Coarse-grained modeling of RNA 3D structure.
Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M
2016-07-01
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
Coarse graining approach to First principles modeling of structural materials
Odbadrakh, Khorgolkhuu; Nicholson, Don M; Rusanu, Aurelian; Samolyuk, German D; Wang, Yang; Stoller, Roger E; Zhang, X.-G.; Stocks, George Malcolm
2013-01-01
Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an e cient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the rst principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force eld. The local moments in the neighborhood of the defect cores are calculated with rst-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs signi cantly and makes large-scale structures amenable to rst principles study. Work is sponsored by the USDoE, O ce of Basic Energy Sciences, Center for Defect Physics, an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the O ce of Science of the USDoE under Contract No. DE-AC05-00OR22725.
Coarse-grained description of cosmic structure from Szekeres models
Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos E-mail: ismael.delgadog@uaem.edu.mx
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
2015-06-01
A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.
Krokhotin, Andrey; Dokholyan, Nikolay V
2015-01-01
Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.
NASA Astrophysics Data System (ADS)
Ganguly, Pritam; Mukherji, Debashish; Junghans, Christoph; van der Vegt, Nico
2012-02-01
Biological organizations depend on a sensitive balance of noncovalent interactions, in particular also those involving interactions of small molecules, including inorganic salts and urea, with biomolecules in aqueous solution. Computer simulations of these types of systems require simple-yet-specific models in order to cover all relevant time and length scales. We present a method to systematically coarse-grain liquid mixtures using Kirkwood-Buff theory of solution combined with an iterative Boltzmann inversion technique that infers single-site interaction potentials for the solution components from the pair correlation functions. Our method preserves both the solution structure at pair level and variations of solution components' chemical potentials with compositions within a unified coarse-graining framework. To test the robustness of our approach, we simulated urea-water and benzene-water systems over a wide-range of concentrations. We also observe the coarse-grained potentials to be reasonably transferable with varying concentrations.
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
NASA Astrophysics Data System (ADS)
Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.
2015-06-01
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
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.
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
NASA Astrophysics Data System (ADS)
Ouldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K.
2011-02-01
We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "average base" description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.
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
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.
Park, Jun-Koo; Jernigan, Robert; Wu, Zhijun
2013-01-01
We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C(α), C, N, and C(β) are considered. Combinations of some of these atoms are also tested. The force constants between the representative atoms are extracted from the Hessian matrix of the energy function and served as the force constants between the corresponding residues. The residue mean-square-fluctuations and their correlations with the experimental B-factors are calculated for a large set of proteins. The results are compared with all-atom normal mode analysis and the residue-level Gaussian Network Model. The coarse-grained methods perform more efficiently than all-atom normal mode analysis, while their B-factor correlations are also higher. Their B-factor correlations are comparable with those estimated by the Gaussian Network Model and in many cases better. The extracted force constants are surveyed for different pairs of residues with different numbers of separation residues in sequence. The statistical averages are used to build a refined Gaussian Network Model, which is able to predict residue-level structural fluctuations significantly better than the conventional Gaussian Network Model in many test cases.
Insights on protein-DNA recognition by coarse grain modelling.
Poulain, P; Saladin, A; Hartmann, B; Prévost, C
2008-11-30
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 acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.
NASA Astrophysics Data System (ADS)
Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.; de Pablo, Juan J.
2013-10-01
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.
Coarse-grained model of glycosaminoglycans.
Samsonov, Sergey A; Bichmann, Leon; Pisabarro, M Teresa
2015-01-26
Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature, GAGs are challenging systems for computational approaches. To deal with the length challenge, coarse-grained (CG) modeling could be a promising approach. In this work, we develop AMBER-compatible CG parameters for GAGs using all-atomic (AA) molecular dynamics (MD) simulations in explicit solvent and the Boltzmann conversion approach. We compare both global and local properties of GAGs obtained in the simulations with AA and CG approaches, and we conclude that our CG model is appropriate for the MD approach of long GAG molecules at long time scales.
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.
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.
Recent Advances in Transferable Coarse-Grained Modeling of Proteins
Kar, Parimal; Feig, Michael
2017-01-01
Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems are employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multi-scale hybrid all-atom/coarse-grained simulations of proteins. PMID:25443957
Dynamical coarse grained models with realistic time dependence
NASA Astrophysics Data System (ADS)
Andersen, Hans
2015-03-01
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. 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 an 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 was studied by Zwanzig [R. Zwanzig, J. Stat. Phys. 9, 215 (1973)]. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics simulation programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. The dynamic CG models have computational requirements that are similar to
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 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
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.
A coarse grain model for protein-surface interactions.
Wei, Shuai; Knotts, Thomas A
2013-09-07
The interaction of proteins with surfaces is important in numerous applications in many fields-such as biotechnology, proteomics, sensors, and medicine--but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.
A coarse grain model for protein-surface interactions
NASA Astrophysics Data System (ADS)
Wei, Shuai; Knotts, Thomas A.
2013-09-01
The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.
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.
Obtaining fully dynamic coarse-grained models from MD.
Español, Pep; Zúñiga, Ignacio
2011-06-14
We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected.
MARTINI Coarse-Grained Models of Polyethylene and Polypropylene.
Panizon, Emanuele; Bochicchio, Davide; Monticelli, Luca; Rossi, Giulia
2015-06-25
The understanding of the interaction of nanoplastics with living organisms is crucial both to assess the health hazards of degraded plastics and to design functional polymer nanoparticles with biomedical applications. In this paper, we develop two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes. The models are compatible with the popular MARTINI force field for lipids, and they are developed using both structural and thermodynamic properties as targets in the parametrization. The models are then validated by showing their reliability at reproducing structural properties of the polymers, both linear and branched, in dilute conditions, in the melt, and in a PE-PP blend. PE and PP radius of gyration is correctly reproduced in all conditions, while PE-PP interactions in the blend are slightly overestimated. Partitioning of PP and PE oligomers in phosphatidylcholine membranes as obtained at CG level reproduces well atomistic data.
One-bead coarse-grained model for RNA dynamics
NASA Astrophysics Data System (ADS)
Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D.
2017-01-01
We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.
One-bead coarse-grained model for RNA dynamics.
Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D
2017-01-28
We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.
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.
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.
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
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.
Knotts, Thomas A; Rathore, Nitin; Schwartz, David C; de Pablo, Juan J
2007-02-28
Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.
NASA Astrophysics Data System (ADS)
Knotts, Thomas A.; Rathore, Nitin; Schwartz, David C.; de Pablo, Juan J.
2007-02-01
Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.
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
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 models for aqueous polyethylene glycol solutions.
Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun
2014-01-09
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.
Coarse Grained Model for Biological Simulations: Recent Refinements and Validation
Vicatos, Spyridon; Rychkova, Anna; Mukherjee, Shayantani; Warshel, Arieh
2014-01-01
Exploring the free energy landscape of proteins and modeling 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 various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinement, extensions and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes and electrolytes and electrodes as well as studies of voltage activated proteins, protein insertion trough the translocon, the action of molecular motors and even the coupling of the stalled ribosome and the translocon. Our example illustrates the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes. PMID:25050439
Parametrizing coarse grained models for molecular systems at equilibrium
NASA Astrophysics Data System (ADS)
Kalligiannaki, E.; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.
2016-10-01
Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.
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
A coarse grained protein-lipid model with application to lipoprotein particles
Shih, Amy Y.; Arkhipov, Anton; Freddolino, Peter L.; Schulten, Klaus
2008-01-01
A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model previously developed by Marrink et al., though further versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces system size about ten-fold and allows integration time steps of 25 to 50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles, involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved reliable in maintaining the shape of pre-assembled particles and in accurately reproducing overall structural features of high-density lipoproteins. Microsecond simulations of lipoprotein assembly revealed formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer. PMID:16494423
Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.
Shen, Lin; Hu, Hao
2014-06-10
We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.
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}.
Capturing the essence of folding and functions of biomolecules using coarse-grained models.
Hyeon, Changbong; Thirumalai, D
2011-09-27
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example, during chromosome organization. Describing phenomena that cover such diverse length, and also time, scales requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.
Na, Hyuntae; Jernigan, Robert L; Song, Guang
2015-10-01
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.
NASA Astrophysics Data System (ADS)
Strom, K. B.
