equilibrate, and its rearrangement is responsible for the appearance of density minima along isobars. We clarify that the minima are not necessarily related to the saturation of the hydrogen bond network. PMID:22129131
NASA Astrophysics Data System (ADS)
Lafitte, Thomas; Avendaño, Carlos; Papaioannou, Vasileios; Galindo, Amparo; Adjiman, Claire S.; Jackson, George; Müller, Erich A.
2012-06-01
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C.S. Adjiman, G. Jackson, and E.A. Müller, J. Phys. Chem. B 115, 11154 (2011)] our methodology for the development of accurate coarse-grained (CG) SAFT-γ force fields for the computer simulation of molecular fluids was introduced with carbon dioxide as a particular case study. The procedure involves the use of a molecular-based equation of state to obtain effective intermolecular parameters (from experimental fluid phase equilibrium data) appropriate for molecular simulation over a wide range of fluid conditions. We now extend the methodology to develop coarse-grained models for benzene (C6H6) that can be used in fluid phase simulations. Our SAFT-γ CG force fields for benzene consist of a simple single-segment spherical model, and a rigid three-segment ring structure of tangent spherical groups interacting via Mie (generalized Lennard-Jones) segment-segment interactions. The description of the fluid phase behaviour of benzene with our simplified CG force fields is found to be comparable to that obtained with the more sophisticated models commonly used in the field; a marked improvement is seen with our SAFT-γ models for the vapour pressure, particularly at lower temperatures. These models of benzene together with the previously developed SAFT-γ three-segment chain model of n-decane are used to develop hetero-group force fields for n-decylbenzene, in the spirit of a group contribution methodology. In our approach, the parameters of the phenyl and n-decyl groups are obtained transferably from the individual models of benzene and n-decane, respectively, and the unlike energetic parameters between the phenyl and decyl segments can be obtained from vapour-liquid equilibria data for n-decylbenzene using the SAFT-γ equation of state. The resulting CG hetero-group models are found to describe the fluid properties of n-decylbenzene over a wide range of conditions, exemplifying how our approach
Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation
Smith, Gregory R.; Xie, Lu; Schwartz, Russell
2016-01-01
The environment of a living cell is vastly different from that of an in vitro reaction system, an issue that presents great challenges to the use of in vitro models, or computer simulations based on them, for understanding biochemistry in vivo. Virus capsids make an excellent model system for such questions because they typically have few distinct components, making them amenable to in vitro and modeling studies, yet their assembly can involve complex networks of possible reactions that cannot be resolved in detail by any current experimental technology. We previously fit kinetic simulation parameters to bulk in vitro assembly data to yield a close match between simulated and real data, and then used the simulations to study features of assembly that cannot be monitored experimentally. The present work seeks to project how assembly in these simulations fit to in vitro data would be altered by computationally adding features of the cellular environment to the system, specifically the presence of nucleic acid about which many capsids assemble. The major challenge of such work is computational: simulating fine-scale assembly pathways on the scale and in the parameter domains of real viruses is far too computationally costly to allow for explicit models of nucleic acid interaction. We bypass that limitation by applying analytical models of nucleic acid effects to adjust kinetic rate parameters learned from in vitro data to see how these adjustments, singly or in combination, might affect fine-scale assembly progress. The resulting simulations exhibit surprising behavioral complexity, with distinct effects often acting synergistically to drive efficient assembly and alter pathways relative to the in vitro model. The work demonstrates how computer simulations can help us understand how assembly might differ between the in vitro and in vivo environments and what features of the cellular environment account for these differences. PMID:27244559
Beguerisse-Díaz, Mariano; Desikan, Radhika; Barahona, Mauricio
2016-08-01
Cellular signal transduction usually involves activation cascades, the sequential activation of a series of proteins following the reception of an input signal. Here, we study the classic model of weakly activated cascades and obtain analytical solutions for a variety of inputs. We show that in the special but important case of optimal gain cascades (i.e. when the deactivation rates are identical) the downstream output of the cascade can be represented exactly as a lumped nonlinear module containing an incomplete gamma function with real parameters that depend on the rates and length of the cascade, as well as parameters of the input signal. The expressions obtained can be applied to the non-identical case when the deactivation rates are random to capture the variability in the cascade outputs. We also show that cascades can be rearranged so that blocks with similar rates can be lumped and represented through our nonlinear modules. Our results can be used both to represent cascades in computational models of differential equations and to fit data efficiently, by reducing the number of equations and parameters involved. In particular, the length of the cascade appears as a real-valued parameter and can thus be fitted in the same manner as Hill coefficients. Finally, we show how the obtained nonlinear modules can be used instead of delay differential equations to model delays in signal transduction. PMID:27581482
Desikan, Radhika
2016-01-01
Cellular signal transduction usually involves activation cascades, the sequential activation of a series of proteins following the reception of an input signal. Here, we study the classic model of weakly activated cascades and obtain analytical solutions for a variety of inputs. We show that in the special but important case of optimal gain cascades (i.e. when the deactivation rates are identical) the downstream output of the cascade can be represented exactly as a lumped nonlinear module containing an incomplete gamma function with real parameters that depend on the rates and length of the cascade, as well as parameters of the input signal. The expressions obtained can be applied to the non-identical case when the deactivation rates are random to capture the variability in the cascade outputs. We also show that cascades can be rearranged so that blocks with similar rates can be lumped and represented through our nonlinear modules. Our results can be used both to represent cascades in computational models of differential equations and to fit data efficiently, by reducing the number of equations and parameters involved. In particular, the length of the cascade appears as a real-valued parameter and can thus be fitted in the same manner as Hill coefficients. Finally, we show how the obtained nonlinear modules can be used instead of delay differential equations to model delays in signal transduction. PMID:27581482
Schindler, Tanja; Kröner, Dietmar; Steinhauser, Martin O
2016-09-01
We present a molecular dynamics simulation study of the self-assembly of coarse-grained lipid molecules from unbiased random initial configurations. Our lipid model is based on a well-tried CG polymer model with an additional potential that mimics the hydrophobic properties of lipid tails. We find that several stages of self-organization of lipid clusters are involved in the dynamics of bilayer formation and that the resulting equilibrium structures sensitively depend on the strength of hydrophobic interactions hc of the lipid tails and on temperature T. The obtained stable lipid membranes are quantitatively analyzed with respect to their local structure and their degree of order. At equilibrium, we obtain self-stabilizing bilayer membrane structures that exhibit a bending stiffness κB and compression modulus KC comparable to experimental measurements under physiological conditions. We present a phase diagram of our lipid model which covers a sol-gel transition, a liquid (or gel-like) phase including stable bilayer structures and vesicle formation, as well as a quasi-crystalline phase. We also determine the exact conditions for temperature T and degree of hydrophobicity hc for stable bilayer formation including closed vesicles. PMID:27216316
Shelley, Michael; McLaughlin, David
2002-01-01
We present a reduction of a large-scale network model of visual cortex developed by McLaughlin, Shapley, Shelley, and Wielaard. The reduction is from many integrate-and-fire neurons to a spatially coarse-grained system for firing rates of neuronal subpopulations. It accounts explicitly for spatially varying architecture, ordered cortical maps (such as orientation preference) that vary regularly across the cortical layer, and disordered cortical maps (such as spatial phase preference or stochastic input conductances) that may vary widely from cortical neuron to cortical neuron. The result of the reduction is a set of nonlinear spatiotemporal integral equations for "phase-averaged" firing rates of neuronal subpopulations across the model cortex, derived asymptotically from the full model without the addition of any extra phenomological constants. This reduced system is used to study the response of the model to drifting grating stimuli-where it is shown to be useful for numerical investigations that reproduce, at far less computational cost, the salient features of the point-neuron network and for analytical investigations that unveil cortical mechanisms behind the responses observed in the simulations of the large-scale computational model. For example, the reduced equations clearly show (1) phase averaging as the source of the time-invariance of cortico-cortical conductances, (2) the mechanisms in the model for higher firing rates and better orientation selectivity of simple cells which are near pinwheel centers, (3) the effects of the length-scales of cortico-cortical coupling, and (4) the role of noise in improving the contrast invariance of orientation selectivity. PMID:12053156
Sarman, Sten; Wang, Yong-Lei; Laaksonen, Aatto
2016-06-22
Thermomechanical coupling in cholesteric liquid crystals, i.e. when a temperature gradient parallel to the cholesteric axis rotates the director, has been studied in a model system of soft ellipsoids where the interaction potential has been augmented by a chiral potential. More specifically, the cross coupling coefficient between the temperature gradient and the director angular velocity, or Leslie coefficient, has been obtained as a function of the pitch by evaluating the corresponding Green-Kubo relation by molecular dynamics simulation. The product of the Leslie coefficient and the pitch has been found to be constant within the statistical uncertainty. This is in accordance with a symmetry condition originally proposed by de Gennes and it means that the Leslie coefficient of systems with longer pitches can be obtained from systems with shorter pitches. Since the pitches of realistic systems are usually very long, it becomes possible to study thermomechanical coupling in these systems which otherwise would have required prohibitively long simulations. Since we also have obtained rather accurate data on the cross correlation function between the director angular velocity and the heat current density, it becomes possible to analyse the mechanism of thermomechanical coupling to some extent. PMID:27279499
Alves, Carla S; Kairys, Visvaldas; Castanho, Miguel A R B; Fernandes, Miguel X
2012-01-01
This work focuses on the conformational and dynamic properties of the antimicrobial peptides (AMPs), BP100 and pepR, when confined within model membrane systems. Brownian dynamics (BD) simulations of a coarse-grained model of each respective peptide in an environment reproducing the phospholipid bilayer were carried out. Simple mean-field potentials were used to reproduce three physically different model phosphatidylcholine (PC) membrane systems. Based on the simplicity of the peptide-membrane models used, 1 micros simulations were performed. With the appropriate choice of parameters, the structure and dynamics of each peptide were recovered from each of the simulated BD trajectories. BP100 was observed to adopt a alpha-helical conformation when confined in each PC membrane. For pepR under the same conditions, the formation of an N-terminal alpha-helix was detected, whereas the C-terminus appeared to be less ordered. The dynamic properties of each peptide were characterized in terms of local and global motions. BP100 tended to localize with no preferred orientation approximately halfway across each membrane leaflet, whereas pepR localized near the membrane core with no preferred orientation. Overall, the peptide dynamics were found to vary according to the size of the peptide, as well as the width of the membrane environment. PMID:23193594
NASA Astrophysics Data System (ADS)
Español, P.; de la Torre, J. A.; Ferrario, M.; Ciccotti, G.
2011-11-01
The method of constraints in molecular dynamics is useful because it avoids the resolution of high frequency motions with very small time steps. However, the price to pay is that both the dynamics and the statistics of a constrained system differ from those of the unconstrained one. Instead of using constraints, we propose to dispose of high frequency motions by a coarse-graining procedure in which fast variables are eliminated. These fast variables are thus modeled as friction and thermal fluctuations. We illustrate the methodology with a simple model case, a diatomic molecule in a monoatomic solvent, in which the bond between the atoms of a diatomic molecule is stiff. Although the example is very simple and does not display the interesting effects of "wrong" statistics of the constrained system (i.e. the well-known issue connected to the Fixman potential), it is well suited to give the proof of concept of the whole procedure.
Coarse-grained description of polymer blends as chains of interacting soft particles
NASA Astrophysics Data System (ADS)
Walton, Kevin; Guenza, Marina
We present an analytic pair potential in a coarse grain description of a polymer blend where each chain is represented as a chain of soft-colloidal particles. This coarse grain model is based on integral theory that can represent the chains at variable levels.The particles have soft repulsion at separation less than the size of each coarse grain unit and a long repulsive tail with small attractive portion. While the short range pieces of the potential dominates the liquid structure, the long range tail dominate the thermodynamics of the system. So an accurate potential in both the short and long range distances is need to keep give correct structure and thermodynamical properties in the coarse grain description.
NASA Astrophysics Data System (ADS)
Higuchi, Yuji; Kubo, Momoji
2016-06-01
We study fracture processes of amorphous and semicrystalline polymers with a coarse-grained molecular dynamics simulation. In the amorphous state, the stress caused by strain mainly arises from the loss of the attractive interaction in the voids. However, in semicrystalline polymers, the elongation of bonding is the dominant factor and it causes much more stress than that in an amorphous state. This is because growth of the voids is prevented by the amorphous regions and it is difficult to relax the folded polymers.
Systematic and Simulation-Free Coarse-Graining of Polymer Melts using Soft Potentials
NASA Astrophysics Data System (ADS)
Yang, Delian; Wang, Qiang
2014-03-01
Full atomistic simulations of multi-chain systems are not feasible at present due to their formidable computational requirements. Molecular simulations with coarse-grained models have to be used instead, where each segment represents, for example, the center-of-mass of a group of atoms or real monomers. While atoms interact with hard excluded-volume interactions (e.g., the Lennard-Jones potential) and cannot overlap, the coarse-grained segments can certainly overlap and should therefore interact with soft potentials that allow complete particle overlapping. Coarse-grained models, however, reduce the chain conformational entropy, which plays an essential role in the behavior of polymeric systems. In this work, we use integral-equation theories, instead of molecular simulations, to perform both the structure-based and relative-entropy-based coarse-graining of homopolymer melts, and systematically examine how the coarse-grained soft potential varies with N (the number of segments on each chain) and how well the coarse-grained models reproduce both the structural and thermodynamic properties of the original system. This provides us with a quantitative basis for choosing small N-values that can still capture the chain conformational entropy, a characteristics of polymers.
Markutsya, Sergiy; Lamm, Monica H
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.
Ardham, Vikram Reddy; Leroy, Frédéric E-mail: f.leroy@theo.chemie.tu-darmstadt.de; Deichmann, Gregor; Vegt, Nico F. A. van der E-mail: f.leroy@theo.chemie.tu-darmstadt.de
2015-12-28
We address the question of how reducing the number of degrees of freedom modifies the interfacial thermodynamic properties of heterogeneous solid-liquid systems. We consider the example of n-hexane interacting with multi-layer graphene which we model both with fully atomistic and coarse-grained (CG) models. The CG models are obtained by means of the conditional reversible work (CRW) method. The interfacial thermodynamics of these models is characterized by the solid-liquid work of adhesion W{sub SL} calculated by means of the dry-surface methodology through molecular dynamics simulations. We find that the CRW potentials lead to values of W{sub SL} that are larger than the atomistic ones. Clear understanding of the relationship between the structure of n-hexane in the vicinity of the surface and W{sub SL} is elucidated through a detailed study of the energy and entropy components of W{sub SL}. We highlight the crucial role played by the solid-liquid energy fluctuations. Our approach suggests that CG potentials should be designed in such a way that they preserve the range of solid-liquid interaction energies, but also their fluctuations in order to preserve the reference atomistic value of W{sub SL}. Our study thus opens perspectives into deriving CG interaction potentials that preserve the thermodynamics of solid-liquid contacts and will find application in studies that intend to address materials driven by interfaces.
Saielli, Giacomo; Wang, Yanting
2016-09-01
In order to investigate the role of the electrostatic interactions in stabilizing various phases of ionic liquids, especially smectic ionic liquid crystals, we have employed a coarse-grained model of 1-hexadecyl-3-methylimidazolium nitrate, [C16mim][NO3], to perform molecular dynamics simulations with the partial charges artificially rescaled by a factor from 0.7 to 1.2. The simulated systems have been characterized by means of orientational and translational order parameters and by distribution functions. We have found that increasing the total charge of the ions strongly stabilizes the ionic smectic phase by shifting the clearing point (melting into the isotropic liquid phase) to higher temperatures, while a smaller effect is observed on the stability of the crystal phase. Our results highlight the importance of the electrostatic interactions in promoting the formation of ionic liquid crystals through microphase segregation. Moreover, as the total charge of the model is increased, we observe a transformation from a homogeneous to a nanosegregated isotropic structure typical of ionic liquids. Therefore, a connection can be established between the degree of nanosegregation of ILs and the stability of ILC phases. All the above can be understood by the competition among electrostatic interactions between charged groups (cationic head groups and anions), van der Waals interactions between nonpolar cationic tail groups, and thermal fluctuations. PMID:27486996
Cao, Zhen; Voth, Gregory A.
2015-12-28
It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.
NASA Astrophysics Data System (ADS)
Trément, Sébastien; Schnell, Benoît.; Petitjean, Laurent; Couty, Marc; Rousseau, Bernard
2014-04-01
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.
Trément, Sébastien; Schnell, Benoît; Petitjean, Laurent; Couty, Marc; Rousseau, Bernard
2014-04-01
We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems. PMID:24712786
Zhang, Deqiang; Konecny, Robert; Baker, Nathan A.; McCammon, J. Andrew
2008-01-01
Although many viruses have been crystallized and the protein capsid structures have been determined by X-ray crystallography, the nucleic acids often can not be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of Cowpea Chlorotic Mottle Virus (CCMV). Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive-charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations. PMID:15386271
NASA Astrophysics Data System (ADS)
Pandey, R. B.; Farmer, B. L.
2009-01-01
Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.
Impact into Coarse Grained Spheres
NASA Technical Reports Server (NTRS)
Barnouin-Jha, O. S.; Cintala, M.; Crawford, D. A.
2005-01-01
Several experimental studies [1,2,3] indicate that differences in the grain size of the target relative to the projectile could influence the cratering process. Impacts into coarse sand grains of size comparable to the projectile show some discrepancies with existing relationships for crater growth [e.g. 4]. Similarly, targets of ne grained, uniform in diameter glass spheres show differences in crater depth, transient crater diameter, and volume of ejecta excavated as a function of grain size [2,3]. The purpose of this work is to continue investigating how the relative grain size may influence early time coupling between a projectile and target, with implications for subsequent ejecta excavation and crater growth. In previous efforts we used numerical techniques to focus on the propagation of shock waves in coarse, granular media emphasizing the influence of relative grain size on crater growth, ejecta production, cratering efficiency, target strength, and crater shape [5,6,7]. In this study, we use experimental techniques - in part as a reality check for the numerical studies - to report on how coarse grained targets might influence ejecta excavation and crater shape. This body of work possesses important implications for ejecta excavation and cratering efficiency on asteroids that may possess rubble pile-like structures, and on planets that may possess either pre-fractured surfaces or large-scale heterogeneities in shock impedance.
NASA Astrophysics Data System (ADS)
Joyeux, Marc
2014-09-01
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes, the precise structure of complexes of DNA and H-NS proteins is still not well understood. In particular, it is not clear whether the structure of DNA/H-NS complexes in the living cell is similar to that of complexes deposited on mica surfaces, which may be observed by AFM microscopy. A coarse-grained model, which helps getting more insight into this question, is described and analyzed in the present paper. This model is able of describing both the bridging of bacterial DNA by H-NS in the bulk and the deposition and equilibration of the complex on a charged surface. Simulations performed with the model reveal that a slight attraction between DNA and the charged surface is sufficient to let DNA/H-NS complexes reorganize from 3D coils to planar plasmids bridged by H-NS proteins similar to those observed by AFM microscopy. They furthermore highlight the antagonistic effects of the interactions between DNA and the surface. Indeed, increasing these interactions slows down the equilibration of naked plasmids on the surface but, on the other hand, enables a faster equilibration of DNA/H-NS complexes. Based on the distribution of the lifetimes of H-NS bridges and the time evolution of the number of trans-binding protein dimers during equilibration of the complexes on the surface, it is argued that the decrease of the equilibration time of the complex upon increase of the interaction strength between DNA and the surface is ascribable to the associated decrease of the probability to form new bridges between DNA and the proteins.
Coarse graining of force fields for metal-organic frameworks.
Dürholt, Johannes P; Galvelis, Raimondas; Schmid, Rochus
2016-03-14
We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four coordinated vertex, was developed as a proof of concept. By adding non-bonded interactions with a modified Buckingham potential, the resulting MOF-FF-CGNB is able to predict local deformation energies of the building blocks as well as bulk properties like the tbovs.pto energy difference or elastic constants in a semi-quantitative way. As expected, the negative thermal expansion of HKUST-1 is not reproduced by the maximally coarse grained model. At the expense of atomic resolution, substantially larger systems (up to tens of nanometers in size) can be simulated with respect to structural and mechanical properties, bridging the gap to the mesoscale. As an example the deformation of the [111] surface of HKUST-1 by a "tip" could be computed without artifacts from periodic images. PMID:26732756
Fan, Yanping; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars
2013-01-01
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. PMID:23418426
Frappier, Vincent; Najmanovich, Rafael J.
2014-01-01
Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569
Measuring Crack Length in Coarse Grain Ceramics
NASA Technical Reports Server (NTRS)
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.
Braun, Daniel; Boresch, Stefan; Steinhauser, Othmar
2014-02-14
Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.
NASA Astrophysics Data System (ADS)
Braun, Daniel; Boresch, Stefan; Steinhauser, Othmar
2014-02-01
Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough.
Braun, Daniel; Boresch, Stefan; Steinhauser, Othmar
2014-02-14
Long-term molecular dynamics simulations are used to compare the single particle dipole reorientation time, the diffusion constant, the viscosity, and the frequency-dependent dielectric constant of the coarse-grained big multipole water (BMW) model to two common atomistic three-point water models, SPC/E and TIP3P. In particular, the agreement between the calculated viscosity of BMW and the experimental viscosity of water is satisfactory. We also discuss contradictory values for the static dielectric properties reported in the literature. Employing molecular hydrodynamics, we show that the viscosity can be computed from single particle dynamics, circumventing the slow convergence of the standard approaches. Furthermore, our data indicate that the Kivelson relation connecting single particle and collective reorientation time holds true for all systems investigated. Since simulations with coarse-grained force fields often employ extremely large time steps, we also investigate the influence of time step on dynamical properties. We observe a systematic acceleration of system dynamics when increasing the time step. Carefully monitoring energy/temperature conservation is found to be a sufficient criterion for the reliable calculation of dynamical properties. By contrast, recommended criteria based on the ratio of fluctuations of total vs. kinetic energy are not sensitive enough. PMID:24527900
Interlaced coarse-graining for the dynamic cluster approximation
NASA Astrophysics Data System (ADS)
Staar, P.; Jiang, M.; Hähner, U. R.; Schulthess, T. C.; Maier, T. A.
2016-04-01
The dynamical cluster approximation (DCA) and its DCA+ extension use coarse-graining of the momentum space to reduce the complexity of quantum many-body problems, thereby mapping the bulk lattice to a cluster embedded in a dynamical mean-field host. Here, we introduce a new form of an interlaced coarse-graining and compare it with the traditional coarse-graining. While it gives a more localized self-energy for a given cluster size, we show that it leads to more controlled results with weaker cluster shape and smoother cluster size dependence, which converge to the results obtained from the standard coarse-graining with increasing cluster size. Most importantly, the new coarse-graining reduces the severity of the fermionic sign problem of the underlying quantum Monte Carlo cluster solver and thus allows for calculations on larger clusters. This enables the treatment of correlations longer ranged than those accessible with the standard coarse-graining and thus can allow for the evaluation of the exact infinite cluster size result via finite size scaling. As a demonstration, we study the hole-doped two-dimensional Hubbard model and show that the interlaced coarse-graining in combination with the extended DCA+ algorithm permits the determination of the superconducting Tc on cluster sizes for which the results can be fit with a Kosterlitz-Thouless scaling law.
Peroxidised phospholipid bilayers: insight from coarse-grained molecular dynamics simulations.
Guo, Yachong; Baulin, Vladimir A; Thalmann, Fabrice
2016-01-01
An original coarse-grained model for peroxidised phospholipids is presented, based on the MARTINI lipid force field. This model results from a combination of thermodynamic modelling and structural information on the area per lipid, which have been made available recently. The resulting coarse-grained lipid molecules form stable bilayers, and a set of elastic coefficients (compressibility and bending moduli) is obtained. We compare the compressibility coefficient to the experimental values [Weber et al., Soft Matter, 2014, 10, 4241]. Predictions for the mechanical properties, membrane thickness and lateral distribution of hydroperoxide groups in the phospholipid bilayer are presented. PMID:26462464
Hasnain, Sabeeha; McClendon, Christopher L; Hsu, Monica T; Jacobson, Matthew P; Bandyopadhyay, Pradipta
2014-01-01
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI. PMID:25180859
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. PMID:26675481
NASA Astrophysics Data System (ADS)
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 60Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60Co 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.
Interlaced coarse-graining for the dynamical cluster approximation
NASA Astrophysics Data System (ADS)
Haehner, Urs; Staar, Peter; Jiang, Mi; Maier, Thomas; Schulthess, Thomas
The negative sign problem remains a challenging limiting factor in quantum Monte Carlo simulations of strongly correlated fermionic many-body systems. The dynamical cluster approximation (DCA) makes this problem less severe by coarse-graining the momentum space to map the bulk lattice to a cluster embedded in a dynamical mean-field host. Here, we introduce a new form of an interlaced coarse-graining and compare it with the traditional coarse-graining. We show that it leads to more controlled results with weaker cluster shape and smoother cluster size dependence, which with increasing cluster size converge to the results obtained using the standard coarse-graining. In addition, the new coarse-graining reduces the severity of the fermionic sign problem. Therefore, it enables calculations on much larger clusters and can allow the evaluation of the exact infinite cluster size result via finite size scaling. To demonstrate this, we study the hole-doped two-dimensional Hubbard model and show that the interlaced coarse-graining in combination with the DCA+ algorithm permits the determination of the superconducting Tc on cluster sizes, for which the results can be fitted with the Kosterlitz-Thouless scaling law. This research used resources of the Oak Ridge Leadership Computing Facility (OLCF) awarded by the INCITE program, and of the Swiss National Supercomputing Center. OLCF is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725.
NASA Astrophysics Data System (ADS)
Meyer, Sam; Everaers, Ralf
2015-02-01
The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.
Holm, Christian; Gompper, Gerhard; Dill, Ken A
2015-12-28
This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling. PMID:26723585
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes
NASA Astrophysics Data System (ADS)
Holm, Christian; Gompper, Gerhard; Dill, Ken A.
2015-12-01
This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes
Holm, Christian; Gompper, Gerhard; Dill, Ken A.
2015-12-28
This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.
Minimizing memory as an objective for coarse-graining
NASA Astrophysics Data System (ADS)
Guttenberg, Nicholas; Dama, James F.; Saunders, Marissa G.; Voth, Gregory A.; Weare, Jonathan; Dinner, Aaron R.
2013-03-01
Coarse-graining a molecular model is the process of integrating over degrees of freedom to obtain a reduced representation. This process typically involves two separate but related steps, selection of the coordinates comprising the reduced system and modeling their interactions. Both the coordinate selection and the modeling procedure present challenges. Here, we focus on the former. Typically, one seeks to integrate over the fast degrees of freedom and retain the slow degrees of freedom. Failure to separate timescales results in memory. With this motivation, we introduce a heuristic measure of memory and show that it can be used to compare competing coordinate selections for a given modeling procedure. We numerically explore the utility of this heuristic for three systems of increasing complexity. The first example is a four-particle linear model, which is exactly solvable. The second example is a sixteen-particle nonlinear model; this system has interactions that are characteristic of molecular force fields but is still sufficiently simple to permit exhaustive numerical treatment. The third example is an atomic-resolution representation of a protein, the class of models most often treated by relevant coarse-graining approaches; we specifically study an actin monomer. In all three cases, we find that the heuristic suggests coordinate selections that are physically intuitive and reflect molecular structure. The memory heuristic can thus serve as an objective codification of expert knowledge and a guide to sites within a model that requires further attention.
Simulating the entropic collapse of coarse-grained chromosomes.
Shendruk, Tyler N; Bertrand, Martin; de Haan, Hendrick W; Harden, James L; Slater, Gary W
2015-02-17
Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition. PMID:25692586
Simulating the Entropic Collapse of Coarse-Grained Chromosomes
Shendruk, Tyler N.; Bertrand, Martin; de Haan, Hendrick W.; Harden, James L.; Slater, Gary W.
2015-01-01
Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition. PMID:25692586
Quan, Xuebo; Peng, ChunWang; Dong, Jiaqi; Zhou, Jian
2016-04-14
In this work, the structural properties of amphiphilic polymer-brush-grafted gold nanoparticles (AuNPs) at the oil-water interface were investigated by coarse-grained simulations. The effects of grafting architecture (diblock, mixed and Janus brush-grafted AuNPs) and hydrophilicity of polymer brushes are discussed. Simulation results indicate that functionalized AuNPs present abundant morphologies including typical core-shell, Janus-type, jellyfish-like, etc., in a water or oil-water solvent environment. It is found that hydrophobic/weak hydrophilic polymer-brush-grafted AuNPs have better phase transfer performance, especially for AuNPs modified with hydrophobic chains as outer blocks and weak hydrophilic chains as inner blocks. This kind of AuNP can cross the interface region and move into the oil phase completely. For hydrophobic/strong hydrophilic polymer-brush-grafted AuNPs, they are trapped in the interface region instead of moving into any phase. The mechanism of phase transfer is ascribed to the flexibility and mobility of outer blocks. Besides, we study the desorption energy by PMF analysis. The results demonstrate that Janus brush-grafted AuNPs show the highest interfacial stability and activity, which can be further strengthened by increasing the hydrophilicity of grafted polymer brushes. This work will promote the industrial applications of polymer-brush-grafted NPs such as phase transfer catalysis and Pickering emulsion catalysis. PMID:26954721
Manzotti, Alessandro; Peloso, Marco; Pietroni, Massimo; Viel, Matteo; Villaescusa-Navarro, Francisco E-mail: peloso@physics.umn.edu E-mail: viel@oats.inaf.it
2014-09-01
Standard cosmological perturbation theory (SPT) for the Large Scale Structure (LSS) of the Universe fails at small scales (UV) due to strong nonlinearities and to multistreaming effects. In ref. [1] a new framework was proposed in which the large scales (IR) are treated perturbatively while the information on the UV, mainly small scale velocity dispersion, is obtained by nonlinear methods like N-body simulations. Here we develop this approach, showing that it is possible to reproduce the fully nonlinear power spectrum (PS) by combining a simple (and fast) 1-loop computation for the IR scales and the measurement of a single, dominant, correlator from N-body simulations for the UV ones. We measure this correlator for a suite of seven different cosmologies, and we show that its inclusion in our perturbation scheme reproduces the fully non-linear PS with percent level accuracy, for wave numbers up to k∼ 0.4 h Mpc{sup -1} down to 0z=. We then show that, once this correlator has been measured in a given cosmology, there is no need to run a new simulation for a different cosmology in the suite. Indeed, by rescaling this correlator by a proper function computable in SPT, the reconstruction procedure works also for the other cosmologies and for all redshifts, with comparable accuracy. Finally, we clarify the relation of this approach to the Effective Field Theory methods recently proposed in the LSS context.
NASA Astrophysics Data System (ADS)
Davris, T.; Lyulin, A. V.
2015-08-01
We present results from molecular-dynamics simulations of a generic bead-spring model of copolymer chains confined between solid walls and report on the glass-transition temperature and segmental dynamics as a function of film thickness and mesh size (the end-to-end distance of the subchains in the crosslinked polymer networks). Apparently, the glass-transition temperature displayed a steep increase for mesh-size values much smaller than the radius of gyration of the bulk chains, otherwise it remained invariant to mesh-size variations. The rise in the glass-transition temperature with decreasing mesh size and film thickness was accompanied by a monotonic slowing-down of segmental dynamics on all studied length scales. This observation is attributed to the correspondingly decreased width of the bulk density layer that was obtained in films whose thickness was larger than the end-to-end distance of the bulk polymer chains. To test this hypothesis, additional simulations were performed in which the crystalline walls were replaced with amorphous or rough walls. In the amorphous case, the high polymer density close to the walls vanished, but the dynamic response of the film was not affected. The rough walls, on the other hand, only slightly decreased the density close to the walls and led to a minor slowing-down in the dynamics at large length-scales.
NASA Astrophysics Data System (ADS)
Quinn, Bonnie; Peyronel, Fernanda; Gordon, Tyler; Marangoni, Alejandro; Hanna, Charles B.; Pink, David A.
2014-11-01
Triacylglycerols (TAGs) are biologically important molecules which form crystalline nanoplatelets (CNPs) and, ultimately, fat crystal networks in edible oils. Characterizing the self-assembled hierarchies of these networks is important to understanding their functionality and oil binding capacity. We have modelled CNPs in multicomponent oils and studied their aggregation. The oil comprises (a) a liquid componentt, and (b) components which phase separately on a nano-scale (nano-phase separation) to coat the surfaces of the CNPs impenetrably, either isotropically or anisotropically, with either liquid-like coatings or crystallites, forming a coating of thickness Δ. We modelled three cases: (i) liquid-liquid nano-phase separation, (ii) solid-liquid nano-phase separation, with CNPs coated isotropically, and (iii) CNPs coated anisotropically. The models were applied to mixes of tristearin and triolein with fully hydrogenated canola oil, shea butter with high oleic sunflower oil, and cotton seed oil. We performed Monte Carlo simulations, computed structure functions and concluded: (1) three regimes arose: (a) thin coating regime, Δ \\lt 0.0701 u (b) transition regime, 0.0701 u≤slant Δ ≤slant 0.0916 u and (c) thick coating regime, Δ \\gt 0.0916 u . (arbitrary units, u) (2) The thin coating regime exhibits 1D TAGwoods, which aggregate, via DLCA/RLCA, into fractal structures which are uniformly distributed in space. (3) In the thick coating regime, for an isotropic coating, TAGwoods are not formed and coated CNPs will not aggregate but will be uniformly distributed in space. For anisotropic coating, TAGwoods can be formed and might form 1D strings but will not form DLCA/RLCA clusters. (4) The regimes are, approximately: thin coating, 0\\lt Δ \\lt 7.0 \\text{nm} transition regime, 7.0\\ltΔ \\lt 9.2 \\text{nm} and thick coating, Δ \\gt 9.2 \\text{nm} (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin
Million atom DFT calculations using coarse graining and petascale computing
NASA Astrophysics Data System (ADS)
Nicholson, Don; Odbadrakh, Kh.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X. G.; Stocks, G. M.