2010-12-01
Mountain streams are the first link in the fluvial system and often have complex bed morphologies which make it difficult to develop simple quantitative expressions for sediment mass flux and stream flow resistance. Such expressions are important for landscape evolution modeling as well as stream management and restoration practices and efforts. Part of the difficulty lies in the fact that stream beds can have large variations in particle size and structural organization - both of which lead to variations in bed strength that can change as a function of time. This study presents a mathematical framework to account for the dynamic impact of surface-structure patches on bed strength and bed load transport under simplified conditions. The framework is based on conservation principles for tracking the exchange of mass between structured and unstructured surface patches in the bed during structure formation and breakup. Two main transport equations are solved for the mobile and stationary phases, and the exchange between the two is modeled using particle collision theory and a simple breakup model (figure 1). The experiments of Strom et al. (2004) are used to parameterize the model initial conditions, and calculated and experimentally observed transport rates are compared as a function of time. Conceptual sketch of the modeling framework for: (A) a gravel bed, and (B) an idealized bed of uniform spherical particles. Mass conservation equations are written for each phase (structured and unstructured) and then solved with time under varying conditions.
Spill, Yannick G; Pasquali, Samuela; Derreumaux, Philippe
2011-05-10
The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.
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.
Insights into DNA-mediated interparticle interactions from a coarse-grained model
NASA Astrophysics Data System (ADS)
Ding, Yajun; Mittal, Jeetain
2014-11-01
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.
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.
Zheng, Wenjun
2017-02-01
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals
2007-11-05
109, 6722–6731. 26. McQuarrie , D. A. Statistical Mechanics . Harper and Row: New York, 1976. 27. Angell, C. A. Proc Natl Acad Sci USA 1995, 92, 6675...favorable. While there are many computational methods that apply force fields or statistical potentials to assess compara- bility of sequences fitted to...sequence-de- pendent, and restraint components. The sequence-specific poten- tial was derived through geometric statistics of known protein structures
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.
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.
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.
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 Model for Water Involving a Virtual Site.
Deng, Mingsen; Shen, Hujun
2016-02-04
In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones.
NASA Astrophysics Data System (ADS)
Knight, Chris; Voth, Gregory A.
2012-05-01
The molecular simulation of condensed phase systems with electronic structure methods can be prohibitively expensive if the length and time scales necessary to observe the desired chemical phenomena are too large. One solution is to map the results of a representative electronic structure simulation onto a computationally more efficient model that reproduces the original calculation, while allowing for statistical sampling relevant to the required length and time scales. The statistical mechanical multiscale coarse-graining procedure is one methodology in which a model can be developed by integrating over the subset of fast degrees of freedom to construct a reduced representation of the original system that reproduces thermodynamic, and in some instances dynamic, properties. The coarse-graining away of electronic structure is one application of this general method, wherein the electronic degrees of freedom are integrated out and the full dimensionality of the system is mapped to that of only the nuclei. The forces on the nuclei in this reduced representation are obtained from a variational force-matching procedure applied to the Hellman-Feynman forces of the original full electron + nuclear system. This work discusses the coarse-graining procedure and its application to ab initio molecular dynamics simulations of the aqueous hydroxide ion.
Coarse-grained modeling of protein unspecifically bound to DNA
NASA Astrophysics Data System (ADS)
Guardiani, Carlo; Cencini, Massimo; Cecconi, Fabio
2014-04-01
There is now a certain consensus that transcription factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D diffusion in solution (jumps), 1D diffusion along DNA (sliding), and small jumps (hopping), achieving association rates higher than for 3D diffusion alone. We investigate the FD phenomenology through molecular dynamics simulations in the framework of coarse-grained modeling. We show that, despite the crude approximations, the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix, leading to a coupling of translation along the DNA axis with rotation around it. The 1D diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument that can be used to quantitatively reproduce the measured values.
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.
Coarse grained model for calculating the ion mobility of hydrocarbons
NASA Astrophysics Data System (ADS)
Kuroboshi, Y.; Takemura, K.
2016-12-01
Hydrocarbons are widely used as insulating compounds. However, their fundamental characteristics in conduction phenomena are not completely understood. A great deal of effort is required to determine reasonable ionic behavior from experiments because of their complicated procedures and tight controls of the temperature and the purity of the liquids. In order to understand the conduction phenomena, we have theoretically calculated the ion mobilities of hydrocarbons and investigated their characteristics using the coarse grained model in molecular dynamics simulations. We assumed a molecule of hydrocarbons to be a bead and simulated its dependence on the viscosity, electric field, and temperature. Furthermore, we verified the suitability of the conformation, scale size, and long-range interactions for the ion mobility. The results of the simulations show that the ion mobility values agree reasonably well with the values from Walden's rule and depend on the viscosity but not on the electric field. The ion mobility and self-diffusion coefficient exponentially increase with increasing temperature, while the activation energy decreases with increasing molecular size. These values and characteristics of the ion mobility are in reasonable agreement with experimental results. In the future, we can understand not only the ion mobilies of hydrocarbons in conduction, but also we can predict general phenomena in electrochemistry with molecular dynamics simulations.
A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.
Srivastava, Anand; Voth, Gregory A
2013-01-08
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.
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
Hadley, K. R.; McCabe, C.
2010-01-01
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. PMID:20387939
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.
Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.
Invernizzi, Michele; Valsson, Omar; Parrinello, Michele
2017-03-28
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.
Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model
Invernizzi, Michele; Valsson, Omar; Parrinello, Michele
2017-01-01
A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890
Moritsugu, Kei; Smith, Jeremy C.
2008-01-01
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 α), plastocyanin (all β), and dihydrofolate reductase (α/β) 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
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
NASA Astrophysics Data System (ADS)
Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.
2015-04-01
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.
Autocorrelation study of the Θ transition for a coarse-grained polymer model.
Qi, Kai; Bachmann, Michael
2014-08-21
By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to critical slowing down, an extremal autocorrelation time can also be considered as an indicator for the collapse transition that helps to locate the transition point. This is particularly useful for finite systems, where response quantities such as the specific heat do not necessarily exhibit clear indications for pronounced thermal activity.
Coarse-grained models of protein folding: toy models or predictive tools?
Clementi, Cecilia
2008-02-01
Coarse-grained models are emerging as a practical alternative to all-atom simulations for the characterization of protein folding mechanisms over long time scales. While a decade ago minimalist toy models were mainly designed to test general hypotheses on the principles regulating protein folding, the latest coarse-grained models are increasingly realistic and can be used to characterize quantitatively the detailed folding mechanism of specific proteins. The ability of such models to reproduce the essential features of folding dynamics suggests that each single atomic degree of freedom is not by itself particularly relevant to folding and supports a statistical mechanical approach to characterize folding transitions. When combined with more refined models and with experimental studies, the systematic investigation of protein systems and complexes using coarse-grained models can advance our theoretical understanding of the actual organizing principles that emerge from the complex network of interactions among protein atomic constituents.
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.
A coarse-grained protein force field for folding and structure prediction.
Maupetit, Julien; Tuffery, P; Derreumaux, Philippe
2007-11-01
We have revisited the protein coarse-grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and 16 protein targets. Because optimization depends on details of how the ensemble of decoys is sampled, trial conformations are generated by molecular dynamics, threading, greedy, and Monte Carlo simulations, or taken from publicly available databases. The OPEP parameters are varied by a genetic algorithm using a scoring function which requires that the native structure has the lowest energy, and the native-like structures have energy higher than the native structure but lower than the remote conformations. Overall, we find that OPEP correctly identifies 24 native or native-like states for 29 targets and has very similar capability to the all-atom discrete optimized protein energy model (DOPE), found recently to outperform five currently used energy models.
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.
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.
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.
Coarse graining approach to First principles modeling of radiation cascade in large Fe super-cells
NASA Astrophysics Data System (ADS)
Odbadrakh, Khorgolkhuu; Nicholson, Don; Rusanu, Aurelian; Wang, Yang; Stoller, Roger; Zhang, Xiaoguang; Stocks, George
2012-02-01
First principles techniques employed to understand systems at an atomistic level are not practical for large systems consisting of millions of atoms. We present an efficient coarse graining approach to bridge the first principles calculations of local electronic properties to classical Molecular Dynamics (MD) simulations of large structures. Local atomic magnetic moments in crystalline Fe are perturbed by radiation generated defects. The effects are most pronounced near the defect core and decay with distance. We develop a coarse grained 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. This work was supported by the Center for Defect Physics, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.
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.