2014-03-01
Researchers performing classical Molecular Dynamics (MD) on defect structures often find it necessary to use millions of atoms in their models. It would be useful to perform density functional calculations on these large configurations in order to observe electron-based properties such as local charge and spin and the Helmann-Feynman forces on the atoms. The great number of atoms usually requires that a subset be ``carved'' from the configuration and terminated in a less that satisfactory manner, e.g. free space or inappropriate periodic boundary conditions. Coarse graining based on the Locally Self-consistent Multiple Scattering method (LSMS) and petascale computing can circumvent this problem by treating the whole system but dividing the atoms into two groups. In Coarse Grained LSMS (CG-LSMS) one group of atoms has its charge and scattering determined prescriptively based on neighboring atoms while the remaining group of atoms have their charge and scattering determined according to DFT as implemented in the LSMS. The method will be demonstrated for a one-million-atom model of a displacement cascade in Fe for which 24,130 atoms are treated with full DFT and the remaining atoms are treated prescriptively. Work supported as part of Center for Defect Physics, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, Basic Energy Sciences, used Oak Ridge Leadership Computing Facility, Oak Ridge National Lab, of DOE Office of Science.
NASA Astrophysics Data System (ADS)
Nunes, Sandra C. C.; Almeida, J. A. S.; Dias, R. S.; Pais, A. A. C. C.
2013-01-01
Cationic systems composed of lipids and/or surfactants are of paramount importance in a variety of applications. Within these, gemini have attracted particular attention, mainly due to their improved aggregation properties and to the possibility of tuning offered by the presence of a spacer. In this work, a Monte Carlo simulation study with a coarse-grained model was employed to assess the interaction of cationic gemini surfactants with a like-charged model membrane. Separating the contribution of the excluded volume and that of the electrostatic effects in the organization of gemini-lipid membranes was the first goal of this work and the role of these factors was assessed varying the concentration, the spacer length and the headgroup charge of gemini surfactants. The results provide a new insight on the organization of lipid headgroups in the vicinity of gemini surfactants. It was found that the surfactant-lipid interaction is strongly affected by the surfactant spacer length, being controlled by an overall balance between excluded volume and surfactant-lipid and surfactant-surfactant electrostatic effects. It is also seen that the out-of-plane motion of the spacer has a significant effect upon membrane organization and counterion condensation. Good agreement was found with results previously obtained from atomistic simulation.
Path-space variational inference for non-equilibrium coarse-grained systems
NASA Astrophysics Data System (ADS)
Harmandaris, Vagelis; Kalligiannaki, Evangelia; Katsoulakis, Markos; Plecháč, Petr
2016-06-01
In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirely data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.
NASA Astrophysics Data System (ADS)
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.
Tadmor, Arbel D.; Tlusty, Tsvi
2008-01-01
We propose a biophysical model of Escherichia coli 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. PMID:18437222
Coarse-grained interaction potentials for anisotropic molecules.
Babadi, M; Everaers, R; Ejtehadi, M R
2006-05-01
We have proposed an efficient parametrization method for a recent variant of the Gay Berne potential for dissimilar and biaxial particles [Phys. Rev. E 67, 041710 (2003)] and demonstrated it for a set of small organic molecules. Compared with the previously proposed coarse-grained models, the new potential exhibits a superior performance in close contact and large distant interactions. The repercussions of thermal vibrations and elasticity have been studied through a statistical method. The study justifies that the potential of mean force is representable with the same functional form, extending the application of this coarse-grained description to a broader range of molecules. Moreover, the advantage of employing coarse-grained models over truncated atomistic summations with large distance cutoffs has been briefly studied. PMID:16689591
NASA Astrophysics Data System (ADS)
Givli, Sefi; Bhattacharya, Kaushik
2009-02-01
A theoretical framework for predicting the macroscopic behavior of a muscle myofibril based on the collective behavior of sarcomeres is presented. The analysis is accomplished by rigorously transforming the nonlinear dynamics of an assemblage of sarcomeres into a partial differential equation for the probability distribution function of sarcomere lengths in the presence of stochastic temporal fluctuations and biological variability. This enables the study of biologically relevant specimens with reasonable computational effort. The model is validated by a comparison to quantitative experimental results. Further, it reproduces experimental observations that cannot be explained by standard single sarcomere models, and provides new insights into muscle function and muscle damage during cyclic loading. We show that the accumulation of overstretched sarcomeres, which is related to muscle damage, depends on a delicate interplay between the dynamics of a large number of sarcomeres and the load characteristics, such as its magnitude and frequency. Further, we show that biological variability rather than stochastic fluctuations are the main source for sarcomere non-uniformities.
García Daza, Fabián A.; Mackie, Allan D.; Colville, Alexander J.
2015-03-21
Microscopic modeling of surfactant systems is expected to be an important tool to describe, understand, and take full advantage of the micellization process for different molecular architectures. Here, we implement a single chain mean field theory to study the relevant equilibrium properties such as the critical micelle concentration (CMC) and aggregation number for three sets of surfactants with different geometries maintaining constant the number of hydrophobic and hydrophilic monomers. The results demonstrate the direct effect of the block organization for the surfactants under study by means of an analysis of the excess energy and entropy which can be accurately determined from the mean-field scheme. Our analysis reveals that the CMC values are sensitive to branching in the hydrophilic head part of the surfactant and can be observed in the entropy-enthalpy balance, while aggregation numbers are also affected by splitting the hydrophobic tail of the surfactant and are manifested by slight changes in the packing entropy.
NASA Astrophysics Data System (ADS)
Lobanova, Olga; Avendaño, Carlos; Lafitte, Thomas; Müller, Erich A.; Jackson, George
2015-05-01
In this work, we develop coarse-grained (CG) force fields for water, where the effective CG intermolecular interactions between particles are estimated from an accurate description of the macroscopic experimental vapour-liquid equilibria data by means of a molecular-based equation of state. The statistical associating fluid theory for Mie (generalised Lennard-Jones) potentials of variable range (SAFT-VR Mie) is used to parameterise spherically symmetrical (isotropic) force fields for water. The resulting SAFT-γ CG models are based on the Mie (8-6) form with size and energy parameters that are temperature dependent; the latter dependence is a consequence of the angle averaging of the directional polar interactions present in water. At the simplest level of CG where a water molecule is represented as a single bead, it is well known that an isotropic potential cannot be used to accurately reproduce all of the thermodynamic properties of water simultaneously. In order to address this deficiency, we propose two CG potential models of water based on a faithful description of different target properties over a wide range of temperatures: our CGW1-vle model is parameterised to match the saturated-liquid density and vapour pressure; our other CGW1-ift model is parameterised to match the saturated-liquid density and vapour-liquid interfacial tension. A higher level of CG corresponding to two water molecules per CG bead is also considered: the corresponding CGW2-bio model is developed to reproduce the saturated-liquid density and vapour-liquid interfacial tension in the physiological temperature range, and is particularly suitable for the large-scale simulation of bio-molecular systems. A critical comparison of the phase equilibrium and transport properties of the proposed force fields is made with the more traditional atomistic models.
Coarse-grained Simulations of Viral Assembly
NASA Astrophysics Data System (ADS)
Elrad, Oren M.
2011-12-01
The formation of viral capsids is a marvel of natural engineering and design. A large number (from 60 to thousands) of protein subunits assemble into complete, reproducible structures under a variety of conditions while avoiding kinetic and thermodynamic traps. Small single-stranded RNA viruses not only assemble their coat proteins in this fashion but also package their genome during the self-assembly process. Recent experiments have shown that the coat proteins are competent to assemble not merely around their own genomes but heterologous RNA, synthetic polyanions and even functionalized gold nanoparticles. Remarkably these viruses can even assemble around cargo not commensurate with their native state by adopting different morphologies. Understanding the properties that confer such exquisite precision and flexibility to the assembly process could aid biomedical research in the search for novel antiviral remedies, drug-delivery vehicles and contrast agents used in bioimaging. At the same time, viral assembly provides an excellent model system for the development of a statistical mechanical understanding of biological self-assembly, in the hopes of that we will identify some universal principles that underly such processes. This work consists of computational studies using coarse-grained representations of viral coat proteins and their cargoes. We find the relative strength of protein-cargo and protein-protein interactions has a profound effect on the assembly pathway, in some cases leading to assembly mechanisms that are markedly different from those found in previous work on the assembly of empty capsids. In the case of polymeric cargo, we find the first evidence for a previously theorized mechanism in which the polymer actively participates in recruiting free subunits to the assembly process through cooperative polymer-protein motions. We find that successful assembly is non-monotonic in protein-cargo affinity, such affinity can be detrimental to assembly if it
Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities
Schneider, Anna R.; Geissler, Phillip L.
2013-01-01
Coarse-grained simulation is a powerful and well-established suite of computational methods for studying structure and dynamics in nanoscale biophysical systems. As our understanding of the plant photosynthetic apparatus has become increasingly nuanced, opportunities have arisen for coarse-grained simulation to complement experiment by testing hypotheses and making predictions. Here, we give an overview of best practices in coarse-grained simulation, with a focus on techniques and results that are applicable to the plant thylakoid membrane–protein system. We also discuss current research topics for which coarse-grained simulation has the potential to play a key role in advancing the field. PMID:24478781
NASA Astrophysics Data System (ADS)
Stanzione, Francesca; Jayaraman, Arthi
Molecular dynamics (MD) is a well established technique to study the structure and dynamics of biomolecular systems. While atomistic simulations maintain chemical details, they are computationally intensive, thus limiting the accessible time, the length scales and the sampling. To overcome these limitations, coarse-grained (CG) models have proven to be successful in reproducing experimentally relevant length and time scales with reasonable computational expense. CG models can be developed to be phenomenological by effectively reproducing experimental results or can be developed by mapping rigorously to structural information provided by atomistic MD simulations. The latter method is recommended for biomolecules and biomaterials since atomistic simulations capture the detailed effect of the medium on interactions that affect the structure, dynamics and functional properties of the biomolecules, and that can be programmed into the CG models. In this poster we highlight three different cases where atomistic MD simulations provide such essential information to guide CG models: Polyethylene glycol, Elastic-like peptides and Collagen-like peptides based biomaterials.
Avendaño, Carlos; Lafitte, Thomas; Adjiman, Claire S; Galindo, Amparo; Müller, Erich A; Jackson, George
2013-03-01
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement
Multiscale coarse graining of liquid-state systems
NASA Astrophysics Data System (ADS)
Izvekov, Sergei; Voth, Gregory A.
2005-10-01
A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system.
Coarse-Grained Molecular Dynamics Simulation of a Red Blood Cell
NASA Astrophysics Data System (ADS)
Jiang, Li-Guo; Wu, Heng-An; Zhou, Xiao-Zhou; Wang, Xiu-Xi
2010-02-01
A worm-like chain model based on a spectrin network is employed to study the biomechanics of red blood cells. Coarse-grained molecular dynamics simulations are performed to obtain a stable configuration free of external loadings. We also discuss the influence of two parameters: the average bending modulus and the persistence length. The change in shape of a malaria-infected red blood cell can contribute to the change in its molecular-based structure. As the persistence length of the membrane network in the infected red blood cell decreases, the deformability decreases and the biconcave shape is destroyed. The numerical results are comparable with previously reported experimental results. The coarse-grained model can be used to study the relationship between macro-mechanical properties and molecular-scale structures of cells.
A coarse-grained framework for spiking neuronal networks: between homogeneity and synchrony.
Zhang, Jiwei; Zhou, Douglas; Cai, David; Rangan, Aaditya V
2014-08-01
Homogeneously structured networks of neurons driven by noise can exhibit a broad range of dynamic behavior. This dynamic behavior can range from homogeneity to synchrony, and often incorporates brief spurts of collaborative activity which we call multiple-firing-events (MFEs). These multiple-firing-events depend on neither structured architecture nor structured input, and are an emergent property of the system. Although these MFEs likely play a major role in the neuronal avalanches observed in culture and in vivo, the mechanisms underlying these MFEs cannot easily be captured using current population-dynamics models. In this work we introduce a coarse-grained framework which illustrates certain dynamics responsible for the generation of MFEs. By using a new kind of ensemble-average, this coarse-grained framework can not only address the nucleation of MFEs, but can also faithfully capture a broad range of dynamic regimes ranging from homogeneity to synchrony. PMID:24338105
A test of systematic coarse-graining of molecular dynamics simulations: Transport properties
NASA Astrophysics Data System (ADS)
Fu, Chia-Chun; Kulkarni, Pandurang M.; Shell, M. Scott; Leal, L. Gary
2013-09-01
To what extent can a "bottom-up" mesoscale fluid model developed through systematic coarse-graining techniques recover the physical properties of a molecular scale system? In a previous paper [C.-C. Fu, P. M. Kulkarni, M. S. Shell, and L. G. Leal, J. Chem. Phys. 137, 164106 (2012)], 10.1063/1.4759463, we addressed this question for thermodynamic properties through the development of coarse-grained (CG) fluid models using modified iterative Boltzmann inversion methods that reproduce correct pair structure and pressure. In the present work we focus on the dynamic behavior. Unlike the radial distribution function and the pressure, dynamical properties such as the self-diffusion coefficient and viscosity in a CG model cannot be matched during coarse-graining by modifying the pair interaction. Instead, removed degrees of freedom require a modification of the equations of motion to simulate their implicit effects on dynamics. A simple but approximate approach is to introduce a friction coefficient, γ, and random forces for the remaining degrees of freedom, in which case γ becomes an additional parameter in the coarse-grained model that can be tuned. We consider the non-Galilean-invariant Langevin and the Galilean-invariant dissipative particle dynamics (DPD) thermostats with CG systems in which we can systematically tune the fraction ϕ of removed degrees of freedom. Between these two choices, only DPD allows both the viscosity and diffusivity to match a reference Lennard-Jones liquid with a single value of γ for each degree of coarse-graining ϕ. This friction constant is robust to the pressure correction imposed on the effective CG potential, increases approximately linearly with ϕ, and also depends on the interaction cutoff length, rcut, of the pair interaction potential. Importantly, we show that the diffusion constant and viscosity are constrained by a simple scaling law that leads to a specific choice of DPD friction coefficient for a given degree of coarse-graining
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA
Poursina, Mohammad; Bhalerao, Kishor D.; Flores, Samuel C.; Anderson, Kurt S.; Laederach, Alain
2011-01-01
Efficient modeling approaches are necessary to accurately predict large-scale structural behavior of biomolecular systems like RNA (Ribonucleic Acid). Coarse grained approximations of such complex systems can significantly reduce the computational costs of the simulation while maintaining sufficient fidelity to capture the biologically significant motions. However, given the coupling and nonlinearity of RNA systems (and effectively all biopolymers), it is expected that different parameters such as geometric and dynamic boundary conditions, states, and applied forces will affect the system’s dynamic behavior. Consequently, static coarse grained models (i.e., models for which the coarse graining is time invariant) are not always able to adequately sample the conformational space of the molecule. We introduce here the concept of adaptive coarse-grained molecular dynamics of RNA, which automatically adapts the coarseness of the model dynamically, in an effort to more optimally increase simulation speed, while maintaining accuracy. Adaptivity requires two basic algorithmic developments; first, a set of integrators that seamlessly allow transitions between higher and lower fidelity models while preserving the laws of motion. Secondly, we propose and validate metrics for determining when and where more or less fidelity needs to be integrated into the model to allow sufficiently accurate dynamics simulation. Given the central role that multibody dynamics plays in the proposed framework, and the nominally large number of dynamic degrees of freedom being considered in these applications, a computationally efficient multibody method which lends itself well to adaptivity is essential to the success of this effort. A suite of Divide-And-Conquer Algorithm (DCA)-based approaches are employed to this end, because these methods offer a good combination of computational efficiency and adaptive structure. PMID:21187222
Quasiclassical coarse graining and thermodynamic entropy
Gell-Mann, Murray; Hartle, James B.
2007-08-15
Our everyday descriptions of the universe are highly coarse grained, following only a tiny fraction of the variables necessary for a perfectly fine-grained description. Coarse graining in classical physics is made natural by our limited powers of observation and computation. But in the modern quantum mechanics of closed systems, some measure of coarse graining is inescapable because there are no nontrivial, probabilistic, fine-grained descriptions. This essay explores the consequences of that fact. Quantum theory allows for various coarse-grained descriptions, some of which are mutually incompatible. For most purposes, however, we are interested in the small subset of 'quasiclassical descriptions' defined by ranges of values of averages over small volumes of densities of conserved quantities such as energy and momentum and approximately conserved quantities such as baryon number. The near-conservation of these quasiclassical quantities results in approximate decoherence, predictability, and local equilibrium, leading to closed sets of equations of motion. In any description, information is sacrificed through the coarse graining that yields decoherence and gives rise to probabilities for histories. In quasiclassical descriptions, further information is sacrificed in exhibiting the emergent regularities summarized by classical equations of motion. An appropriate entropy measures the loss of information. For a 'quasiclassical realm' this is connected with the usual thermodynamic entropy as obtained from statistical mechanics. It was low for the initial state of our universe and has been increasing since.
A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation
Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng
2012-01-01
Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075
Coarse grained dynamics in the glass phase
NASA Astrophysics Data System (ADS)
Smessaert, Anton; Rottler, Jörg
2013-03-01
Atomic scale dynamics in glasses is dominated by extended periods of localized vibration, where the crowded surroundings of a particle act as a cage. Collective motion is necessary to escape the cage, and the succession of particle jumps or hops leads to diffusion. Each jump is an elementary relaxation event since the local structure is stable until a jump occurs. The link between local dynamics and structural properties has become of increasing interest in recent years. Aging of the mechanical response has been tied to a power-law distribution of persistence times in the cages, and concentration of hops into dynamical heterogeneities (DH) was observed in granular media and simulations of supercooled liquids in 2D. These studies were limited to small systems or hop detection in subsets, because of the post processing requirements. We present results based on a new algorithm that allows us to detect the hops of all particles during a molecular dynamics simulation. This complete coarse-grained ``map'' of the dynamics allows us to directly investigate temporal and spatial correlations between relaxation events. Furthermore, we can readily identify DH using a cluster algorithm and we explore the impact of aging and deformation on the size and shape of DH.
Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units.
Tunbridge, Ian; Best, Robert B; Gain, James; Kuttel, Michelle M
2010-11-01
We report a hybrid parallel central and graphics processing units (CPU-GPU) implementation of a coarse-grained model for replica exchange Monte Carlo (REMC) simulations of protein assemblies. We describe the design, optimization, validation, and benchmarking of our algorithms, particularly the parallelization strategy, which is specific to the requirements of GPU hardware. Performance evaluation of our hybrid implementation shows scaled speedup as compared to a single-core CPU; reference simulations of small 100 residue proteins have a modest speedup of 4, while large simulations with thousands of residues are up to 1400 times faster. Importantly, the combination of coarse-grained models with highly parallel GPU hardware vastly increases the length- and time-scales accessible for protein simulation, making it possible to simulate much larger systems of interacting proteins than have previously been attempted. As a first step toward the simulation of the assembly of an entire viral capsid, we have demonstrated that the chosen coarse-grained model, together with REMC sampling, is capable of identifying the correctly bound structure, for a pair of fragments from the human hepatitis B virus capsid. Our parallel solution can easily be generalized to other interaction functions and other types of macromolecules and has implications for the parallelization of similar N-body problems that require random access lookups. PMID:26617104
NASA Astrophysics Data System (ADS)
Maiolo, M.; Vancheri, A.; Krause, R.; Danani, A.
2015-11-01
In this paper, we apply Multiresolution Analysis (MRA) to develop sparse but accurate representations for the Multiscale Coarse-Graining (MSCG) approximation to the many-body potential of mean force. We rigorously framed the MSCG method into MRA so that all the instruments of this theory become available together with a multitude of new basis functions, namely the wavelets. The coarse-grained (CG) force field is hierarchically decomposed at different resolution levels enabling to choose the most appropriate wavelet family for each physical interaction without requiring an a priori knowledge of the details localization. The representation of the CG potential in this new efficient orthonormal basis leads to a compression of the signal information in few large expansion coefficients. The multiresolution property of the wavelet transform allows to isolate and remove the noise from the CG force-field reconstruction by thresholding the basis function coefficients from each frequency band independently. We discuss the implementation of our wavelet-based MSCG approach and demonstrate its accuracy using two different condensed-phase systems, i.e. liquid water and methanol. Simulations of liquid argon have also been performed using a one-to-one mapping between atomistic and CG sites. The latter model allows to verify the accuracy of the method and to test different choices of wavelet families. Furthermore, the results of the computer simulations show that the efficiency and sparsity of the representation of the CG force field can be traced back to the mathematical properties of the chosen family of wavelets. This result is in agreement with what is known from the theory of multiresolution analysis of signals.
The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation.
Davtyan, Aram; Dama, James F; Sinitskiy, Anton V; Voth, Gregory A
2014-12-01
The increasing interest in the modeling of complex macromolecular systems in recent years has spurred the development of numerous coarse-graining (CG) techniques. However, many of the CG models are constructed assuming that all details beneath the resolution of CG degrees of freedom are fast and average out, which sets limits on the resolution of feasible coarse-grainings and on the range of applications of the CG models. Ultra-coarse-graining (UCG) makes it possible to construct models at any desired resolution while accounting for discrete conformational or chemical changes within the CG sites that can modulate the interactions between them. Here, we discuss the UCG methodology and its numerical implementation. We pay particular attention to the numerical mechanism for including state transitions between different conformations within CG sites because this has not been discussed previously. Using a simple example of 1,2-dichloroethane, we demonstrate the ability of the UCG model to reproduce the multiconfigurational behavior of this molecular liquid, even when each molecule is modeled with only one CG site. The methodology can also be applied to other molecular liquids and macromolecular systems with time scale separation between conformational transitions and other intramolecular motions and rotations. PMID:26583210
Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach
Zhou, Lei; Siegelbaum, Steven A.
2008-01-01
Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant atoms, including surface water molecules, into the coarse-grained protein motions. The importance of such improvements is demonstrated by the effect of surface water to shift vibrational modes to higher frequencies and by an increase in overlap of the coarse-grained eigenvector space (the motion directions) with that obtained from molecular dynamics simulations of solvated protein in a water box. These results not only confirm the quality of our method but also point out the importance of incorporating surface structural water in studying protein dynamics. PMID:18212016
Coarse-grained molecular simulations of allosteric cooperativity
NASA Astrophysics Data System (ADS)
Nandigrami, Prithviraj; Portman, John J.
2016-03-01
Interactions between a protein and a ligand are often accompanied by a redistribution of the population of thermally accessible conformations. This dynamic response of the protein's functional energy landscape enables a protein to modulate binding affinities and control binding sensitivity to ligand concentration. In this paper, we investigate the structural origins of binding affinity and allosteric cooperativity of binding two Ca2+ 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 Ca2+ 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.
First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids
NASA Astrophysics Data System (ADS)
Lyubimov, I.; Guenza, M. G.
2011-09-01
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov, J. McCarty, A. Clark, and M. G. Guenza, J. Chem. Phys.JCPSA60021-960610.1063/1.3450301 132, 224903 (2010)). Starting from the first-principle Liouville equation and applying the Mori-Zwanzig projection operator technique, we derive the generalized Langevin equations (GLEs) for the coarse-grained representations of the liquid. The chosen slow variables in the projection operators define the length scale of coarse graining. Each polymer is represented at two levels of coarse graining: monomeric as a bead-and-spring model and molecular as a soft colloid. In the long-time regime where the center-of-mass follows Brownian motion and the internal dynamics is completely relaxed, the two descriptions must be equivalent. By enforcing this formal relation we derive from the GLEs the analytical rescaling factors to be applied to dynamical data in the coarse-grained representation to recover the monomeric description. Change in entropy and change in friction are the two corrections to be accounted for to compensate the effects of coarse graining on the polymer dynamics. The solution of the memory functions in the coarse-grained representations provides the dynamical rescaling of the friction coefficient. The calculation of the internal degrees of freedom provides the correction of the change in entropy due to coarse graining. The resulting rescaling formalism is a function of the coarse-grained model and thermodynamic parameters of the system simulated. The rescaled dynamics obtained from mesoscale simulations of polyethylene, represented as soft-colloidal particles, by applying our rescaling approach shows a good agreement with data of translational diffusion measured experimentally and from simulations. The proposed method is used to predict self-diffusion coefficients of new polyethylene samples.
Bayesian calibration of coarse-grained forces: Efficiently addressing transferability
NASA Astrophysics Data System (ADS)
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.
Coarse-graining the electrostatic potential via distributed multipole expansions
Gramada, Apostol; Bourne, Philip E.
2011-01-01
Multipole expansions offer a natural path to coarse-graining the electrostatic potential. However, the validity of the expansion is restricted to regions outside a spherical enclosure of the distribution of charge and, therefore, not suitable for most applications that demand accurate representation at arbitrary positions around the molecule. We propose and demonstrate a distributed multipole expansion approach that resolves this limitation. We also provide a practical algorithm for the computational implementation of this approach. The method allows the partitioning of the charge distribution into subsystems so that the multipole expansion of each component of the partition, and therefore of their superposition, is valid outside an enclosing surface of the molecule of arbitrary shape. The complexity of the resulting coarse-grained model of electrostatic potential is dictated by the area of the molecular surface and therefore, for a typical three-dimensional molecule, it scale as N2/3 with N, the number of charges in the system. This makes the method especially useful for coarse-grained studies of biological systems consisting of many large macromolecules provided that the configuration of the individual molecules can be approximated as fixed. PMID:21572587
Coarse-graining Landau-Lifshitz damping
NASA Astrophysics Data System (ADS)
Feng, Xuebing; Visscher, P. B.
2001-06-01
High speed switching in magnetic materials is usually studied with the Landau-Lifshitz (LL) equation, which describes damping through a phenomenological coefficient. The results of micromagnetic calculations based on the LL equation have been observed to depend strongly on the cell size. We take a coarse-graining or renormalization-group approach to this cell size dependence: from a simulation using cell size L, we look at the dynamics of a cell of size 2L and determine an effective damping coefficient that describes the larger-scale dynamics. This can be thought of as a Green-Kubo calculation of the effective damping coefficient. In principle, this makes it possible to coarse grain from the atomic scale to determine the micromagnetic damping coefficient.
Critical time scale of coarse-graining entropy production
NASA Astrophysics Data System (ADS)
Sohn, Jang-il
2016-04-01
We study coarse-grained entropy production in an asymmetric random walk system on a periodic one-dimensional lattice. In coarse-grained systems, the original dynamics are unavoidably destroyed, but the coarse-grained entropy production is not hidden below the critical time-scale separation. The hidden entropy production is rapidly increasing near the critical time-scale separation.
Cellulose microfibril formation within a coarse grained molecular dynamics
NASA Astrophysics Data System (ADS)
Nili, Abdolmadjid; Shklyaev, Oleg; Crespi, Vincent; Zhao, Zhen; Zhong, Linghao; CLSF Collaboration
2014-03-01
Cellulose in biomass is mostly in the form of crystalline microfibrils composed of 18 to 36 parallel chains of polymerized glucose monomers. A single chain is produced by cellular machinery (CesA) located on the preliminary cell wall membrane. Information about the nucleation stage can address important questions about intermediate region between cell wall and the fully formed crystalline microfibrils. Very little is known about the transition from isolated chains to protofibrils up to a full microfibril, in contrast to a large body of studies on both CesA and the final crystalline microfibril. In addition to major experimental challenges in studying this transient regime, the length and time scales of microfibril nucleation are inaccessible to atomistic molecular dynamics. We have developed a novel coarse grained model for cellulose microfibrils which accounts for anisotropic interchain interactions. The model allows us to study nucleation, kinetics, and growth of cellulose chains/protofibrils/microfibrils. This work is supported by the US Department of Energy, Office of Basic Energy Sciences as part of The Center for LignoCellulose Structure and Formation, an Energy Frontier Research Center.
The power of coarse graining in biomolecular simulations
Ingólfsson, Helgi I; Lopez, Cesar A; Uusitalo, Jaakko J; de Jong, Djurre H; Gopal, Srinivasa M; Periole, Xavier; Marrink, Siewert J
2014-01-01
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling. PMID:25309628
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.
Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P
2016-09-01
Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR). PMID:27566318
Coarse grained open system quantum dynamics
Thanopulos, Ioannis; Brumer, Paul; Shapiro, Moshe
2008-11-21
We show that the quantum dynamics of a system comprised of a subspace Q coupled to a larger subspace P can be recast as a reduced set of 'coarse grained' ordinary differential equations with constant coefficients. These equations can be solved by a single diagonalization of a general complex matrix. The method makes no assumptions about the strength of the couplings between the Q and the P subspaces, nor is there any limitation on the initial population in P. The utility of the method is demonstrated via computations in three following areas: molecular compounds, photonic materials, and condensed phases.
Shen, Hujun; Li, Yan; Xu, Peijun; Li, Xiaofang; Chu, Huiying; Zhang, Dinglin; Li, Guohui
2015-06-01
In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay-Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay-Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (DHH), area per lipid ( AL) and volume per lipid ( VL). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. PMID:25788250
Coarse-grained distributions and superstatistics
NASA Astrophysics Data System (ADS)
Chavanis, Pierre-Henri
2006-01-01
We show an interesting connection between non-standard (non-Boltzmannian) distribution functions arising in the theory of violent relaxation for collisionless stellar systems [D. Lynden-Bell, Mon. Not. R. Astron. Soc. 136 (1967) 101.] and the notion of superstatistics recently introduced by [Beck and Cohen Physica A 322 (2003) 267]. The common link between these two theories is the emergence of coarse-grained distributions arising out of fine-grained distributions. The coarse-grained distribution functions are written as a superposition of Boltzmann factors weighted by a non-universal function. Even more general distributions can arise in case of incomplete violent relaxation (non-ergodicity). They are stable stationary solutions of the Vlasov equation. We also discuss analogies and differences between the statistical equilibrium state of a multi-components self-gravitating system and the metaequilibrium (or quasi-equilibrium) states of a collisionless stellar system. Finally, we stress the important distinction between entropies, generalized entropies, relative entropies and H-functions. We discuss applications of these ideas in two-dimensional turbulence and for other systems with long-range interactions.
Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto
2015-12-01
Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins. PMID:26597989
Statistical coarse-graining of molecular dynamics into peridynamics.
Silling, Stewart Andrew; Lehoucq, Richard B.
2007-10-01
This paper describes an elegant statistical coarse-graining of molecular dynamics at finite temperature into peridynamics, a continuum theory. Peridynamics is an efficient alternative to molecular dynamics enabling dynamics at larger length and time scales. In direct analogy with molecular dynamics, peridynamics uses a nonlocal model of force and does not employ stress/strain relationships germane to classical continuum mechanics. In contrast with classical continuum mechanics, the peridynamic representation of a system of linear springs and masses is shown to have the same dispersion relation as the original spring-mass system.
Coarse Graining to Investigate Membrane Induced Peptide Folding of Anticancer Peptides
NASA Astrophysics Data System (ADS)
Ganesan, Sai; Xu, Hongcheng; Matysiak, Silvina
Information about membrane induced peptide folding mechanisms using all-atom molecular dynamics simulations is a challenge due to time and length scale issues.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model by adding oppositely charged dummy particles inside protein backbone beads.These two dummy particles represent a fluctuating dipole,thus introducing structural polarization into the coarse-grained model.With this model,we were able to achieve significant α- β secondary structure content de novo,without any added bias.We extended the model to zwitterionic and anionic lipids,by adding oppositely charged dummy particles inside polar beads, to capture the ability of the head group region to form hydrogen bonds.We use zwitterionic POPC and anionic POPS as our model lipids, and a cationic anticancer peptide,SVS1,as our model peptide.We have characterized the driving forces for SVS1 folding on lipid bilayers with varying anionic and zwitterionic lipid compositions.Based on our results, dipolar interactions between peptide backbone and lipid head groups contribute to stabilize folded conformations.Cooperativity in folding is induced by both intra peptide and membrane-peptide interaction.
Effective surface coverage of coarse-grained soft matter.
Craven, Galen T; Popov, Alexander V; Hernandez, Rigoberto
2014-12-11
The surface coverage of coarse-grained macromolecules bound to a solid substrate is not simply proportional to the two-dimensional number density because macromolecules can overlap. As a function of the overlap probability δ, we have developed analytical formulas and computational models capable of characterizing this nonlinear relationship. For simplicity, we ignore site-site interactions that would be induced by length-scale mismatches between binding sites and the radius of gyration of the incident coarse-grained macromolecular species. The interactions between macromolecules are modeled with a finite bounded potential that allows multiple macromolecules to occupy the same binding site. The softness of the bounded potential is thereby reduced to the single parameter δ. Through variation of this parameter, completely hard (δ = 0) and completely soft (δ = 1) behavior can be bridged. For soft macromolecular interactions (δ > 0), multiple occupancy reduces the fraction of sites ϕ occupied on the substrate. We derive the exact transition probability between sequential configurations and use this probability to predict ϕ and the distribution of occupied sites. Due to the complexity of the exact ϕ expressions and their analytical intractability at the thermodynamic limit, we apply a simplified mean-field (MF) expression for ϕ. The MF model is found to be in excellent agreement with the exact result. Both the exact and MF models are applied to an example dynamical system with multibody interactions governed by a stochastic bounded potential. Both models show agreement with results measured from simulation. PMID:25059882
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
NASA Astrophysics Data System (ADS)
Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu
2011-10-01
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu
2011-01-01
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338
Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent.
Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu
2011-10-21
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338
Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description
NASA Astrophysics Data System (ADS)
Pantawane, Sanwardhini; Choudhury, Niharendu
2016-05-01
In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degree of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.
Deformation Behaviour of Coarse Grain Alumina under Shock Loading
NASA Astrophysics Data System (ADS)
Gupta, Satish
2013-06-01
To develop better understanding of the shock wave induced deformation behavior of coarse grain alumina ceramics, and for measurement of its Hugoniot Elastic Limit (HEL), in-situ and recovery gas gun experiments have been carried out on coarse grain alumina (grain size ~ 10 μm), prepared in the form of discs (>99.9% TMD) by pressure-less sintering of alpha alumina powder at 1583 K. The HEL value of 1.9 GPa has been determined from the kink in the pressure history recorded using piezoresistance gauge and also from the free surface velocity history of the sample shocked to 9 GPa. The nano-indentation measurements on the alumina samples shocked to 6.5 GPa showed hardness value 15% lower than 21.3 GPa for unshocked alumina, and strong Indentation Size Effect (ISE); the hardness value was still lower and the ISE was stronger for the sample shocked to 12 GPa. The XRD measurements showed reduced particle size and increased microstrains in the shocked alumina fragments. SEM, FESEM and TEM measurements on shock treated samples showed presence of grain localized micro- and nano-scale deformations, micro-cleavages, grain-boundary microcracks, extensive shear induced deformations, and localized micro-fractures, etc. These observations led to the development of a qualitative model for the damage initiation and its subsequent growth mechanisms in shocked alumina. The work performed in collaboration with K.D. Joshi of BARC and A.K. Mukhopadhyay of CGCRI.