Wang, Yaohong; Sigurdsson, Jon Karl; Brandt, Erik; Atzberger, Paul J
2013-08-01
We introduce a thermostat based on fluctuating hydrodynamics for dynamic simulations of implicit-solvent coarse-grained models of lipid bilayer membranes. We show our fluctuating hydrodynamics approach captures interesting correlations in the dynamics of lipid bilayer membranes that are missing in simulations performed using standard Langevin dynamics. Our momentum conserving thermostat accounts for solvent-mediated momentum transfer by coupling coarse-grained degrees of freedom to stochastic continuum fields that account for both the solvent hydrodynamics and thermal fluctuations. We present both a general framework and specific methods to couple the particle and continuum degrees of freedom in a manner consistent with statistical mechanics and amenable to efficient computational simulation. For self-assembled vesicles, we study the diffusivity of lipids and their spatial correlations. We find the hydrodynamic coupling yields within the bilayer interesting correlations between diffusing lipids that manifest as a vortex-like structure similar to those observed in explicit-solvent simulations. We expect the introduced fluctuating hydrodynamics methods to provide a way to extend implicit-solvent models for use in a wide variety of dynamic studies.
Integral equation analysis of single-site coarse-grained models for polymer-colloid mixtures
NASA Astrophysics Data System (ADS)
Menichetti, Roberto; D'Adamo, Giuseppe; Pelissetto, Andrea; Pierleoni, Carlo
2015-09-01
We discuss the reliability of integral equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterised by mutually interacting soft- and hard-core particles. Specifically, we consider a set of potentials appropriate to describe a system of hard-sphere colloids and linear homopolymers in good solvent, and investigate the behaviour when the soft particles are smaller than the colloids, which is the regime of validity of the coarse-grained models. Using computer-simulation results as a benchmark, we find that the hypernetted-chain approximation provides accurate estimates of thermodynamics and structure in the colloid-gas phase in which the density of colloids is small. On the other hand, all closures considered appear to be unable to describe the behaviour of the mixture in the colloid-liquid phase, as they cease to converge at polymer densities significantly smaller than those at the binodal. As a consequence, integral equations appear to be unable to predict a quantitatively correct phase diagram.
Zimmermann, Eva; Seifert, Udo
2015-02-01
Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.
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
A Coarse-grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS
Moore, Timothy C.; Iacovella, Christopher R.; Hartkamp, Remco; Bunge, Annette L.; McCabe, Clare
2017-01-01
Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and timescales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869
Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.
Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej
2013-05-10
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
NASA Astrophysics Data System (ADS)
Hsu, David D.
Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational
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).
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
2015-11-24
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.
Toward multiscale modeling of the chromatin fiber: a coarse grain model for DNA
NASA Astrophysics Data System (ADS)
Savelyev, Alexey; Papoian, Garegin
2008-03-01
In eukaryotic cells DNA is compacted a million-fold into a chromatin. Understanding the mechanism of chromatin folding is of great biological importance. All-atom Molecular Dynamics (MD) simulations could provide crucial insights into the electrostatic and structural mechanisms of chromatin folding. However, because of the enormous size of even short chromatin fiber segment and long folding time-scales, atomistic simulations are computationally impractical. Our long-term aim is to build an accurate coarse-grain (CG) model of the chromatin, derived systematically from all-atom simulations of its smaller parts. Here we report the development of the CG model for a linear DNA chain, playing the role of a linker DNA segment in the chromatin. We derived CG inter-DNA electrostatic potential from atomistic simulations with explicit solvent and mobile ions, instead of relying on the standard models of continuum electrostatics, which are inadequate at small intermolecular distances. In addition, we used the ideas of renormalization group theory to construct an optimization scheme for parameterizing the CG force field. This novel approach is designed to accurately reproduce correlations among various CG degrees of freedom. The implementation of these correlations was left as an open question in the prior studies of CG polymer models.
Fast coarse-grained model for RNA titration
NASA Astrophysics Data System (ADS)
Barroso da Silva, Fernando Luís; Derreumaux, Philippe; Pasquali, Samuela
2017-01-01
A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.
Coarse-grained models for interacting, flapping swimmers
NASA Astrophysics Data System (ADS)
Oza, Anand; Ristroph, Leif; Shelley, Michael; Courant Institute Applied Math Lab Collaboration
2016-11-01
We present the results of a theoretical investigation into the dynamics of interacting flapping swimmers. Our study is motivated by ongoing experiments in the NYU Applied Math Lab, in which freely-translating, heaving airfoils interact hydrodynamically to choose their relative positions and velocities. We develop a discrete dynamical system in which flapping swimmers shed point vortices during each flapping cycle, which in turn exert forces on the swimmers. We present a framework for finding exact solutions to the evolution equations and for assessing their stability, giving physical insight into the preference for certain observed "schooling states". The model may be extended to arrays of flapping swimmers, and configurations in which the swimmers' flapping frequencies are incommensurate. Generally, our results indicate how hydrodynamics may mediate schooling and flocking behavior in biological contexts. A. Oza acknowledges the support of the NSF Mathematical Sciences Postdoctoral Fellowship.
Representing environment-induced helix-coil transitions in a coarse grained peptide model
NASA Astrophysics Data System (ADS)
Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine
2016-10-01
Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that
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
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.
A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments
NASA Astrophysics Data System (ADS)
Weik, Florian; Kesselheim, Stefan; Holm, Christian
2016-11-01
We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
Wei, Zonghui
2015-01-01
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. PMID:26723631
Protein simulation using coarse-grained two-bead multipole force field with polarizable water models
NASA Astrophysics Data System (ADS)
Li, Min; Zhang, John Z. H.
2017-02-01
A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.
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.
Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei
2016-02-09
In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths.
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.
Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik
2016-08-31
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.
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
NASA Astrophysics Data System (ADS)
Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik
2016-08-01
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.
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.
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
NASA Astrophysics Data System (ADS)
Glukhova, O. E.; Kolesnikova, A. S.; Grishina, O. A.; Slepchenkov, M. M.
2015-03-01
At the present time actual task of the modern materials is the creation of biodegradable biocompatible composite materials possessing high strength properties for medical purposes. One of the most promising biomaterials from a position of creation on their basis super strong nanofibres is chitosan. The aim of this work is a theoretical study of the structural features and physico-mechanical properties of biocomposite materials based on chitosan and carbon nanostructures. As matrix nanocomposite we considered various carbon nano-objects, namely carbon nanotubes and graphene. Using the developed original software complex KVAZAR we built atomistic and coarse-grained models of the biocomposite material. To identify regularities of influence of the configuration of the carbon matrix on the mechanical and electronic properties of biocomposite we carried out a series of numerical experiments using a classical algorithm of molecular dynamics and semi-empirical methods. The obtained results allow us to suggest that the generated biocomposite based on chitosan and carbon nanostructures has high stability and strength characteristics. Such materials can be used in biomedicine as a base material for creating of artificial limbs.
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.
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.
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.
NASA Astrophysics Data System (ADS)
McCarty, J.; Clark, A. J.; Copperman, J.; Guenza, M. G.
2014-05-01
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.
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.
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.
RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models
Leonarski, Filip; Trylska, Joanna
2015-01-01
Coarse-grained (CG) models in molecular dynamics (MD) are powerful tools to simulate the dynamics of large biomolecular systems on micro- to millisecond timescales. However, the CG model, potential energy terms, and parameters are typically not transferable between different molecules and problems. So parameterizing CG force fields, which is both tedious and time-consuming, is often necessary. We present RedMDStream, a software for developing, testing, and simulating biomolecules with CG MD models. Development includes an automatic procedure for the optimization of potential energy parameters based on metaheuristic methods. As an example we describe the parameterization of a simple CG MD model of an RNA hairpin. PMID:25902423
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.
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
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.
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.
Computational Study of Uniaxial Deformations in Silica Aerogel Using a Coarse-Grained Model.
Ferreiro-Rangel, Carlos A; Gelb, Lev D
2015-07-09
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.
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.
Moussavi-Baygi, R.; Jamali, Y.; Karimi, R.; Mofrad, M.R.K.