Masella, Michel; Borgis, Daniel; Cuniasse, Philippe
2008-08-01
The dynamic coupling between a polarizable protein force field and a particle-based implicit solvent model is described. The polarizable force field, TCPEp, developed recently to simulate protein systems, is characterized by a reduced number of polarizable sites, with a substantial gain in efficiency for an equal chemical accuracy. The Polarizable Pseudo-Particle (PPP) solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile Lennard-Jones pseudo-particles. The solvent-induced dipoles are sensitive to the solute electric field, but not to each other, so that the computational cost of solvent-solvent interactions is basically negligible. The solute and solvent induced dipoles are determined self-consistently and the equations of motion are solved using an efficient iterative multiple time step procedure. The solvation cost with respect to vacuum simulations is shown to decrease with solute size: the estimated multiplicative factor is 2.5 for a protein containing about 1000 atoms, and as low as 1.15 for 8000 atoms. The model is tested for six 20 ns molecular dynamics trajectories of a traditional benchmark system: the hydrated Bovine Pancreatic Trypsin Inhibitor (BPTI). Even though the TCPEp parameters have not been refined to be used with the solvent PPP model, we observe a good conservation of the BPTI structure along the trajectories. Moreover, our approach is able to provide a description of the protein solvation thermodynamic at the same accuracy as the standard Poisson-Boltzman continuum methods. It provides in addition a good description of the microscopic structural aspects concerning the solute/solvent interaction. PMID:18351600
A coarse-grain force field for RDX: Density dependent and energy conserving
NASA Astrophysics Data System (ADS)
Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.
2016-03-01
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.
Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
Spijker, Peter; van Hoof, Bram; Debertrand, Michel; Markvoort, Albert J.; Vaidehi, Nagarajan; Hilbers, Peter A.J.
2010-01-01
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. PMID:20640160
A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales
Ayton, Gary S.; Voth, Gregory A.
2009-01-01
A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analyticsystematic as one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, while the remaining component utilizes an analytic potential. The systematic component models the in-plane center of mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well known Gay-Berne ellipsoid of revolution liquid crystal model, and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an “aggressive” CG methodology designed to model multi-component biological membranes at very large length and timescales. PMID:19281167
Hybrid coarse-graining approach for lipid bilayers at large length and time scales.
Ayton, Gary S; Voth, Gregory A
2009-04-01
A hybrid analytic-systematic (HAS) coarse-grained (CG) lipid model is developed and employed in a large-scale simulation of a liposome. The methodology is termed hybrid analytic-systematic because one component of the interaction between CG sites is variationally determined from the multiscale coarse-graining (MS-CG) methodology, whereas the remaining component utilizes an analytic potential. The systematic component models the in-plane center-of-mass interaction of the lipids as determined from an atomistic-level MD simulation of a bilayer. The analytic component is based on the well-known Gay-Berne ellipsoid-of-revolution liquid-crystal model and is designed to model the highly anisotropic interactions at a highly coarse-grained level. The HAS CG approach is the first step in an "aggressive" CG methodology designed to model multicomponent biological membranes at very large length and time scales. PMID:19281167
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
NASA Astrophysics Data System (ADS)
Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.
2015-11-01
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
NASA Astrophysics Data System (ADS)
Xia, Wenjie; Hsu, David; Keten, Sinan
Understanding and predicting the thermomechanical responses of nanoscale polymer systems are very challenging as their responses are greatly influenced by many factors, such as interfacial energy, filler volume fraction and molecule weight, giving rise to the presence of nanoscale interface and free surface. To overcome these issues, here we employ a novel atomistically informed coarse-grained computational technique, called thermomechanically consistent coarse graining (TCCG), to investigate how the nanoscale interface and free surface influence the elastic modulus (E) and glass transition temperature (Tg) of polymer films and nanocomposites. By performing tensile tests and nanoindentation simulations, we are able to predict the size dependent elastic properties of polymer films and quantify the length scale of the local mechanical interphase. Finally, taking cellulose nanocrystal (CNC) and poly(methyl-methacrylate) (PMMA) nanocomposites as a relevant model system, we present a multi-scale framework built upon our CG approach to allow the prediction of Tg of nanocomposite as a function of interfacial energy and filler volume fractions by drawing the analogy between thin film and nanocomposites. Our established multi-scale framework is validated by recent experiments and breaks new ground in predicting, without any empirical parameters, key structure-property relationships for polymer nanomaterials.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.
Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L
2015-11-01
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene. PMID:26547161
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
Heinemann, Thomas Klapp, Sabine H. L.; Palczynski, Karol Dzubiella, Joachim
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.
A coarse grained stochastic particle interacting system for tropical convection
NASA Astrophysics Data System (ADS)
Khouider, B.
2012-12-01
Climate models (GCMs) fail to represent adequately the variability associated with organized convection in the tropics. This deficiency is believed to hinder medium and long range weather forecasts, over weeks to months. GCMs use very complex sub-grid models, known as cumulus parameterizations, to represent the effects of clouds and convection as well as other unresolved processes. Cumulus parameterizations are intrinsically deterministic and are typically based on the quasi-equilibrium theory, which assumes that convection instantaneously consumes the atmospheric instability produced by radiation. In this talk, I will discuss a stochastic model for organized tropical convection based on a particle interacting system defined on a microscopic lattice. An order parameter is assumed to take the values 0,1,2,3 at a any given lattice site according to whether it is a clear site or it is occupied by a cloud of a one of the three types: congestus, deep, or stratiform, following intuitive rules motivated by recent satellite observations and various field campaigns conducted over the Indian Ocean and Western Pacific. The microscopic Markov process is coarse-grained systematically to obtain a multidimensional birth-death process with immigration, following earlier work done by Katsoulakis, Majda, and Vlachos (JCP 2003) for the case of the Ising model where the order parameter takes the values 0 and 1. The coarse grained birth-death process is a stochastic model, intermediate between the microscopic lattice model and the deterministic mean field limit, that is used to represent the sub-grid scale variability of the underlying physical process (here the cloud cover) with a negligible computational overhead and yet permits both local interactions between lattice sites and two-way interactions between the cloud cover and the large-scale climate dynamics. The new systematic coarse-graining, developed here for the multivalued order parameter, provides a unifying framework
Misra, R D K; Nune, C; Pesacreta, T C; Somani, M C; Karjalainen, L P
2013-04-01
Metallic biomedical devices with nanometer-sized grains (NGs) provide surfaces that are different from their coarse-grained (CG) (tens of micrometer) counterparts in terms of increased fraction of grain boundaries (NG>50%; CG<2-3%). The novel concept of 'phase-reversion' involving a controlled deformation-annealing sequence is used to obtain a wide range of grain structures, starting from the NG regime to the CG regime, to demonstrate that the grain structure significantly impacts cellular interactions and osteoblast functions. The uniqueness of this concept is the ability to address the critical aspect of cellular activity in nanostructured materials, because a range of grain sizes from NG to CG are obtained in a single material using an identical set of parameters. This is in addition to a high strength/weight ratio and superior wear and corrosion resistance. These multiple attributes are important for the long-term stability of biomedical devices. Experiments on the interplay between grain structure from the NG regime to CG in austenitic stainless steel on osteoblast functions indicated that cell attachment, proliferation, viability, morphology and spread varied with grain size and were favorably modulated on the NG and ultrafine-grain structure. Furthermore, immunofluorescence studies demonstrated stronger vinculin signals associated with actin stress fibers in the outer regions of the cells and cellular extensions on the NG surface. The differences in the cellular response with change in grain structure are attributed to grain structure and degree of hydrophilicity. The study lays the foundation for a new branch of nanostructured materials for biomedical applications. PMID:23232208
A general method for spatially coarse-graining Metropolis Monte Carlo simulations onto a lattice
NASA Astrophysics Data System (ADS)
Liu, Xiao; Seider, Warren D.; Sinno, Talid
2013-03-01
A recently introduced method for coarse-graining standard continuous Metropolis Monte Carlo simulations of atomic or molecular fluids onto a rigid lattice of variable scale [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012)], 10.1103/PhysRevE.86.026708 is further analyzed and extended. The coarse-grained Metropolis Monte Carlo technique is demonstrated to be highly consistent with the underlying full-resolution problem using a series of detailed comparisons, including vapor-liquid equilibrium phase envelopes and spatial density distributions for the Lennard-Jones argon and simple point charge water models. In addition, the principal computational bottleneck associated with computing a coarse-grained interaction function for evolving particle positions on the discretized domain is addressed by the introduction of new closure approximations. In particular, it is shown that the coarse-grained potential, which is generally a function of temperature and coarse-graining level, can be computed at multiple temperatures and scales using a single set of free energy calculations. The computational performance of the method relative to standard Monte Carlo simulation is also discussed.
Xu, Peijun; Shen, Hujun; Yang, Lu; Ding, Yang; Li, Beibei; Shao, Ying; Mao, Yingchen; Li, Guohui
2013-02-01
Coarse-grained studies of CH(3)SH, CH(3)CHO and CHCl(3) liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen. PMID:22961621
Biomembranes in atomistic and coarse-grained simulations
NASA Astrophysics Data System (ADS)
Pluhackova, Kristyna; Böckmann, Rainer A.
2015-08-01
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure.
Koslover, Elena F; Spakowitz, Andrew J
2014-07-01
Simulating the dynamics of a semiflexible polymer across time and length scales that bridge the rigid and flexible regimes requires a physically sound method for generating coarse-grained representations of the polymer. Here, we study the dynamic behavior of the discrete stretchable, shearable wormlike chain model, which can be used to coarse-grain a continuous semi-elastic chain at an arbitrary discretization. We show that the dynamics of this universal model match those of the wormlike chain at length scales above the discretization length. The evolution of the stress correlation, as probed through Brownian dynamics simulations, is found to reproduce the predicted behavior in both the rigid and flexible regimes, spanning over six orders of magnitude in time scales. The coarse-graining approach employed here thus enables dynamic simulation of semiflexible polymers at lengths and times that were previously inaccessible with conventional methods. PMID:25122407
Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure
NASA Astrophysics Data System (ADS)
Koslover, Elena F.; Spakowitz, Andrew J.
2014-07-01
Simulating the dynamics of a semiflexible polymer across time and length scales that bridge the rigid and flexible regimes requires a physically sound method for generating coarse-grained representations of the polymer. Here, we study the dynamic behavior of the discrete stretchable, shearable wormlike chain model, which can be used to coarse-grain a continuous semi-elastic chain at an arbitrary discretization. We show that the dynamics of this universal model match those of the wormlike chain at length scales above the discretization length. The evolution of the stress correlation, as probed through Brownian dynamics simulations, is found to reproduce the predicted behavior in both the rigid and flexible regimes, spanning over six orders of magnitude in time scales. The coarse-graining approach employed here thus enables dynamic simulation of semiflexible polymers at lengths and times that were previously inaccessible with conventional methods.
A unified data representation theory for network visualization, ordering and coarse-graining
NASA Astrophysics Data System (ADS)
Kovács, István A.; Mizsei, Réka; Csermely, Péter
2015-09-01
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form.
A unified data representation theory for network visualization, ordering and coarse-graining
Kovács, István A.; Mizsei, Réka; Csermely, Péter
2015-01-01
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no underlying theoretical framework linking these problems. Here we show an elegant, information theoretic data representation approach as a unified solution of network visualization, data ordering and coarse-graining. The optimal representation is the hardest to distinguish from the original data matrix, measured by the relative entropy. The representation of network nodes as probability distributions provides an efficient visualization method and, in one dimension, an ordering of network nodes and edges. Coarse-grained representations of the input network enable both efficient data compression and hierarchical visualization to achieve high quality representations of larger data sets. Our unified data representation theory will help the analysis of extensive data sets, by revealing the large-scale structure of complex networks in a comprehensible form. PMID:26348923
Supramolecular polymerization: a coarse grained molecular dynamics study.
Bejagam, Karteek K; Balasubramanian, Sundaram
2015-04-30
A coarse-grained (CG) force field to model the self-assembly of benzene-1,3,5-tricarboxamide (BTA) class of compounds in nonpolar solvents has been developed. The model includes an intrinsic point dipole embedded on one of the CG beads so as to impart a macrodipole moment to the oligomer, one of its characteristic feature. Chemical specificity has been preserved by benchmarking against results, including dimerization and solvation free energies, obtained from an all-atom representation. Starting from a well-dispersed configuration in n-nonane, BTA molecules self-assemble to form one-dimensional stacks. Free energy (FE) changes for the various manner in which short oligomers can exchange between the assembled and the dispersed states have been calculated. These calculations show BTA to self-assemble via a downhill cooperative mechanism with a nucleus size of three. PMID:25853485
Hoffman, F.; Chiarappa, M.L.
1998-03-01
One of the serious impediments to the remediation of ground water contaminated with volatile organic compounds (VOCs) is that the VOCs are retarded with respect to the movement of the ground water. Although the processes that result in VOC retardation are poorly understood, we have developed a conceptual model that includes several retarding mechanisms. These include adsorption to inorganic surfaces, absorption to organic carbon, and diffusion into areas of immobile waters. This project was designed to evaluate the relative contributions of these mechanisms; by improving our understanding, we hope to inspire new remediation technologies or approaches. Our project consisted of a series of column experiments designed to measure the retardation, in different geological media, of four common ground water VOCs (chloroform, carbon tetrachloride, trichloroethylene, and tetrachloroethylene) which have differing physical and chemical characteristics. It also included a series of diffusion parameters that constrain the model, we compared the data from these experiments to the output of a computational model.
Lu, Jibao; Chakravarty, Charusita; Molinero, Valeria
2016-06-21
Liquid water has several anomalous properties, including a non-monotonous dependence of density with temperature and an increase of thermodynamic response functions upon supercooling. Four thermodynamic scenarios have been proposed to explain the anomalies of water, but it is not yet possible to decide between them from experiments because of the crystallization and cavitation of metastable liquid water. Molecular simulations provide a versatile tool to study the anomalies and phase behavior of water, assess their agreement with the phenomenology of water under conditions accessible to experiments, and provide insight into the behavior of water in regions that are challenging to probe in the laboratory. Here we investigate the behavior of the computationally efficient monatomic water models mW and mTIP4P/2005(REM), with the aim of unraveling the relationships between the lines of density extrema in the p-T plane, and the lines of melting, liquid-vapor spinodal and non-equilibrium crystallization and cavitation. We focus particularly on the conditions for which the line of density maxima (LDM) in the liquid emerges and disappears as the pressure is increased. We find that these models present a retracing LDM, same as previously found for atomistic water models and models of other tetrahedral liquids. The low-pressure end of the LDM occurs near the pressure of maximum of the melting line, a feature that seems to be general to models that produce tetrahedrally coordinated crystals. We find that the mW water model qualitatively reproduces several key properties of real water: (i) the LDM is terminated by cavitation at low pressures and by crystallization of ice Ih at high pressures, (ii) the LDM meets the crystallization line close to the crossover in crystallization from ice Ih to a non-tetrahedral four-coordinated crystal, and (iii) the density of the liquid at the crossover in crystallization from ice Ih to a four-coordinated non-tetrahedral crystal coincides with
NASA Astrophysics Data System (ADS)
Lu, Jibao; Chakravarty, Charusita; Molinero, Valeria
2016-06-01
Liquid water has several anomalous properties, including a non-monotonous dependence of density with temperature and an increase of thermodynamic response functions upon supercooling. Four thermodynamic scenarios have been proposed to explain the anomalies of water, but it is not yet possible to decide between them from experiments because of the crystallization and cavitation of metastable liquid water. Molecular simulations provide a versatile tool to study the anomalies and phase behavior of water, assess their agreement with the phenomenology of water under conditions accessible to experiments, and provide insight into the behavior of water in regions that are challenging to probe in the laboratory. Here we investigate the behavior of the computationally efficient monatomic water models mW and mTIP4P/2005REM, with the aim of unraveling the relationships between the lines of density extrema in the p-T plane, and the lines of melting, liquid-vapor spinodal and non-equilibrium crystallization and cavitation. We focus particularly on the conditions for which the line of density maxima (LDM) in the liquid emerges and disappears as the pressure is increased. We find that these models present a retracing LDM, same as previously found for atomistic water models and models of other tetrahedral liquids. The low-pressure end of the LDM occurs near the pressure of maximum of the melting line, a feature that seems to be general to models that produce tetrahedrally coordinated crystals. We find that the mW water model qualitatively reproduces several key properties of real water: (i) the LDM is terminated by cavitation at low pressures and by crystallization of ice Ih at high pressures, (ii) the LDM meets the crystallization line close to the crossover in crystallization from ice Ih to a non-tetrahedral four-coordinated crystal, and (iii) the density of the liquid at the crossover in crystallization from ice Ih to a four-coordinated non-tetrahedral crystal coincides with the
Mesoscopic coarse-grained simulations of lysozyme adsorption.
Yu, Gaobo; Liu, Jie; Zhou, Jian
2014-05-01
Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale. PMID:24785197
NASA Astrophysics Data System (ADS)
Turner, T. J.; Semiatin, S. L.
2011-09-01
Isothermal, uniaxial compression tests and accompanying numerical simulations were conducted on Waspaloy-ingot specimens to quantify deformation heterogeneity during hot working of coarse, columnar-grain materials. This was used as a means to approximate deformation processing in ingot materials. Electron-backscatter-diffraction (EBSD) measurements were made before and after compression testing to quantify microstructure evolution. A crystal-plasticity finite-element-method model, in which the starting microstructure was instantiated using EBSD scans of the undeformed material, was used to simulate the deformation. Good agreement was found between observations and simulation predictions of specimen profiles and intra-grain misorientations. The simulation results also revealed that the grain neighborhood appeared to be a principal factor controlling the heterogeneity of deformation at the grain scale. Significant differences in the simulated deformation of a given grain were noted for various arrangements of the orientations of its neighbors. In particular, the first- and second-nearest neighbors of a given grain have the most significant effect on heterogeneous deformation behavior.
NASA Astrophysics Data System (ADS)
Glade, R.; Jerolmack, D. J.; Pelletier, J. D.
2014-12-01
Coarse-grained ripples, also known as "megaripples," are large sand ripples found in both aeolian and aquatic environments on Earth, and are common on Mars. The formation and morphology of coarse-grained ripples are not as well understood as more common splash ripples. Current understanding suggests that formative wind speeds are above the saltation threshold for the fine grains, but below this threshold for coarse grains found on the crests, such that they creep. Based on this idea, we hypothesize that wind speeds above this coarse-grain saltation threshold will destroy the ripples. We further hypothesize that these ripples do not have an equilibrium size; rather, their size is related to the persistence of formative winds in a given direction. To test this model, we studied windblown coarse-grained ripples in White Sands, New Mexico. Terrestrial LiDAR was used to obtain high resolution ripple morphology and migration over a three month period. Wind velocity profiles and concurrent saltating grain size data were collected during a wind storm to directly relate modes of transport to particle size and wind stress. These local data were used to calibrate wind records from a nearby meteorological station to estimate local fluid stress using a long-term record. LiDAR data indicate that these ripples were destroyed and reoriented between March and June 2013, while the wind record shows that the coarse-grain saltation threshold was indeed exceeded during this time. Morphological analysis indicates that the lee slope of these ripples is set by saltation impact - similar to splash ripples - but that height, wavelength and stoss slope are not related to instantaneous transport conditions. The historical wind record also shows that the range of wind directions decreases rapidly with increasing speed, restricting strong winds to a narrow range of direction. From these results we explore the idea that coarse-grained ripples are typically larger and less frequently destroyed
NASA Astrophysics Data System (ADS)
Yamamoto, Umi; Wang, Zhen-Gang
We present results from coarse-grained simulation for ion dynamics and structures in dry polymer electrolytes. To capture the thermodynamic, kinetic, and system-specific aspects of ion solvation and clustering, cation-monomer complexation is modeled via functionalized physical bonds whose functionality and lifetime vary due to local availability of binding monomers and competition with Coulombic interaction. By varying salt concentration, cation-monomer binding energy, dielectric constant, and maximal functionality of the physical bonds, we systematically study the growth of ion clustering activity as characterized by packing structures, and associated changes in electric conductivity via single-ion and collective charge mobility. Deviations from Nernst-Einstein predictions, and comparisons with existing experiments for concentration dependence of conductivity will be discussed.
Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.
Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone
2015-04-14
A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed. PMID:26574390
Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.
Wassenaar, Tsjerk A; Ingólfsson, Helgi I; Priess, Marten; Marrink, Siewert J; Schäfer, Lars V
2013-04-01
Hybrid molecular dynamics simulations of atomistic (AA) solutes embedded in coarse-grained (CG) environment can substantially reduce the computational cost with respect to fully atomistic simulations. However, interfacing both levels of resolution is a major challenge that includes a balanced description of the relevant interactions. This is especially the case for polar solvents such as water, which screen the electrostatic interactions and thus require explicit electrostatic coupling between AA and CG subsystems. Here, we present and critically test computationally efficient hybrid AA/CG models. We combined the Gromos atomistic force field with the MARTINI coarse-grained force field. To enact electrostatic coupling, two recently developed CG water models with explicit electrostatic interactions were used: the polarizable MARTINI water model and the BMW model. The hybrid model was found to be sensitive to the strength of the AA-CG electrostatic coupling, which was adjusted through the relative dielectric permittivity εr(AA-CG). Potentials of mean force (PMFs) between pairs of amino acid side chain analogues in water and partitioning free enthalpies of uncharged amino acid side chain analogues between apolar solvent and water show significant differences between the hybrid simulations and the fully AA or CG simulations, in particular for charged and polar molecules. For apolar molecules, the results obtained with the hybrid AA/CG models are in better agreement with the fully atomistic results. The structures of atomistic ubiquitin solvated in CG water and of a single atomistic transmembrane α-helix and the transmembrane portion of an atomistic mechanosensitive channel in CG lipid bilayers were largely maintained during 50-100 ns of AA/CG simulations, partly due to an overstabilization of intramolecular interactions. This work highlights some key challenges on the way toward hybrid AA/CG models that are both computationally efficient and sufficiently accurate for
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
Qin, Feng
2015-01-01
The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362
Coarse-grained molecular dynamics: Nonlinear finite elements and finite temperature
Rudd, R E; Broughton, J Q
2005-05-30
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are modeled on a mesh in a formulation that generalizes conventional finite element modeling (FEM) of continuum elasticity. CGMD is derived solely from the MD model, however, and has no continuum parameters. As a result, it provides a coupling that is smooth and provides control of errors that arise at the coupling between the atomistic and coarse-grained regions. In this article, we elaborate on the formulation of CGMD, describing in detail how CGMD is applied to anharmonic solids and finite temperature simulations. As tests of CGMD, we present in detail the calculation of the phonon spectra for solid argon and tantalum in 3D, demonstrating how CGMD provides a better description of the elastic waves than that provided by FEM. We also present elastic wave scattering calculations that show the elastic wave scattering is more benign in CGMD than FEM. We also discuss the dependence of scattering on the properties of the mesh. We introduce a rigid approximation to CGMD that eliminates internal relaxation, similar to the Quasicontinuum technique, and compare it to the full CGMD.
Coarse-grained molecular dynamics simulations of nanopatterning with multivalent inks
NASA Astrophysics Data System (ADS)
Cieplak, Marek; Thompson, Damien
2008-06-01
A coarse-grained molecular dynamics (MD) model is developed to study the multivalent, or multisite, binding of small functionalized dendrimer molecules to β-cyclodextrin-terminated self-assembled monolayers, the so-called ``molecular printboards'' used to print ``ink'' molecules on surfaces with a high degree of positional control and specificity. Some current and future bionanotechnology applications are in the creation of nanoparticle assemblies, directed protein assembly, platforms for biosensing, and cell:surface attachment. The coarse-grained model allows us to probe up to microsecond timescales and model ink diffusion, crucial for the application of the printboard in, for example, medical diagnostics. Recent all-atom MD simulations identified and quantified the molecular strain limiting the stability of nanopatterns created with small dendrimer inks, and explained the different patterns obtained experimentally with different dendrimer inks. In the present work, the all-atom simulations are ``scaled up'' to longer timescales via coarse graining, without incurring significant additional computational expense, and, crucially, without significant loss in atom-scale detail, the coarse-grained MD simulations yielding properties similar to those obtained from the all-atom simulations. The anchoring of the ink molecules to the monolayer is of multivalent nature and the degree of multivalency shows a sharp dependence on temperature, control of temperature thus providing a further operational ``switch'' for directed molecular assembly. The computational protocol developed can, in principle, be extended to model any multivalent assembly, for example, virus-cell complexation.
Emergence of attraction in simulations of coarse-grained double stranded DNA
NASA Astrophysics Data System (ADS)
Ghanbarian, Shahzad; Rottler, Joerg
2015-03-01
DNA condensation induced by multivalent counterions is believed to play an important role in DNA bundling and packing into the cell nucleus. We present a coarse-grained, implicit solvent representation of rigid ds-DNA molecules in the presence of divalent counterions. In order to include solvation effects arising from the discrete nature of the water molecules, short-ranged corrections are added to the pairwise interaction potentials such that the structure of counterions is consistent with results from corresponding explicit solvent simulations. The effective force between two DNA strands generated by these potentials provides an excellent match to that observed in the explicit solvent model. Importantly, this interaction features multiple minima and reproduces the like-charge attraction effect between DNA molecules observed in full atomistic simulations at significantly reduced computational expense. This result proves that it is possible to capture complex multibody interactions between polyelectrolyte strands with two-body potentials.
Kinetics of formation of bile salt micelles from coarse-grained Langevin dynamics simulations.
Vila Verde, Ana; Frenkel, Daan
2016-06-21
We examine the mechanism of formation of micelles of dihydroxy bile salts using a coarse-grained, implicit solvent model and Langevin dynamics simulations. We find that bile salt micelles primarily form via addition and removal of monomers, similarly to surfactants with typical head-tail molecular structures, and not via a two-stage mechanism - involving formation of oligomers and their subsequent aggregation to form larger micelles - originally proposed for bile salts. The free energy barrier to removal of single bile monomers from micelles is ≈2kBT, much less than what has been observed for head-tail surfactants. Such a low barrier may be biologically relevant: it allows for rapid release of bile monomers into the intestine, possibly enabling the coverage of fat droplets by bile salt monomers and subsequent release of micelles containing fats and bile salts - a mechanism that is not possible for ionic head-tail surfactants of similar critical micellar concentrations. PMID:27199094
All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.
Zheng, Wenjun
2014-07-01
The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. PMID:24403006
Chemically transferable coarse-grained potentials from conditional reversible work calculations.
Brini, E; van der Vegt, N F A
2012-10-21
The representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of n-alkanes, the coarse-grained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a free-energy-based coarse-graining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRW-CG potentials may be readily obtained from a single simulation of the liquid state using the free energy perturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules. PMID:23083154
NASA Astrophysics Data System (ADS)
Zheng, Wenjun; Glenn, Paul
2015-01-01
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.
Zheng, Wenjun Glenn, Paul
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.
Aramoon, Amin; Breitzman, Timothy D; Woodward, Christopher; El-Awady, Jaafar A
2016-09-01
In this work, a coarse-grained model is developed for highly cross-linked bisphenol A diglycidyl ether epoxy resin with diaminobutane hardener. In this model, all conformationally relevant coarse-grained degrees of freedom are accounted for by sampling over the free-energy surfaces of the atomic structures using quantum mechanical simulations. The interaction potentials between nonbonded coarse-grained particles are optimized to accurately predict the experimentally measured density and glass-transition temperature of the system. In addition, a new curing algorithm is also developed to model the creation of highly cross-linked epoxy networks. In this algorithm, to create a highly cross-linked network, the reactants are redistributed from regions with an excessive number of reactive molecules to regions with a lower number of reactants to increase the chances of cross-linking. This new algorithm also dynamically controls the rate of cross-linking at each local region to ensure uniformity of the resulting network. The curing simulation conducted using this algorithm is able to develop polymeric networks having a higher average degree of cross-linking, which is more uniform throughout the simulation cell as compared to that in the networks cured using other curing algorithms. The predicted gel point from the current curing algorithm is in the acceptable theoretical and experimental range of measured values. Also, the resulting cross-linked microstructure shows a volume shrinkage of 5%, which is close to the experimentally measured volume shrinkage of the cured epoxy. Finally, the thermal expansion coefficients of materials in the glassy and rubbery states show good agreement with the experimental values. PMID:27504803
NASA Astrophysics Data System (ADS)
Calzetta, E. A.; Hu, B. L.; Mazzitelli, Francisco D.
2001-10-01
usefully applied. This is followed by an introduction to the influence functional in the (Feynman-Vernon) formulation of quantum open systems, illustrated by the quantum Brownian motion models. We show its relation to the CTP CGEA, and indicate how to identify the noise and dissipation kernels therein. We derive the master and Langevin equations for interacting quantum fields, represented in the works of Lombardo and Mazzitelli and indicate how they can be applied to the problem of coarse-graining, decoherence and structure formation in de Sitter universe. We perform a nonperturbative evaluation of the CTP CGEA and show how to derive the renormalization group equations under an adiabatic approximation adopted for the modes by Dalvit and Mazzitelli. We assert that this approximation is incomplete as the effect of noise is suppressed. We then discuss why noise is expected in the RG equations for nonequilibrium processes. In Part IV (Sections /9, /10), following Lombardo and Mazzitelli, we use the RG equations to derive the Einstein-Langevin equation in stochastic semiclassical gravity. As an example, we calculate the quantum correction to the Newtonian potential. We end with a discussion on why a stochastic component of RG equations is expected for nonequilibrium processes.
Coarse-grained mechanics of viral shells
NASA Astrophysics Data System (ADS)
Klug, William S.; Gibbons, Melissa M.
2008-03-01
We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.
Coarse-grained force field; general folding theory
Liwo, Adam; He, Yi; Scheraga, Harold A.
2012-01-01
We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described. PMID:21643583
Coarse grained molecular simulations of melting kinetics of DPPC vesicles
NASA Astrophysics Data System (ADS)
Bolling-Patel, Lara A.; Kindt, James T.
2015-03-01
Phase transitions in unilamellar vesicles are of particular interest as the increase in permeability of lipid bilayers around the main phase transition temperature makes them candidates for drug encapsulation and temperature-responsive delivery. We study the transition between the gel and fluid phases of a unilamellar vesicle of MARTINI coarse grain DPPC lipids with a diameter of 40 nm following temperature jumps from 280 K to temperatures near the transition temperature of 295 K. At 290 K and 295 K vesicles show single exponential melting kinetics in qualitative agreement with the early stages of melting measured in IR temperature-jump experiments. These trajectories exhibit partial melting over 500 ns, accompanied by a decrease in the number of gel domains from 8 domains in the initial faceted structure to 5 and 3 respectively. Melting at 295 K results in a shape change to an asymmetric structure that appears to be transforming into an oblate solid. Complete melting is seen for temperature jumps to 300 K and 310 K, in which cases vesicles undergo shape transitions into prolate dumbbell shapes. The shape changes that accompany the phase transition indicate that the phase transition kinetics are correlated to changes in curvature. NSF CHE-1213904.
Coarse-grained potentials of single-walled carbon nanotubes
NASA Astrophysics Data System (ADS)
Zhao, Junhua; Jiang, Jin-Wu; Wang, Lifeng; Guo, Wanlin; Rabczuk, Timon
2014-11-01
We develop the coarse-grained (CG) potentials of single-walled carbon nanotubes (SWCNTs) in CNT bundles and buckypaper for the study of the static and dynamic behaviors. The explicit expressions of the CG stretching, bending and torsion potentials for the nanotubes are obtained by the stick-spiral and the beam models, respectively. The non-bonded CG potentials between two different CG beads are derived from analytical results based on the cohesive energy between two parallel and crossing SWCNTs from the van der Waals interactions. We show that the CG model is applicable to large deformations of complex CNT systems by combining the bonded potentials with non-bonded potentials. Checking against full atom molecular dynamics calculations and our analytical results shows that the present CG potentials have high accuracy. The established CG potentials are used to study the mechanical properties of the CNT bundles and buckypaper efficiently at minor computational cost, which shows great potential for the design of micro- and nanomechanical devices and systems.
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. PMID:26723603
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.
NASA Astrophysics Data System (ADS)
Español, Pep; Donev, Aleksandar
2015-12-01
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our "bottom-up" and previous "top-down" approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a "linear for spiky" weak approximation which replaces microscopic "fields" with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics simulations as input
Español, Pep; Donev, Aleksandar
2015-12-21
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our “bottom-up” and previous “top-down” approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a “linear for spiky” weak approximation which replaces microscopic “fields” with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics
Español, Pep; Donev, Aleksandar
2015-12-21
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our "bottom-up" and previous "top-down" approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a "linear for spiky" weak approximation which replaces microscopic "fields" with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics simulations as input
Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales
Ayton, Gary S.; Lyman, Edward
2014-01-01
An overall multiscale simulation strategy for large scale coarse-grain simulations of membrane protein systems is presented. The protein is modeled as a heterogeneous elastic network, while the lipids are modeled using the hybrid analytic-systematic (HAS) methodology, where in both cases atomistic level information obtained from molecular dynamics simulation is used to parameterize the model. A feature of this approach is that from the outset liposome length scales are employed in the simulation (i.e., on the order of ½ a million lipids plus protein). A route to develop highly coarse-grained models from molecular-scale information is proposed and results for N-BAR domain protein remodeling of a liposome are presented. PMID:20158037
Tensor network algorithm by coarse-graining tensor renormalization on finite periodic lattices
NASA Astrophysics Data System (ADS)
Zhao, Hui-Hai; Xie, Zhi-Yuan; Xiang, Tao; Imada, Masatoshi
2016-03-01
We develop coarse-graining tensor renormalization group algorithms to compute physical properties of two-dimensional lattice models on finite periodic lattices. Two different coarse-graining strategies, one based on the tensor renormalization group and the other based on the higher-order tensor renormalization group, are introduced. In order to optimize the tensor network model globally, a sweeping scheme is proposed to account for the renormalization effect from the environment tensors under the framework of second renormalization group. We demonstrate the algorithms by the classical Ising model on the square lattice and the Kitaev model on the honeycomb lattice, and show that the finite-size algorithms achieve substantially more accurate results than the corresponding infinite-size ones.