2011-01-01
The nuclear pore complex (NPC) is the gatekeeper of the nucleus, capable of actively discriminating between the active and inert cargo while accommodating a high rate of translocations. The biophysical mechanisms underlying transport, however, remain unclear due to the lack of information about biophysical factors playing role in transport. Based on published experimental data, we have established a coarse-grained model of an intact NPC structure to examine nucleocytoplasmic transport with refined spatial and temporal resolutions. Using our model, we estimate the transport time versus cargo sizes. Our findings suggest that the mean transport time of cargos smaller than 15 nm is independent of size, while beyond this size, there is a sharp increase in the mean transport time. The model confirms that kap-FG hydrophobicity is sufficient for active cargo transport. Moreover, our model predicts that during translocation, small and large cargo-complexes are hydrophobically attached to FG-repeat domains for 86 and 96% of their transport time, respectively. Inside the central channel FG-repeats form a thick layer on the wall leaving an open tube. The cargo-complex is almost always attached to this layer and diffuses back and forth, regardless of the cargo size. Finally, we propose a plausible model for transport in which the NPC can be viewed as a lubricated gate. This model incorporates basic assumptions underlying virtual-gate and reduction-of-dimensionality models with the addition of the FG-layer inside the central channel acting as a lubricant. PMID:21402022
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.
Yang, Kengran; White, Claire E
2016-11-08
Alkali-activated materials (AAMs) are currently being pursued as viable alternatives to conventional ordinary Portland cement because of their lower carbon footprint and established mechanical performance. However, our understanding of the mesoscale morphology (∼1 to 100 nm) of AAMs and related amorphous aluminosilicate gels, including the development of the three-dimensional aluminosilicate network and nanoscale porosity, is severely limited. This study investigates the structural changes that occur during the formation of AAM gels at the mesoscale by utilizing a coarse-grained Monte Carlo (CGMC) modeling technique that exploits density functional theory calculations. The model is capable of simulating the reaction of an aluminosilicate particle in a highly alkaline solution (sodium hydroxide or sodium silicate). Two precursor morphologies have been investigated (layered alumina and silica sheets mimicking metakaolin and spherical aluminosilicate particles reminiscent of coal-derived fly ash) to determine if the precursor morphology has an impact on the structural evolution of the resulting alkali-activated aluminosilicate gel. The CGMC model can capture the three major stages of the alkali-activation process-dissolution, polycondensation, and reorganization-revealing that the dissolved silicate and aluminate species, ranging from monomers to nanoprecipitates (100s of monomers in size), exist in the pore solution of the hardened gel. The model also reveals that the silica concentration of the activating solution controls the extent of dissolution of the precursor particle. From the analysis of the aluminosilicate cluster size distributions, the mechanisms of AAM gel growth have been elucidated, revealing that Ostwald ripening occurs in systems containing free silica at the start of the reaction. On the other hand, growth of the hydroxide-activated systems (metakaolin and fly ash) occurs via the formation of intermediate-sized clusters in addition to continual
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 [Formula: see text]-carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific [Formula: see text]/[Formula: see text]-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C
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
Refining the Treatment of Membrane Proteins by Coarse-Grained Models
Vorobyov, Igor; Kim, Ilsoo; Chu, Zhen T.; Warshel, Arieh
2015-01-01
Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al Proteins 2014; 82: 1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data. PMID:26531155
Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing
2017-03-20
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.
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
2012-01-04
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.
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
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.
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.
Sovová, Žofie; Berka, Karel; Otyepka, Michal; Jurečka, Petr
2015-03-12
Ceramides are lipids that are involved in numerous biologically important structures (e.g., the stratum corneum and ceramide-rich platforms) and processes (e.g., signal transduction and membrane fusion), but their behavior is not fully understood. We report coarse-grain force field parameters for N-lignocerylsphingosine (ceramide NS, also known as ceramide 2) that are consistent with the Martini force field. These parameters were optimized for simulations in the gel phase and validated against atomistic simulations. Coarse-grained simulations with our parameters provide areas per lipid, membrane thicknesses, and electron density profiles that are in good agreement with atomistic simulations. Properties of the simulated membranes are compared with available experimental data. The obtained parameters were used to model the phase behavior of ceramide NS as a function of temperature and hydration. At low water content and above the main phase transition temperature, the bilayer melts into an irregular phase, which may correspond to the unstructured melted-chain phase observed in X-ray diffraction experiments. The developed parameters also reproduce the extended conformation of ceramide, which may occur in the stratum corneum. The parameters presented herein will facilitate studies on important complex functional structures such as the uppermost layer of the skin and ceramide-rich platforms in phospholipid membranes.
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.
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
NASA Astrophysics Data System (ADS)
Schöberl, Markus; Zabaras, Nicholas; Koutsourelakis, Phaedon-Stelios
2017-03-01
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a probabilistic coarse-to-fine map. This corresponds to a directed probabilistic model where the coarse variables play the role of latent generators of the fine scale (all-atom) data. From an information-theoretic perspective, the framework proposed provides an improvement upon the relative entropy method [1] and is capable of quantifying the uncertainty due to the information loss that unavoidably takes place during the coarse-graining process. Furthermore, it can be readily extended to a fully Bayesian model where various sources of uncertainties are reflected in the posterior of the model parameters. The latter can be used to produce not only point estimates of fine-scale reconstructions or macroscopic observables, but more importantly, predictive posterior distributions on these quantities. Predictive posterior distributions reflect the confidence of the model as a function of the amount of data and the level of coarse-graining. The issues of model complexity and model selection are seamlessly addressed by employing a hierarchical prior that favors the discovery of sparse solutions, revealing the most prominent features in the coarse-grained model. A flexible and parallelizable Monte Carlo - Expectation-Maximization (MC-EM) scheme is proposed for carrying out inference and learning tasks. A comparative assessment of the proposed methodology is presented for a lattice spin system and the SPC/E water model.
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.
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
2016-08-07
A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.
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
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.
Chng, Choon-Peng; Yang, Lee-Wei
2008-01-01
Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774
NASA Astrophysics Data System (ADS)
Song, Bo; Yuan, Huajun; Jameson, Cynthia J.; Murad, Sohail
2012-09-01
How nanoparticles interact with biological membranes is of significant importance in determining the toxicity of nanoparticles as well as their potential applications in phototherapy, imaging and gene/drug delivery. It has been shown that such interactions are often determined by nanoparticle physicochemical factors such as size, shape, hydrophobicity and surface charge density. Surface modification of the nanoparticle offers the possibility of creating site-specific carriers for both drug delivery and diagnostic purposes. In this work, we use coarse-grained molecular dynamic simulations to explore the permeation characteristics of ligand-coated nanoparticles through a model membrane. We compare permeation behaviors of ligand-coated nanoparticles with bare nanoparticles to provide insights into how the ligands affect the permeation process. A series of simulations is carried out to validate a coarse-grained model for nanoparticles and a lipid membrane system. The minimum driving force for nanoparticles to penetrate the membrane and the mechanism of nanoparticle-membrane interaction were investigated. The potential of the mean force profile, nanoparticle velocity profile, force profile and density profiles (planar and radial) were obtained to explore the nanoparticle permeation process. The structural properties of both nanoparticles and lipid membrane during the permeation, which are of considerable fundamental interest, are also studied in our work. The findings described in our work will lead to a better understanding of nanoparticle-lipid membrane interactions and cell cytotoxicity and help develop more efficient nanocarrier systems for intracellular delivery of therapeutics.
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
Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
Hills, Ronald D.; Brooks, Charles L.
2009-01-01
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions. PMID:19399227
A coarse-grained model for synergistic action of multiple enzymes on cellulose
Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; Shen, Tongye; Langan, Paul; Redondo, Antonio; Gnanakaran, Sandrasegaram
2012-08-01
In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo
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.
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.
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.
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Theodorakis, Panagiotis E.; Dellago, Christoph; Kahl, Gerhard
2013-01-01
We discuss a coarse-grained model recently proposed by Starr and Sciortino [J. Phys.: Condens. Matter 18, L347 (2006), 10.1088/0953-8984/18/26/L02] 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.
Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect.
Xiao, Qiang; Guo, Hongxia
2016-11-02
In this paper, we construct an efficient and simple coarse grained (CG) model for atactic polystyrene (PS) by using a 1 : 1 mapping scheme at 463 K and 1 atm pressure and derive the corresponding bonded and non-bonded potentials in the CG force field (FF) via a direct Boltzmann inversion approach and a combined structure-based and thermodynamic quantities-based CG method, respectively. For computational considerations, the non-bonded interaction between CG particles is described by Lennard-Jones (LJ) type potentials, and both the radial distribution function (RDF) and the bulk density of the atomistic simulations are taken as target properties in the parameterization of the two LJ parameters. To shed light on the choice of LJ forms of CG non-bonded potentials when designing the CG models, a series of CG models with different LJ potentials are constructed and compared in order to understand how the quality of a CG model in reproducing the structure and thermodynamic properties of chemically realistic systems is affected by the choice of non-bonded potentials. We find that with our structural and thermodynamics combined CG method to construct the CG FF at a single thermodynamic state point without any temperature dependent LJ potential correction and/or pressure optimization, the resulting CG models possess good temperature transferability in a wide range of temperatures 300-600 K, where both the target properties and several other static properties (such as thermal expansion coefficient and mean-square radius of gyration) are generally reproduced. Furthermore, the non-bonded LJ potential influences the density response of CG models to the temperature change, i.e., CG models with harder LJ potentials show better temperature transferability than the softer ones. Meanwhile, the derived Tg increases with increasing LJ repulsion strength while thermal expansion coefficients in both melt and glass states are lowered as the LJ potential hardens. With regard to the
Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics.