Quantum particles from coarse grained classical probabilities in phase space
Wetterich, C.
2010-07-15
Quantum particles can be obtained from a classical probability distribution in phase space by a suitable coarse graining, whereby simultaneous classical information about position and momentum can be lost. For a suitable time evolution of the classical probabilities and choice of observables all features of a quantum particle in a potential follow from classical statistics. This includes interference, tunneling and the uncertainty relation.
7 CFR 457.113 - Coarse grains crop insurance provisions.
Code of Federal Regulations, 2013 CFR
2013-01-01
... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...
7 CFR 457.113 - Coarse grains crop insurance provisions.
Code of Federal Regulations, 2012 CFR
2012-01-01
... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...
7 CFR 457.113 - Coarse grains crop insurance provisions.
Code of Federal Regulations, 2014 CFR
2014-01-01
... Grains Crop Provisions 1. Definitions Coarse grains. Corn, grain sorghum, and soybeans. Grain sorghum... cash grain price per bushel for the U.S. No. 2 yellow corn, U.S. No. 2 grain sorghum, or U.S. No. 1... yellow corn and grain sorghum, or U.S. No. 1 grade for soybeans. Factors not associated with...
NASA Astrophysics Data System (ADS)
Dold, C.; Henerichs, M.; Gilgen, P.; Wegener, K.
Manufacturing of cutting edges in PCD cutting tool inserts (CTI) using picosecond pulsewidth laser sources is presented. Cutting edge radii of redge = 5 to 6 μm are achieved. Validation experiments are carried out on a turning lathe using lasered and ground CTI on machining carbon fibre reinforced plastics (CFRP) which is mainly used for aircraft structures. Experiments are done on fine and coarse grain PCD structures (average grain sizes are 2-4 μm and 25 μm resepectively) which are not economical in the latter case if manufactured conventionally, e.g. using grinding processes. Wear resistance, tool lifetime and process forces can be improved if laser processed coarse grain cutting tools are employed.
Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons.
Moon, Sung Joon; Cook, Katherine A; Rajendran, Karthikeyan; Kevrekidis, Ioannis G; Cisternas, Jaime; Laing, Carlo R
2015-12-01
The formation of oscillating phase clusters in a network of identical Hodgkin-Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition-through [Formula: see text] (possibly perturbed) period-doubling and subsequent bifurcations-to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar "fine" states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron's "identity" (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established "identity-state" correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics. PMID:26458901
Quantitative comparison of alternative methods for coarse-graining biological networks
Bowman, Gregory R.; Meng, Luming; Huang, Xuhui
2013-01-01
Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717
Quantitative comparison of alternative methods for coarse-graining biological networks.
Bowman, Gregory R; Meng, Luming; Huang, Xuhui
2013-09-28
Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717
Quantitative comparison of alternative methods for coarse-graining biological networks
NASA Astrophysics Data System (ADS)
Bowman, Gregory R.; Meng, Luming; Huang, Xuhui
2013-09-01
Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results.
Ramírez, Claudia L; Petruk, Ariel; Bringas, Mauro; Estrin, Dario A; Roitberg, Adrian E; Marti, Marcelo A; Capece, Luciana
2016-07-12
Heme proteins are ubiquitous in nature and perform many diverse functions in all kingdoms of life. Many of these functions are related to large-scale conformational transitions and allosteric processes. Sampling of these large conformational changes is computationally very challenging. In this context, coarse-grain simulations emerge as an efficient approach to explore the conformational landscape. In this work, we present a coarse-grained model of the heme group and thoroughly validate this model in different benchmark examples, which include the monomeric heme proteins myoglobin and neuroglobin and the tetrameric human hemoglobin where we evaluated the method's ability to explore conformational changes (as the formation of hexacoordinated species) and allosteric transitions (as the well-known R → T transition). The obtained results are compared with atomistic molecular dynamics simulations. Overall, the results indicate that this approach conserves the essential dynamical information on different allosteric processes. PMID:27267322
A coarse-grain force field for RDX: Density dependent and energy conserving.
Moore, Joshua D; Barnes, Brian C; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S; Taylor, DeCarlos E; Brennan, John K
2016-03-14
We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions. PMID:26979691
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity
NASA Astrophysics Data System (ADS)
Frigori, Rafael B.; Rizzi, Leandro G.; Alves, Nelson A.
2013-01-01
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.
Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity.
Frigori, Rafael B; Rizzi, Leandro G; Alves, Nelson A
2013-01-01
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process. PMID:23298062
NASA Astrophysics Data System (ADS)
Rudzinski, J. F.; Bereau, T.
2016-07-01
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent, dynamics. In this work, we rely on Markov state models to simultaneously characterize the static and kinetic properties of two CG peptide force fields—one top-down and one bottom-up. Instead of a rigorous evolution of CG dynamics (e.g., using a generalized Langevin equation), we attempt to improve the description of kinetics by simply altering the existing CG models, which employ standard Langevin dynamics. By varying masses and relevant force-field parameters, we can improve the timescale separation of the slow kinetic processes, achieve a more consistent ratio of mean-first-passage times between metastable states, and refine the relative free-energies between these states. Importantly, we show that the incorporation of kinetic information into a structure-based parametrization improves the description of the helix-coil transition sampled by a minimal CG model. While structure-based models understabilize the helical state, kinetic constraints help identify CG models that improve the ratio of forward/backward timescales by effectively hindering the sampling of spurious conformational intermediate states.
Coarse-grained Simulation of Complexation between Small Interfering RNA and Polycations
NASA Astrophysics Data System (ADS)
Wei, Zonghui; Ren, Yong; Williford, John-Michael; Mao, Hai-Quan; Luijten, Erik; Northwestern University Collaboration; Johns Hopkins University Collaboration
Nanoparticles formed through self-assembly of polycations and nucleic acids are promising systems for gene delivery. A full understanding of the behavior of these particles in physiological context requires detailed knowledge of their physical properties. All-atom molecular dynamics simulations can provide insight into the interaction of polymeric carriers with genomic material, but only at limited time and length scales. To overcome these limitations and explore the full complexation process, a reliable coarse-grained model is needed. Here, we systematically develop such a model for a system comprised of small interfering RNA (siRNA) and polyethyleneimine-based carriers, and evaluate the quality of the coarse-grained model through comparison with all-atom simulations. We show that our coarse-grained model provides a reliable description of detailed binding pictures, charge characteristics, and water dynamics, while accelerating the simulations by two orders of magnitude. This makes it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.
Coarse-graining using the VOTCA package
Junghans, Christoph
2012-06-07
Coarsegraining is a systematic way of reducing the number of degrees of freedom representing a system of interest. Several coarsegraining techniques have so far been developed, such as iterative Boltzmann inversion, forcematching, and inverse Monte Carlo. However, there is no unified framework that implements these methods and allows their direct comparison. We present a versatile objectoriented toolkit for coarsegraining applications that implements these techniques and provides a flexible modular platform for the further development of coarsegraining techniques. All methods are illustrated and compared by coarsegraining the SPCE water model and liquid propane.
Leonard, T.; Lander, B.; Seifert, U.; Speck, T.
2013-11-28
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for the work still hold albeit for a different, apparent, change of free energy.
A coarse-grained kinetic equation for neutral particles in turbulent fusion plasmas
Mekkaoui, A.; Marandet, Y.; Genesio, P.; Rosato, J.; Stamm, R.; Capes, H.; Koubiti, M.; Godbert-Mouret, L.; Catoire, F.
2012-06-15
A coarse-grained kinetic equation for neutral particles (atoms, molecules) in magnetized fusion plasmas, valid on time scales large compared to the turbulence correlation time, is presented. This equation includes the effects of plasma density fluctuations, described by gamma statistics, on the transport of neutral particles. These effects have so far been neglected in plasma edge modeling, in spite of the fact that the amplitude of fluctuations can be of order unity. Density fluctuations are shown to have a marked effect on the screening of neutrals and on the spatial localization of the ionization source, in particular at high density. The coarse-grained equations obtained in this work are readily implemented in edge code suites currently used for fusion plasma analysis and future divertor design (ITER, DEMO).
NASA Astrophysics Data System (ADS)
Leonard, T.; Lander, B.; Seifert, U.; Speck, T.
2013-11-01
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example, simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski relation connecting work with the change of free energy holds if the time evolution of the density follows the Kawasaki-Dean equation. Specifically, we study the work distributions for the compression and expansion of a two-dimensional colloidal model suspension implementing a practical coarse-graining scheme of the microscopic particle positions. We demonstrate that even if coarse-grained dynamics and density functional do not match, the fluctuation relations for the work still hold albeit for a different, apparent, change of free energy.
Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em
2016-07-28
We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn. PMID:27475343
NASA Astrophysics Data System (ADS)
Li, Zhen; Bian, Xin; Yang, Xiu; Karniadakis, George Em
2016-07-01
We construct effective coarse-grained (CG) models for polymeric fluids by employing two coarse-graining strategies. The first one is a forward-coarse-graining procedure by the Mori-Zwanzig (MZ) projection while the other one applies a reverse-coarse-graining procedure, such as the iterative Boltzmann inversion (IBI) and the stochastic parametric optimization (SPO). More specifically, we perform molecular dynamics (MD) simulations of star polymer melts to provide the atomistic fields to be coarse-grained. Each molecule of a star polymer with internal degrees of freedom is coarsened into a single CG particle and the effective interactions between CG particles can be either evaluated directly from microscopic dynamics based on the MZ formalism, or obtained by the reverse methods, i.e., IBI and SPO. The forward procedure has no free parameters to tune and recovers the MD system faithfully. For the reverse procedure, we find that the parameters in CG models cannot be selected arbitrarily. If the free parameters are properly defined, the reverse CG procedure also yields an accurate effective potential. Moreover, we explain how an aggressive coarse-graining procedure introduces the many-body effect, which makes the pairwise potential invalid for the same system at densities away from the training point. From this work, general guidelines for coarse-graining of polymeric fluids can be drawn.
Systematic coarse-graining in nucleation theory
Schweizer, M.; Sagis, L. M. C.
2015-08-21
In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.
Systematic coarse-graining in nucleation theory.
Schweizer, M; Sagis, L M C
2015-08-21
In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 - 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters. PMID:26298141
Systematic coarse-graining in nucleation theory
NASA Astrophysics Data System (ADS)
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.
Role of neutral lipids in tear fluid lipid layer: coarse-grained simulation study.
Telenius, Jelena; Koivuniemi, Artturi; Kulovesi, Pipsa; Holopainen, Juha M; Vattulainen, Ilpo
2012-12-11
Tear fluid lipid layer (TFLL) residing at the air-water interface of tears has been recognized to play an important role in the development of dry eye syndrome. Yet, the composition, structure, and mechanical properties of TFLL are only partly known. Here, we report results of coarse-grained simulations of a lipid layer comprising phospholipids, free fatty acids, cholesteryl esters, and triglycerides at the air-water interface to shed light on the properties of TFLL. We consider structural as well as dynamical properties of the lipid layer as a function of surface pressure. Simulations revealed that neutral lipids reside heterogeneously between phospholipids at relatively low pressures but form a separate hydrophobic phase with increasing surface pressure, transforming the initial lipid monolayer to a two-layered structure. When the model of TFLL was compared to a one-component phospholipid monolayer system, we found drastic differences in both structural and dynamical properties that explain the prominent role of neutral lipids as stabilizers of the TFLL. Based on our results, we suggest that neutral lipids are able to increase the stability of the TFLL by modulating its dynamical and structural behavior, which is important for the proper function of tear film. PMID:23151187
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. PMID:26885845
NASA Astrophysics Data System (ADS)
Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.
2015-12-01
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.
2015-12-28
We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.
Coarse-Grained Molecular Dynamics: Dissipation Due to Internal Modes
Rudd, R E
2001-12-21
We describe progress on the issue of pathological elastic wave reflection in atomistic and multiscale simulation. First we briefly review Coarse-Grained Molecular Dynamics (CGMD). Originally CGMD was formulated as a Hamiltonian system in which energy is conserved. This formulation is useful for many applications, but recently CGMD has been extended to include generalized Langevin forces. Here we describe how Langevin dynamics arise naturally in CGMD, and we examine the implication for elastic wave scattering.
Coarse-graining stochastic biochemical networks: adiabaticity and fast simulations
Nemenman, Ilya; Sinitsyn, Nikolai; Hengartner, Nick
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.
High capacitance of coarse-grained carbide derived carbon electrodes
NASA Astrophysics Data System (ADS)
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury
2016-02-01
We report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. Using a titanium carbide (TiC) precursor, we synthesized 70-250 μm sized particles with high surface area and a narrow pore size distribution. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. The material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250-1000 micron thick dense CDC films with up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.
High capacitance of coarse-grained carbide derived carbon electrodes
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury
2016-01-01
Here, we report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. We synthesized 70–250 μm sized particles with high surface area and a narrow pore size distribution, using a titanium carbide (TiC) precursor. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. Moreover, the material showcased capacitance above 100 F g-1 at sweep rates as high as 250 mV s-1 in organic electrolyte. 250–1000 micron thick dense CDC films withmore » up to 80 mg cm-2 loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.« less
High capacitance of coarse-grained carbide derived carbon electrodes
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; Zozulya, Yuliya; Simon, Patrice; Gogotsi, Yury
2016-01-01
Here, we report exceptional electrochemical properties of supercapacitor electrodes composed of large, granular carbide-derived carbon (CDC) particles. We synthesized 70–250 μm sized particles with high surface area and a narrow pore size distribution, using a titanium carbide (TiC) precursor. Electrochemical cycling of these coarse-grained powders defied conventional wisdom that a small particle size is strictly required for supercapacitor electrodes and allowed high charge storage densities, rapid transport, and good rate handling ability. Moreover, the material showcased capacitance above 100 F g^{-1} at sweep rates as high as 250 mV s^{-1} in organic electrolyte. 250–1000 micron thick dense CDC films with up to 80 mg cm^{-2} loading showed superior areal capacitances. The material significantly outperformed its activated carbon counterpart in organic electrolytes and ionic liquids. Furthermore, large internal/external surface ratio of coarse-grained carbons allowed the resulting electrodes to maintain high electrochemical stability up to 3.1 V in ionic liquid electrolyte. In addition to presenting novel insights into the electrosorption process, these coarse-grained carbons offer a pathway to low-cost, high-performance implementation of supercapacitors in automotive and grid-storage applications.
Eby, D Matthew; Johnson, Glenn R; Farmer, Barry L; Pandey, Ras B
2011-01-21
Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide- and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate-peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitro KSL and silaffin systems. PMID:21072418
Coarse-grained simulations of poly(propylene imine) dendrimers in solution.
Smeijers, A F; Markvoort, A J; Pieterse, K; Hilbers, P A J
2016-02-21
The behavior of poly(propylene imine) (PPI) dendrimers in concentrated solutions has been investigated using molecular dynamics simulations containing up to a thousand PPI dendrimers of generation 4 or 5 in explicit water. To deal with large system sizes and time scales required to study the solutions over a wide range of dendrimer concentrations, a previously published coarse-grained model was applied. Simulation results on the radius of gyration, structure factor, intermolecular spacing, dendrimer interpenetration, and water penetration are compared with available experimental data, providing a clear concentration dependent molecular picture of PPI dendrimers. It is shown that with increasing concentration the dendrimer volume diminishes accompanied by a reduction of internalized water, ultimately resulting in solvent filled cavities between stacked dendrimers. Concurrently dendrimer interpenetration increases only slightly, leaving each dendrimer a separate entity also at high concentrations. Moreover, we compare apparent structure factors, as calculated in experimental studies relying on the decoupling approximation and the constant atomic form factor assumption, with directly computed structure factors. We demonstrate that these already diverge at rather low concentrations, not because of small changes in form factor, but rather because the decoupling approximation fails as monomer positions of separate dendrimers become correlated at concentrations well below the overlap concentration. PMID:26896998
2015-01-01
Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (LettieriS.; ZuckermanD. M.J. Comput. Chem.2012, 33, 268−27522120971) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70–90% of the α-helical structure while providing a factor of 3–10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding–unfolding transitions of the peptide were observed, along with a factor of 10–100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a “resolution exchange” setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange
Peridynamics as a rigorous coarse-graining of atomistics for multiscale materials design.
Lehoucq, Richard B.; Aidun, John Bahram; Silling, Stewart Andrew; Sears, Mark P.; Kamm, James R.; Parks, Michael L.
2010-09-01
This report summarizes activities undertaken during FY08-FY10 for the LDRD Peridynamics as a Rigorous Coarse-Graining of Atomistics for Multiscale Materials Design. The goal of our project was to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. The goal of our project is to develop a coarse-graining of finite temperature molecular dynamics (MD) that successfully transitions from statistical mechanics to continuum mechanics. Our coarse-graining overcomes the intrinsic limitation of coupling atomistics with classical continuum mechanics via the FEM (finite element method), SPH (smoothed particle hydrodynamics), or MPM (material point method); namely, that classical continuum mechanics assumes a local force interaction that is incompatible with the nonlocal force model of atomistic methods. Therefore FEM, SPH, and MPM inherit this limitation. This seemingly innocuous dichotomy has far reaching consequences; for example, classical continuum mechanics cannot resolve the short wavelength behavior associated with atomistics. Other consequences include spurious forces, invalid phonon dispersion relationships, and irreconcilable descriptions/treatments of temperature. We propose a statistically based coarse-graining of atomistics via peridynamics and so develop a first of a kind mesoscopic capability to enable consistent, thermodynamically sound, atomistic-to-continuum (AtC) multiscale material simulation. Peridynamics (PD) is a microcontinuum theory that assumes nonlocal forces for describing long-range material interaction. The force interactions occurring at finite distances are naturally accounted for in PD. Moreover, PDs nonlocal force model is entirely consistent with those used by atomistics methods, in stark contrast to classical continuum mechanics. Hence, PD can be employed for mesoscopic phenomena that are beyond the realms of classical continuum mechanics and
Self-assembly of Spherical Macroions in Solution: A Coarse-grained Molecular Dynamics Study
NASA Astrophysics Data System (ADS)
Liu, Zhuonan; Liu, Tianbo; Tsige, Mesfin
2015-03-01
Macroions (such as polyoxometalates) in solution can form a stable hollow spherical super-molecular structure called blackberry when they have moderate surface charge density and size (1-10 nm). Depending on the surface charge density of macroions, the size of the blackberry can be from 20 to more than 100 nm. Other macroions such as dendrimers can also self-assemble into similar super-molecular structure in solution. Existing theories such as Debye-Hückel and DLVO theories cannot explain this phenomenon and we are not aware of any other theory that can explain this. Previous studies using all-atom Molecular Dynamics simulations have shown identical macroions forming oligomers mediated by counterions. Due to the limitations in all-atom simulation and available computational capabilities, these studies handled only small systems with simple macroions, leading to less conclusive but still relevant results on the self-assembly behavior. To overcome these limitations, in this work large-scale coarse-grained modeling of macroions in solution is used. In order to understand the origin of the attractive force that is responsible for the self-assembly of macroions, different types of macroions in different solution conditions are studied. This work was supported by NSF Grant DMR0847580.
Bieler, Noah S.; Knowles, Tuomas P. J.; Frenkel, Daan; Vácha, Robert
2012-01-01
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 -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. PMID:23071427
Lu, Qing; Straub, John E
2016-03-10
The solid-to-liquid phase transition in water nanofilms confined between plates, with varying separations and water-plate interactions ranging from strongly hydrophobic to strongly hydrophilic, was simulated using a coarse-grained monatomic water model (mW) and the generalized replica exchange method (gREM). Extensive gREM simulations combined with the statistical temperature weighted histogram analysis method (ST-WHAM) provide a detailed description of the thermodynamic properties intrinsic to the phase transition, including the transition temperature, isobaric heat capacity, phase change enthalpy, entropy, and their dependence on the interplate distance and the plate-water interaction. The ice structure of water nanofilms was characterized at various conditions using the transverse density profile and the distribution of angles formed by hydrogen-bonded neighboring molecules. Flat bilayer ice was observed to be the dominant solid phase at close interplate distance, while puckered bilayer ice, similar to a slab of ice Ih, is the predominant structure at larger interplates. Stable puckered bilayer ice, previously observed to have a low melting point, is observed to have enhanced stability with high melting temperature when confined between hydrophilic plates. These results demonstrate the strong dependence of phase stability and coexistence in nanoconfined systems on the geometry and physical properties of the confining environment. PMID:26906259
Equation of state for a coarse-grained DPPC monolayer at the air/water interface
NASA Astrophysics Data System (ADS)
Adhangale, Parag S.; Gaver, Donald P., III
Pulmonary surfactant, a complex mixture of phospholipids and proteins, secreted by the type II epithelial cells in the lungs, is crucial to reducing the effort required for breathing. A lack of adequate amounts of pulmonary surfactant in underdeveloped lungs of premature infants results in infant respiratory distress syndrome (RDS). Surfactant replacement therapy (SRT) is the approved method of mitigating the effects of RDS. The development of new SRT regimens requires a fundamental understanding of the links between surfactant biochemistry and functionality. We use a coarse-grained (CG) model to predict the surface pressure-surface concentration relationship (equation of state) for pure DPPC, which is a major component of endogenous and synthetic pulmonary surfactant mixtures. We show that the model can be efficiently used to predict the equation of state in excellent agreement with experimental results. We also study the structure of the monolayer as a function of the surface tension of the system. We show that a decrease in the applied surface tension results in an increase in order in the head group region and a decrease in order in the tail region of DPPC. This technique may be useful in the prediction of equations of state for surfactant replacements.
NASA Astrophysics Data System (ADS)
Bereau, Tristan; Wang, Zun-Jing; Deserno, Markus
2014-03-01
Interfacial systems are at the core of fascinating phenomena in many disciplines, such as biochemistry, soft-matter physics, and food science. However, the parametrization of accurate, reliable, and consistent coarse-grained (CG) models for systems at interfaces remains a challenging endeavor. In the present work, we explore to what extent two independently developed solvent-free CG models of peptides and lipids—of different mapping schemes, parametrization methods, target functions, and validation criteria—can be combined by only tuning the cross-interactions. Our results show that the cross-parametrization can reproduce a number of structural properties of membrane peptides (for example, tilt and hydrophobic mismatch), in agreement with existing peptide-lipid CG force fields. We find encouraging results for two challenging biophysical problems: (i) membrane pore formation mediated by the cooperative action of several antimicrobial peptides, and (ii) the insertion and folding of the helix-forming peptide WALP23 in the membrane.
Li, Xiaoxu; Gao, Lianghui; Fang, Weihai
2016-01-01
In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop. PMID:27137463
Li, Xiaoxu; Gao, Lianghui; Fang, Weihai
2016-01-01
In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop. PMID:27137463
Yoo, Jejoong; Cui, Qiang
2009-01-01
Abstract Although many membrane additives are known to modulate the activities of membrane proteins via perturbing the properties of lipid membrane, the underlying mechanism is often not precisely understood. In this study, we investigate the impact of asymmetrically incorporating single-tailed lysophosphatidylcholine (LPC) into a membrane bilayer using coarse-grained molecular dynamics simulations. Using a simple computational protocol designed to approximately mimic a micropipette setting, we show that asymmetric incorporation of LPC can lead to significant curvature in a bilayer. Detailed analysis of geometrical and mechanical properties (pressure profile) of the resulting mound structure indicates that the degree of pressure profile perturbation is determined not by the local curvature per se but by the packing of lipid headgroups (i.e., area-per-lipid). The findings help provide a concrete basis for understanding the activation mechanism of mechanosensitive channels by asymmetric incorporation of LPC into membrane patches in patch-clamp experiments. The calculated local pressure profiles are valuable to the construction of realistic membrane models for the analysis of mechanosensation in a continuum mechanics framework. PMID:19843459
Flores-Canales, Jose C; Vargas-Uribe, Mauricio; Ladokhin, Alexey S; Kurnikova, Maria
2015-06-01
Diphtheria toxin translocation (T) domain inserts in lipid bilayers upon acidification of the environment. Computational and experimental studies have suggested that low pH triggers a conformational change of the T-domain in solution preceding membrane binding. The refolded membrane-competent state was modeled to be compact and mostly retain globular structure. In the present work, we investigate how this refolded state interacts with membrane interfaces in the early steps of T-domain's membrane association. Coarse-grained molecular dynamics simulations suggest two distinct membrane-bound conformations of the T-domain in the presence of bilayers composed of a mixture of zwitteronic and anionic phospholipids (POPC:POPG with a 1:3 molar ratio). Both membrane-bound conformations show a common near parallel orientation of hydrophobic helices TH8-TH9 relative to the membrane plane. The most frequently observed membrane-bound conformation is stabilized by electrostatic interactions between the N-terminal segment of the protein and the membrane interface. The second membrane-bound conformation is stabilized by hydrophobic interactions between protein residues and lipid acyl chains, which facilitate deeper protein insertion in the membrane interface. A theoretical estimate of a free energy of binding of a membrane-competent T-domain to the membrane is provided. PMID:25650178
Spreading of a Unilamellar Liposome on Charged Substrates: A Coarse-Grained Molecular Simulation.
Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng
2016-04-19
Supported lipid bilayers (SLBs) are able to accommodate membrane proteins useful for diverse biomimetic applications. Although liposome spreading represents a common procedure for preparation of SLBs, the underlying mechanism is not yet fully understood, particularly from a molecular perspective. The present study examines the effects of the substrate charge on unilamellar liposome spreading on the basis of molecular dynamics simulations for a coarse-grained model of the solvent and lipid molecules. Liposome transformation into a lipid bilayer of different microscopic structures suggests three types of kinetic pathways depending on the substrate charge density, that is, top-receding, parachute, and parachute with wormholes. Each pathway leads to a unique distribution of the lipid molecules and thereby distinctive properties of SLBs. An increase of the substrate charge density results in a magnified asymmetry of the SLBs in terms of the ratio of charged lipids, parallel surface movements, and the distribution of lipid molecules. While the lipid mobility in the proximal layer is strongly correlated with the substrate potential, the dynamics of lipid molecules in the distal monolayer is similar to that of a freestanding lipid bilayer. For liposome spreading on a highly charged surface, wormhole formation promotes lipid exchange between the SLB monolayers thus reduces the asymmetry on the number density of lipid molecules, the lipid order parameter, and the monolayer thickness. The simulation results reveal the important regulatory role of electrostatic interactions on liposome spreading and the properties of SLBs. PMID:27019394
NASA Astrophysics Data System (ADS)
Chushak, Y.; Travesset, A.
2005-12-01
Multiblock polymers in aqueous solution, where one or several blocks are hydrophobic, exhibit a rich variety of phases and states of aggregation. In this paper, we investigate a pentablock system ABCBA, where the B block is always hydrophilic and the A and C blocks have varying degrees of hydrophobicity depending on external conditions. We report coarse-grained molecular-dynamics simulations where the solvent is included explicitly and monomers interact via a 6-9 Lennard Jones potential function. The hydrophobic interaction is modeled by tuning the parameter controlling the strength of the interaction between the hydrophobic monomers and the solvent. We investigate the structure and morphology of the micelles for two concrete situations representing changes in temperature and the pH level. The simulated system is directly relevant to a recently synthesized pentablock system consisting of a triblock Pluronic® with an added pH-sensitive end group [B. C. Anderson et al., Macromolecules 36, 1670 (2003)].
NASA Astrophysics Data System (ADS)
Nguyen, Hung; Van, Thanh Dac; Le, Ly
2015-10-01
The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.
Effective mobility of dislocations from systematic coarse-graining
NASA Astrophysics Data System (ADS)
Kooiman, M.; Hütter, M.; Geers, MGD
2015-06-01
The dynamics of large amounts of dislocations governs the plastic response of crystalline materials. In this contribution we discuss the relation between the mobility of discrete dislocations and the resulting flow rule for coarse-grained dislocation densities. The mobilities used in literature on these levels are quite different, for example in terms of their intrinsic the stress dependence. To establish the relation across the scales, we have derived the macroscopic evolution equations of dislocation densities from the equations of motion of individual dislocations by means of systematic coarse-graining. From this, we can identify a memory kernel relating the driving force and the flux of dislocations. This kernel can be considered as an effective macroscopic mobility with two contributions; a direct contribution related to the overdamped motion of individual dislocations, and an emergent contribution that arises from time correlations of fluctuations in the Peach-Koehler force. Scaling analysis shows that the latter contribution is dominant for dislocations in metals at room temperature. We also discuss several concerns related to the separation of timescales.
NASA Astrophysics Data System (ADS)
Srinivas, Goundla; Klein, Michael L.
2004-01-01
The interaction of surfactant diblock poly(ethylene oxide)-poly(ethylethylene) copolymers (PEO-PEE) with a lipid bilayer of dimyristoylphosphatidylcholine has been studied by means of coarse-grain molecular dynamics simulations. The effect of the surfactants on the lipid bilayer was studied over a wide range of diblock copolymer concentrations. The simulations show that the hydrophilic PEO chains adopt different structures at low and high concentrations. In particular, the computed density profiles reveal that the PEO chains extend over a longer range from the bilayer surface, with increasing copolymer concentration. The simulated density profiles are in agreement with the scaling law predictions.
Ramanan, B; Holmes, W M; Sloan, W T; Phoenix, V R
2012-01-01
Quantifying nanoparticle (NP) transport inside saturated porous geological media is imperative for understanding their fate in a range of natural and engineered water systems. While most studies focus upon finer grained systems representative of soils and aquifers, very few examine coarse-grained systems representative of riverbeds and gravel based sustainable urban drainage systems. In this study, we investigated the potential of magnetic resonance imaging (MRI) to image transport behaviors of nanoparticles (NPs) through a saturated coarse-grained system. MRI successfully imaged the transport of superparamagnetic NPs, inside a porous column composed of quartz gravel using T(2)-weighted images. A calibration protocol was then used to convert T(2)-weighted images into spatially resolved quantitative concentration maps of NPs at different time intervals. Averaged concentration profiles of NPs clearly illustrates that transport of a positively charged amine-functionalized NP within the column was slower compared to that of a negatively charged carboxyl-functionalized NP, due to electrostatic attraction between positively charged NP and negatively charged quartz grains. Concentration profiles of NPs were then compared with those of a convection-dispersion model to estimate coefficients of dispersivity and retardation. For the amine functionalized NPs (which exhibited inhibited transport), a better model fit was obtained when permanent attachment (deposition) was incorporated into the model as opposed to nonpermanent attachment (retardation). This technology can be used to further explore transport processes of NPs inside coarse-grained porous media, either by using the wide range of commercially available (super)paramagnetically tagged NPs or by using custom-made tagged NPs. PMID:22091923
Collu, Francesca; Spiga, Enrico; Lorenz, Christian D.; Fraternali, Franca
2015-01-01
Membrane fusion is critical to eukaryotic cellular function and crucial to the entry of enveloped viruses such as influenza and human immunodeficiency virus. Influenza viral entry in the host cell is mediated by a 20–23 amino acid long sequence, called the fusion peptide (FP). Recently, possible structures for the fusion peptide (ranging from an inverted V shaped α-helical structure to an α-helical hairpin, or to a complete α-helix) and their implication in the membrane fusion initiation have been proposed. Despite the large number of studies devoted to the structure of the FP, the mechanism of action of this peptide remains unclear with several mechanisms having been suggested, including the induction of local disorder, promoting membrane curvature, and/or altering local membrane composition. In recent years, several research groups have employed atomistic and/or coarse-grained molecular dynamics (MD) simulations to investigate the matter. In all previous works, the behavior of a single FP monomer was studied, while in this manuscript, we use a simplified model of a tripeptide (TP) monomer of FP (TFP) instead of a single FP monomer because each Influenza Hemagglutinin contains three FP molecules in the biological system. In this manuscript we report findings targeted at understanding the fusogenic properties and the collective behavior of these trimers of FP peptides on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine model membrane. Here we show how the TFP monomers self-assemble into differently sized oligomers in the presence of the membrane. We measure the perturbation to the structure of the phospholipid membrane caused by the presence of these TFP oligomers. Our work (i) shows how self-assembly of TFP in the presence of the membrane induces non negligible deformation to the membrane and (ii) could be a useful starting point to stimulate discussion and further work targeted to fusion pore formation. PMID:26636093
NASA Astrophysics Data System (ADS)
Jiang, H.; Wang, P.; Thompson, J.; Ding, Z.; Lu, Y.
2009-12-01
OSL dating, grain-size analysis and magnetic susceptibility measurements were conducted on the Fanjiaping loess section, the western Chinese Loess Plateau. The results confirm that last glacial high-frequency climatic shifts were documented in mid-latitude continental archives. Comparison and analysis of grain-size distribution features indicated that the sequence was generally dominated by silt, indicating wind-blown dust sedimentation. Nevertheless, the lower part of the sequence was marked by high fluctuations of coarse-grained sand content with horizontal bedding and washing-refilling structures, implying a fluvial process. These coarse-grain sedimentations were probably a response to brief intensifications of Asian summer monsoon at the start of MIS 4 and during the early to middle stage of MIS 3. During the stage 5-4 transition, the relatively high sea-surface temperatures of high latitudes probably led to a small meridional temperature gradient, which may have helped the Asian summer monsoon to penetrate northward, bringing more precipitation to Lanzhou. The early to middle stage of MIS 3 was a relatively warm and humid climate not only regionally in the low-latitude Yunnan Province and the mid-latitude Lanzhou, but also in the high-latitude East Siberian Arctic. During this period, instability of the ice sheets around the Arctic Ocean enhanced significantly and enormous icebergs were discharged, coincident with the moderate summer insolation. Because modeling results indicate that the boreal forest warmed both winter and summer air temperatures (relative to bare ground or tundra vegetation) during the last glacial period, the interstadial events observed in the middle to high latitude of Northern Hemisphere may be caused by a combination of enhanced insolation, ice sheet instability and the boreal forest recovery. This study thus provides new significant information about the response of terrestrial loessic palaeoenvironments to millennial
NASA Astrophysics Data System (ADS)
Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue
2016-05-01
Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.
Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue
2016-01-01
Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user's specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program. PMID:27188541
Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue
2016-01-01
Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program. PMID:27188541
Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der
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 ato