Shen, Hujun; Deng, Mingsen; Zhang, Yachao
2017-05-15
It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse-grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW-like water model (namely CAVS model) with the ELBA-like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.
A coarse-grained model for synergistic action of multiple enzymes on cellulose
Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; ...
2012-08-01
In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose,more » several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo
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.
Universal and non-universal features in coarse-grained models of flow in disordered solids.
Nicolas, Alexandre; Martens, Kirsten; Bocquet, Lydéric; Barrat, Jean-Louis
2014-07-14
We study the two-dimensional (2D) shear flow of amorphous solids within variants of an elastoplastic model, paying particular attention to spatial correlations and time fluctuations of, e.g., local stresses. The model is based on the local alternation between an elastic regime and plastic events during which the local stress is redistributed. The importance of a fully tensorial description of the stress and of the inclusion of (coarse-grained) convection in the model is investigated; scalar and tensorial models yield similar results, while convection enhances fluctuations and breaks the spurious symmetry between the flow and velocity gradient directions, for instance when shear localisation is observed. Besides, correlation lengths measured with diverse protocols are discussed. One class of such correlation lengths simply scale with the spacing between homogeneously distributed, simultaneous plastic events. This leads to a scaling of the correlation length with the shear rate as γ̇(-1/2) in 2D in the athermal regime, regardless of the details of the model. The radius of the cooperative disk, defined as the near-field region in which plastic events induce a stress redistribution that is not amenable to a mean-field treatment, notably follows this scaling. On the other hand, the cooperative volume measured from the four-point stress susceptibility and its dependence on the system size and the shear rate are model-dependent.
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.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F
2007-02-19
Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.
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.
Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane
Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V.
2016-01-07
Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.
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.
Predicting Partition Coefficients with a Simple All-Atom/Coarse-Grained Hybrid Model.
Genheden, Samuel
2016-01-12
The solvation free energy is an essential quantity in force field development and in numerous applications. Here, we present the estimation of solvation free energies in polar (water, hexanol, octanol, and nonanol) and in apolar (hexane, octane, and nonane) media. The estimates are produced using molecular dynamics simulations employing a simple all-atom/coarse-grained hybrid model (AA/ELBA) and are therefore very efficient. More than 150 solutes were taken from the Minnesota solvation database and represent small, organic molecules. The mean absolute deviation for the different solvents ranges between 2.0 and 4.1 kJ/mol, and the correlation coefficient ranges between 0.78 and 0.99, indicating that the predictions are accurate. Outliers are identified, and potential avenues for improvements are discussed. Furthermore, partition coefficients between water and the organic solvents were estimated, and the percentage of the predictions that has the correct sign ranges between 74% (for octane) and 92% (for octanol and hexanol). Finally, membrane/water partition coefficients are replaced with hexane/water and octanol/water partition coefficients, and the latter is found to be as accurate as the expensive membrane calculations, indicating a wider application area.
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
Derivation of free energy expressions for tube models from coarse-grained slip-link models
NASA Astrophysics Data System (ADS)
Steenbakkers, Rudi J. A.; Schieber, Jay D.
2012-07-01
We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)], 10.1063/1.3314727 by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)], 10.1515/JNETDY.2003.010 can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)], 10.1021/ma8009855 starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)], 10.1122/1.1595099. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)], 10.1063/1.1553764. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical
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.
de Oliveira, Tiago E.; Netz, Paulo A.; Kremer, Kurt; ...
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.
A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.
Chiu, See-Wing; Scott, H Larry; Jakobsson, Eric
2010-03-09
In order to extend the time and distance scales of molecular dynamics simulations, it is essential to create accurate coarse-grained force fields, in which each particle contains several atoms. Coarse-grained force fields that utilize the Lennard-Jones potential form for pairwise nonbonded interactions have been shown to suffer from serious inaccuracy, notably with respect to describing the behavior of water. In this paper, we describe a coarse-grained force field for water, in which each particle contains four water molecules, based on the Morse potential form. By molecular dynamics simulations, we show that our force field closely replicates important water properties. We also describe a Morse potential force field for alkanes and a simulation method for alkanes in which individual particles may have variable size, providing flexibility in constructing complex molecules comprised partly or solely of alkane groups. We find that, in addition to being more accurate, the Morse potential also provides the ability to take larger time steps than the Lennard-Jones, because the short distance repulsion potential profile is less steep. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations.
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.
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
Chen, Chunxia; Depa, Praveen; Sakai, Victoria García; Maranas, Janna K; Lynn, Jeffrey W; Peral, Inmaculada; Copley, John R D
2006-06-21
We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each model's accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.
Choi, Eunsong; Yethiraj, Arun
2015-07-23
We study the conformational properties of polymers in room temperature ionic liquids using theory and simulations of a coarse-grained model. Atomistic simulations have shown that single poly(ethylene oxide) (PEO) molecules in the ionic liquid 1-butyl 3-methyl imidazolium tetrafluoroborate ([BMIM][BF4]) are expanded at room temperature (i.e., the radius of gyration, Rg), scales with molecular weight, Mw, as Rg ∼ Mw(0.9), instead of the expected self-avoiding walk behavior. The simulations were restricted to fairly short chains, however, which might not be in the true scaling regime. In this work, we investigate a coarse-grained model for the behavior of PEO in [BMIM][BF4]. We use existing force fields for PEO and [BMIM][BF4] and Lorentz–Berthelot mixing rules for the cross interactions. The coarse-grained model predicts that PEO collapses in the ionic liquid. We also present an integral equation theory for the structure of the ionic liquid and the conformation properties of the polymer. The theory is in excellent agreement with the simulation results. We conclude that the properties of polymers in ionic liquids are unusually sensitive to the details of the intermolecular interactions. The integral equation theory is sufficiently accurate to be a useful guide to computational work.
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.
Cheng, Yuan; Li, Dechang; Ji, Baohua; Shi, Xinghua; Gao, Huajian
2010-09-01
Nanoparticles such as fullerenes and carbon nanotubes have been extensively studied for biomedical applications. In this paper, we report the design of carbon nanotubes as HIV-1 protease inhibitors. Docking and molecular dynamics calculations are performed using an atomistic model to explore the optimal interaction structure and free energy between the nanotube and HIV-1 protease. A coarse-grained model is then developed based on the atomistic model, allowing us to investigate the dynamic behaviors of the protease in the bound and unbound states. The dynamic process reveals that the carbon nanotube is able to bind to the active site of the protease and prevent the active flaps from opening up, thus blocking the function of the protease. This process is strongly influenced by the size of the nanotube. The binding of carbon nanotubes to an alternative binding site other than the active site is also explored. Therefore, carbon nanotube-based inhibitors have great potential for application as HIV-1 protease inhibitors.
Euston, Stephen R
2010-10-11
The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.
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
2015-01-01
Recent studies have shown that simple stereochemical constraints encoded at the RNA secondary structure level significantly restrict the orientation of RNA helices across two-way junctions and yield physically reasonable distributions of RNA 3D conformations. Here we develop a new coarse-grain model, TOPRNA, that is optimized for exploring detailed aspects of these topological constraints in complex RNA systems. Unlike prior models, TOPRNA effectively treats RNAs as collections of semirigid helices linked by freely rotatable single strands, allowing us to isolate the effects of secondary structure connectivity and sterics on 3D structure. Simulations of bulge junctions show that TOPRNA captures new aspects of topological constraints, including variations arising from deviations in local A-form structure, translational displacements of the helices, and stereochemical constraints imposed by bulge-linker nucleotides. Notably, these aspects of topological constraints define free energy landscapes that coincide with the distribution of bulge conformations in the PDB. Our simulations also quantitatively reproduce NMR RDC measurements made on HIV-1 TAR at low salt concentrations, although not for different TAR mutants or at high salt concentrations. Our results confirm that topological constraints are an important determinant of bulge conformation and dynamics and demonstrate the utility of TOPRNA for studying the topological constraints of complex RNAs. PMID:24547945
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.
Highly Coarse-Grained Representations of Transmembrane Proteins
2017-01-01
Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3–30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies. PMID:28043122
NASA Astrophysics Data System (ADS)
Knott, Michael; Best, Robert B.
2014-05-01
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.
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
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.
Rottler, Jörg; Plotkin, Steven S.
2016-01-01
Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered. PMID:27898663
Lei, Huan; Karniadakis, George Em
2013-01-01
Sickle red blood cells (SS-RBCs) exhibit heterogeneous cell morphologies (sickle, holly leaf, granular, etc.) in the deoxygenated state due to the polymerization of the sickle hemoglobin. Experimental evidence points to a close relationship between SS-RBC morphology and intracellular aligned hemoglobin polymers. Here, we develop a coarse-grained (CG) stochastic model to represent the growth of the intracellular aligned hemoglobin polymer domain. The CG model is calibrated based on the mechanical properties (Young’s modulus, bending rigidity) of the sickle hemoglobin fibers reported in experiments. The process of the cell membrane transition is simulated for physiologic aligned hemoglobin polymer configurations and mean corpuscular hemoglobin concentration. Typical SS-RBC morphologies observed in experiments can be obtained from the current model as a result of the intracellular aligned hemoglobin polymer development without introducing any further ad hoc assumptions. It is found that the final shape of SS-RBCs is primarily determined by the angular width of the aligned hemoglobin polymer domain, but it also depends, to a lesser degree, on the polymer growth rate and the cell membrane rigidity. Cell morphologies are quantified by structural shape factors, which agree well with experimental results from medical images. PMID:24307912
Ando, Tadashi; Skolnick, Jeffrey
2014-12-01
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.
A hybrid all-atom/coarse grain model for multiscale simulations of DNA.
Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio
2011-10-28
Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulations. Our method allows us to forthrightly link a state-of-the-art force field for AA simulations of DNA with a CG representation developed by our group. We show that no modification is needed for any of the existing residues (neither AA nor CG). Only the bonding parameters at the hybrid interface are enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems, which are studied by molecular dynamics simulations using an implicit solvent. The simplicity of the approach potentially permits us to study the effect of mutations/modifications as well as DNA binding molecules at the atomistic level within a significantly larger DNA scaffold considered at the CG level. Since all the interactions are computed within the same classical Hamiltonian, the extension to a quantum/classical/coarse-grain multilayer approach using QM/MM modules implemented in widely used simulation packages is straightforward.
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
Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep
2014-10-16
Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of
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.
NASA Astrophysics Data System (ADS)
Davtyan, Aram; Voth, Gregory A.; Andersen, Hans C.
2016-12-01
We recently developed a dynamic force matching technique for converting a coarse-grained (CG) model of a molecular system, with a CG potential energy function, into a dynamic CG model with realistic dynamics [A. Davtyan et al., J. Chem. Phys. 142, 154104 (2015)]. This is done by supplementing the model with additional degrees of freedom, called "fictitious particles." In that paper, we tested the method on CG models in which each molecule is coarse-grained into one CG point particle, with very satisfactory results. When the method was applied to a CG model of methanol that has two CG point particles per molecule, the results were encouraging but clearly required improvement. In this paper, we introduce a new type (called type-3) of fictitious particle that exerts forces on the center of mass of two CG sites. A CG model constructed using type-3 fictitious particles (as well as type-2 particles previously used) gives a much more satisfactory dynamic model for liquid methanol. In particular, we were able to construct a CG model that has the same self-diffusion coefficient and the same rotational relaxation time as an all-atom model of liquid methanol. Type-3 particles and generalizations of it are likely to be useful in converting more complicated CG models into dynamic CG models.
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.
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.
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.
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.
NASA Astrophysics Data System (ADS)
Sellers, Michael S.; Lísal, Martin; Schweigert, Igor; Larentzos, James P.; Brennan, John K.
2017-01-01
In discrete particle simulations, when an atomistic model is coarse-grained, a tradeoff is made: a boost in computational speed for a reduction in accuracy. The Dissipative Particle Dynamics (DPD) methods help to recover lost accuracy of the viscous and thermal properties, while giving back a relatively small amount of computational speed. Since its initial development for polymers, one of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. In 2007, Maillet, Soulard, and Stoltz introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We present an extended and generalized version of the DPD-RX method, and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Demonstration simulations of reacting RDX are performed under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its transition to hot product gases within DPD-RX is presented. Additionally, we discuss several examples of the effect of shock speed and microstructure on the corresponding material chemistry.
Koehl, Patrice; Poitevin, Frédéric; Navaza, Rafael; Delarue, Marc
2017-03-14
Understanding the dynamics of biomolecules is the key to understanding their biological activities. Computational methods ranging from all-atom molecular dynamics simulations to coarse-grained normal-mode analyses based on simplified elastic networks provide a general framework to studying these dynamics. Despite recent successes in studying very large systems with up to a 100,000,000 atoms, those methods are currently limited to studying small- to medium-sized molecular systems due to computational limitations. One solution to circumvent these limitations is to reduce the size of the system under study. In this paper, we argue that coarse-graining, the standard approach to such size reduction, must define a hierarchy of models of decreasing sizes that are consistent with each other, i.e., that each model contains the information of the dynamics of its predecessor. We propose a new method, Decimate, for generating such a hierarchy within the context of elastic networks for normal-mode analysis. This method is based on the concept of the renormalization group developed in statistical physics. We highlight the details of its implementation, with a special focus on its scalability to large systems of up to millions of atoms. We illustrate its application on two large systems, the capsid of a virus and the ribosome translation complex. We show that highly decimated representations of those systems, containing down to 1% of their original number of atoms, still capture qualitatively and quantitatively their dynamics. Decimate is available as an OpenSource resource.
Coarse-grained protein molecular dynamics simulations.
Derreumaux, Philippe; Mousseau, Normand
2007-01-14
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Abeta16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50 ns time scale. Based on two 220 ns trajectories starting from disordered chains, we find that four Abeta16-22 peptides can form a three-stranded beta sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
Coarse-grained protein molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's Aβ16-22 peptides. We find that coarse-grained isolated proteins are stable at room temperature within 50ns time scale. Based on two 220ns trajectories starting from disordered chains, we find that four Aβ16-22 peptides can form a three-stranded β sheet. We also demonstrate that the reptation move of one chain over the others, first observed using the activation-relaxation technique, is a kinetically important mechanism during aggregation. These results show that MD-OPEP is a particularly appropriate tool to study qualitatively the dynamics of long biological processes and the thermodynamics of molecular assemblies.
NASA Astrophysics Data System (ADS)
Balaji, V.; Benson, Rusty; Wyman, Bruce; Held, Isaac
2016-10-01
Climate models represent a large variety of processes on a variety of timescales and space scales, a canonical example of multi-physics multi-scale modeling. Current hardware trends, such as Graphical Processing Units (GPUs) and Many Integrated Core (MIC) chips, are based on, at best, marginal increases in clock speed, coupled with vast increases in concurrency, particularly at the fine grain. Multi-physics codes face particular challenges in achieving fine-grained concurrency, as different physics and dynamics components have different computational profiles, and universal solutions are hard to come by. We propose here one approach for multi-physics codes. These codes are typically structured as components interacting via software frameworks. The component structure of a typical Earth system model consists of a hierarchical and recursive tree of components, each representing a different climate process or dynamical system. This recursive structure generally encompasses a modest level of concurrency at the highest level (e.g., atmosphere and ocean on different processor sets) with serial organization underneath. We propose to extend concurrency much further by running more and more lower- and higher-level components in parallel with each other. Each component can further be parallelized on the fine grain, potentially offering a major increase in the scalability of Earth system models. We present here first results from this approach, called coarse-grained component concurrency, or CCC. Within the Geophysical Fluid Dynamics Laboratory (GFDL) Flexible Modeling System (FMS), the atmospheric radiative transfer component has been configured to run in parallel with a composite component consisting of every other atmospheric component, including the atmospheric dynamics and all other atmospheric physics components. We will explore the algorithmic challenges involved in such an approach, and present results from such simulations. Plans to achieve even greater levels of
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.
Yuan, Hongyan; Huang, Changjin; Li, Ju; Lykotrafitis, George; Zhang, Sulin
2010-07-01
Biological membranes are involved in numerous intriguing biophysical and biological cellular phenomena of different length scales, ranging from nanoscale raft formation, vesiculation, to microscale shape transformations. With extended length and time scales as compared to atomistic simulations, solvent-free coarse-grained membrane models have been exploited in mesoscopic membrane simulations. In this study, we present a one-particle-thick fluid membrane model, where each particle represents a cluster of lipid molecules. The model features an anisotropic interparticle pair potential with the interaction strength weighed by the relative particle orientations. With the anisotropic pair potential, particles can robustly self-assemble into fluid membranes with experimentally relevant bending rigidity. Despite its simple mathematical form, the model is highly tunable. Three potential parameters separately and effectively control diffusivity, bending rigidity, and spontaneous curvature of the model membrane. As demonstrated by selected examples, our model can naturally simulate dynamics of phase separation in multicomponent membranes and the topological change of fluid vesicles.
Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang
2016-07-07
Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.
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.
Genheden, Samuel; Eriksson, Leif A
2016-09-13
Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.
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.
Devaurs, Didier; Antunes, Dinler A.; Papanastasiou, Malvina; Moll, Mark; Ricklin, Daniel; Lambris, John D.; Kavraki, Lydia E.
2017-01-01
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a single conformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins. PMID:28344973
NASA Astrophysics Data System (ADS)
De Nicola, Antonio; Kawakatsu, Toshihiro; Müller-Plathe, Florian; Milano, Giuseppe
2016-10-01
Polymer composites attract large attention for their industrial use because of their unique features. The preparation of equilibrated melts of long entangled chains in the presence of a solid nanoparticle in molecular dynamics simulations is a very difficult task due to the slow relaxation time. We present a coarse-grained (CG) model suitable for polymer nanocomposites which combines Iterative-Boltzmann-Inversion derived polymer models, the hybrid particle-field representation of non-bonded interactions, and a convenient description of a solid nanoparticle suitable for hybrid particle-field models. The proposed approach is applied to test simulations of well characterized polystyrene-silica nanocomposites models. Finally, procedures for an efficient relaxation of pure polymer melts and interphase structures of large molecular weight nanocomposites are proposed.
RNA pseudo-knots simulated with a one-bead coarse-grained model
NASA Astrophysics Data System (ADS)
Taxilaga-Zetina, Oscar; Pliego-Pastrana, Patricia; Carbajal-Tinoco, Mauricio D.
2014-03-01
We present a revised version of a Monte Carlo simulation model for RNA molecules that was introduced in a previous communication [O. Taxilaga-Zetina, P. Pliego-Pastrana, and M. D. Carbajal-Tinoco, Phys. Rev. E 81, 041914 (2010)]. The basic model consists of a series of knowledge-based pair potentials that were obtained from the statistical analysis of large RNAs belonging to the Protein Data Bank. These effective interactions are then used to dress a polymeric chain that reproduces relatively simple secondary structures (e.g., small hairpins). In order to describe more complicated three-dimensional structures such as pseudo-knots, here we include orientational information for the interaction between nucleotides forming hydrogen bonds, as in the case of the Watson-Crick base pairs. As a result, the simulated molecules obtained through the modified model are now consistent with their corresponding experimental configurations.
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)
Tunuguntla, Deepak R.; Weinhart, Thomas; Thornton, Anthony R.
2016-10-01
Over the last 12 years, numerous new theoretical continuum models have been formulated to predict particle segregation in the size-based bidisperse granular flows over inclined channels. Despite their presence, to our knowledge, no attempts have been made to compare and contrast the fundamental basis upon which these continuum models have been formulated. In this paper, firstly, we aim to illustrate the difference in these models including the incompatible nomenclature which impedes direct comparison. Secondly, we utilise (i) our robust and efficient in-house particle solver MercuryDPM, and (ii) our accurate micro-macro (discrete to continuum) mapping tool called coarse-graining, to compare several proposed models. Through our investigation involving size-bidisperse mixtures, we find that (i) the proposed total partial stress fraction expressions do not match the results obtained from our simulation, and (ii) the kinetic partial stress fraction dominates over the total partial stress fraction and the contact partial stress fraction. However, the proposed theoretical total stress fraction expressions do capture the kinetic partial stress fraction profile, obtained from simulations, very well, thus possibly highlighting the reason why mixture theory segregation models work for inclined channel flows. However, further investigation is required to strengthen the basis upon which the existing mixture theory segregation models are built upon.
Allison, Stuart A; Wu, Hengfu; Moyher, Avery; Soegiarto, Linda; Truong, Bi; Nguyen, Duy; Nguyen, Tam; Park, Donghyun
2014-03-20
The coarse-grained continuum primitive model is developed and used to characterize the titration and electrical conductance behavior of aqueous solutions of fullerene hexa malonic acid (FHMA). The spherical FHMA molecule, a highly charged electrolyte with an absolute valence charge as large as 12, is modeled as a dielectric sphere in Newtonian fluid, and electrostatics are treated numerically at the level of the non-linear Poisson-Boltzmann equation. Transport properties (electrophoretic mobilities and conductances) of the various charge states of FHMA are numerically computed using established numerical algorithms. For reasonable choices of the model parameters, good agreement between experiment (published literature) and modeling is achieved. In order to accomplish this, however, a moderate degree of specific binding of principal counterion and FHMA must be included in the modeling. It should be emphasized, however, that alternative explanations are possible. This comparison is made at 25 °C for both Na(+) and Ca(2+) principal counterions. The model is also used to characterize the different charge states and degree of counterion binding to those charge states as a function of pH.
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.
Discrete breathers in a realistic coarse-grained model of proteins.
Luccioli, Stefano; Imparato, Alberto; Lepri, Stefano; Piazza, Francesco; Torcini, Alessandro
2011-08-01
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin, discrete breathers (DBs), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. DBs are time-periodic, space-localized vibrational modes that exist generically in nonlinear discrete systems and are known for their resilience and ability to concentrate energy for long times. In the case of the small β-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, DBs stabilize the structure by concentrating energy on a few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of these two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.
Chu, Jhih-Wei; Voth, Gregory A
2007-12-01
In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle points, and is hence a "rough" free energy landscape. In this implementation of the DWNM, the free energy function is reduced to an elastic-network model representation near the two reference states. The effects of free energy function roughness on the reaction pathways of protein conformational change is demonstrated by applying the DWNM to the conformational changes of two protein systems: the coil-to-helix transition of the DB-loop in G-actin and the open-to-closed transition of adenylate kinase. In both systems, the rough free energy function of the DWNM leads to the identification of distinct minimum free energy paths connecting two conformational states. These results indicate that while the elastic-network model captures the low-frequency vibrational motions of a protein, the roughness in the free energy function introduced by the DWNM can be used to characterize the transition mechanism between protein conformations.
Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water.
Haji-Akbari, Amir; DeFever, Ryan S; Sarupria, Sapna; Debenedetti, Pablo G
2014-12-21
Freezing in the vicinity of water-vapor interfaces is of considerable interest to a wide range of disciplines, most notably the atmospheric sciences. In this work, we use molecular dynamics and two advanced sampling techniques, forward flux sampling and umbrella sampling, to study homogeneous nucleation of ice in free-standing thin films of supercooled water. We use a coarse-grained monoatomic model of water, known as mW, and we find that in this model a vapor-liquid interface suppresses crystallization in its vicinity. This suppression occurs in the vicinity of flat interfaces where no net Laplace pressure in induced. Our free energy calculations reveal that the pre-critical crystalline nuclei that emerge near the interface are thermodynamically less stable than those that emerge in the bulk. We investigate the origin of this instability by computing the average asphericity of nuclei that form in different regions of the film, and observe that average asphericity increases closer to the interface, which is consistent with an increase in the free energy due to increased surface-to-volume ratios.
Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field
Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio
2017-01-01
We present the first investigation of the kinetic and thermodynamic stability of two homologous thermophilic and mesophilic proteins based on the coarse-grained model OPEP. The object of our investigation is a pair of G-domains of relatively large size, 200 amino acids each, with an experimental stability gap of about 40 K. The OPEP force field is able to maintain stable the fold of these relatively large proteins within the hundrend-nanosecond time scale without including external constraints. This makes possible to characterize the conformational landscape of the folded protein as well as to explore the unfolding. In agreement with all-atom simulations used as a reference, we show that the conformational landscape of the thermophilic protein is characterized by a larger number of substates with slower dynamics on the network of states and more resilient to temperature increase. Moreover, we verify the stability gap between the two proteins using replica-exchange simulations and estimate a difference between the melting temperatures of about 23 K, in fair agreement with experiment. The detailed investigation of the unfolding thermodynamics, allows to gain insight into the mechanism underlying the enhanced stability of the thermophile relating it to a smaller heat capacity of unfolding. PMID:28100926
Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field.
Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio
2015-01-01
We present the first investigation of the kinetic and thermodynamic stability of two homologous thermophilic and mesophilic proteins based on the coarse-grained model OPEP. The object of our investigation is a pair of G-domains of relatively large size, 200 amino acids each, with an experimental stability gap of about 40 K. The OPEP force field is able to maintain stable the fold of these relatively large proteins within the hundrend-nanosecond time scale without including external constraints. This makes possible to characterize the conformational landscape of the folded protein as well as to explore the unfolding. In agreement with all-atom simulations used as a reference, we show that the conformational landscape of the thermophilic protein is characterized by a larger number of substates with slower dynamics on the network of states and more resilient to temperature increase. Moreover, we verify the stability gap between the two proteins using replica-exchange simulations and estimate a difference between the melting temperatures of about 23 K, in fair agreement with experiment. The detailed investigation of the unfolding thermodynamics, allows to gain insight into the mechanism underlying the enhanced stability of the thermophile relating it to a smaller heat capacity of unfolding.
de los Santos, Francisco; Franzese, Giancarlo
2011-12-08
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.
Preparation of Entangled Polymer Melts of Various Architecture for Coarse-Grained Models
2011-09-01
thermostat, see the original papers by Hoogerbrugge and Koelman (7) and Español and Warren (8). 3. Generation of Initial Structure Using gel 3.1...1–19. 7. Koelman, J. M. V. A.; Hoogerbrugge, P. J. Europhys. Lett. 1993, 21, 363–368. 8. Español , P.; Warren, P. B. Europhys. Lett. 1995, 30, 191
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
Electro-acoustic behavior of the mitotic spindle: a semi-classical coarse-grained model.
Havelka, Daniel; Kučera, Ondřej; Deriu, Marco A; Cifra, Michal
2014-01-01
The regulation of chromosome separation during mitosis is not fully understood yet. Microtubules forming mitotic spindles are targets of treatment strategies which are aimed at (i) the triggering of the apoptosis or (ii) the interruption of uncontrolled cell division. Despite these facts, only few physical models relating to the dynamics of mitotic spindles exist up to now. In this paper, we present the first electromechanical model which enables calculation of the electromagnetic field coupled to acoustic vibrations of the mitotic spindle. This electromagnetic field originates from the electrical polarity of microtubules which form the mitotic spindle. The model is based on the approximation of resonantly vibrating microtubules by a network of oscillating electric dipoles. Our computational results predict the existence of a rapidly changing electric field which is generated by either driven or endogenous vibrations of the mitotic spindle. For certain values of parameters, the intensity of the electric field and its gradient reach values which may exert a not-inconsiderable force on chromosomes which are aligned in the spindle midzone. Our model may describe possible mechanisms of the effects of ultra-short electrical and mechanical pulses on dividing cells--a strategy used in novel methods for cancer treatment.
Electro-Acoustic Behavior of the Mitotic Spindle: A Semi-Classical Coarse-Grained Model
Havelka, Daniel; Kučera, Ondřej; Deriu, Marco A.; Cifra, Michal
2014-01-01
The regulation of chromosome separation during mitosis is not fully understood yet. Microtubules forming mitotic spindles are targets of treatment strategies which are aimed at (i) the triggering of the apoptosis or (ii) the interruption of uncontrolled cell division. Despite these facts, only few physical models relating to the dynamics of mitotic spindles exist up to now. In this paper, we present the first electromechanical model which enables calculation of the electromagnetic field coupled to acoustic vibrations of the mitotic spindle. This electromagnetic field originates from the electrical polarity of microtubules which form the mitotic spindle. The model is based on the approximation of resonantly vibrating microtubules by a network of oscillating electric dipoles. Our computational results predict the existence of a rapidly changing electric field which is generated by either driven or endogenous vibrations of the mitotic spindle. For certain values of parameters, the intensity of the electric field and its gradient reach values which may exert a not-inconsiderable force on chromosomes which are aligned in the spindle midzone. Our model may describe possible mechanisms of the effects of ultra-short electrical and mechanical pulses on dividing cells—a strategy used in novel methods for cancer treatment. PMID:24497952
Definition of the persistence length in the coarse-grained models of DNA elasticity.
Fathizadeh, A; Eslami-Mossallam, B; Ejtehadi, M R
2012-11-01
By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA.
Definition of the persistence length in the coarse-grained models of DNA elasticity
NASA Astrophysics Data System (ADS)
Fathizadeh, A.; Eslami-Mossallam, B.; Ejtehadi, M. R.
2012-11-01
By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA.
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
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.
Sequence determines degree of knottedness in a coarse-grained protein model.
Wüst, Thomas; Reith, Daniel; Virnau, Peter
2015-01-16
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.
Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa
2015-04-14
We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.
Li, Min; Zhang, John Z H
2017-03-08
The development of polarizable water models at coarse-grained (CG) levels is of much importance to CG molecular dynamics simulations of large biomolecular systems. In this work, we combined the newly developed two-bead multipole force field (TMFF) for proteins with the two-bead polarizable water models to carry out CG molecular dynamics simulations for benchmark proteins. In our simulations, two different two-bead polarizable water models are employed, the RTPW model representing five water molecules by Riniker et al. and the LTPW model representing four water molecules. The LTPW model is developed in this study based on the Martini three-bead polarizable water model. Our simulation results showed that the combination of TMFF with the LTPW model significantly stabilizes the protein's native structure in CG simulations, while the use of the RTPW model gives better agreement with all-atom simulations in predicting the residue-level fluctuation dynamics. Overall, the TMFF coupled with the two-bead polarizable water models enables one to perform an efficient and reliable CG dynamics study of the structural and functional properties of large biomolecules.
NASA Astrophysics Data System (ADS)
Markutsya, Sergiy; Lamm, Monica H.
2014-11-01
We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.
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.
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.
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.
Atomistic and Coarse-grained Simulations of Hexabenzocoronene Crystals
NASA Astrophysics Data System (ADS)
Ziogos, G.; Megariotis, G.; Theodorou, D. N.
2016-08-01
This study concerns atomistic and coarse-grained Molecular Dynamics simulations of pristine hexabenzocoronene (HBC) molecular crystals. HBC is a symmetric graphene flake of nanometric size that falls in the category of polyaromatic hydrocarbons, finding numerous applications in the field of organic electronics. The HBC molecule is simulated in its crystalline phase initially by means of an all-atom representation, where the molecules self- organize into well aligned molecular stacks, which in turn create a perfect monoclinic molecular crystal. The atomistic model reproduces fairly well the structural experimental properties and thus can be used as a reliable starting point for the development of a coarsegrained model following a bottom-up approach. The coarse-grained model is developed by applying Iterative Boltzmann Inversion, a systematic coarse-graining method which reproduces a set of target atomistic radial distribution functions and intramolecular distributions at the coarser level of description. This model allows the simulation of HBC crystals over longer time and length scales. The crystalline phase is analyzed in terms of the Saupe tensor and thermomechanical properties are probed at the atomistic level.
Coarse graining flow of spin foam intertwiners
NASA Astrophysics Data System (ADS)
Dittrich, Bianca; Schnetter, Erik; Seth, Cameron J.; Steinhaus, Sebastian
2016-12-01
Simplicity constraints play a crucial role in the construction of spin foam models, yet their effective behavior on larger scales is scarcely explored. In this article we introduce intertwiner and spin net models for the quantum group SU (2 )k×SU (2 )k, which implement the simplicity constraints analogous to four-dimensional Euclidean spin foam models, namely the Barrett-Crane (BC) and the Engle-Pereira-Rovelli-Livine/Freidel-Krasnov (EPRL/FK) model. These models are numerically coarse grained via tensor network renormalization, allowing us to trace the flow of simplicity constraints to larger scales. In order to perform these simulations we have substantially adapted tensor network algorithms, which we discuss in detail as they can be of use in other contexts. The BC and the EPRL/FK model behave very differently under coarse graining: While the unique BC intertwiner model is a fixed point and therefore constitutes a two-dimensional topological phase, BC spin net models flow away from the initial simplicity constraints and converge to several different topological phases. Most of these phases correspond to decoupling spin foam vertices; however we find also a new phase in which this is not the case, and in which a nontrivial version of the simplicity constraints holds. The coarse graining flow of the BC spin net models indicates furthermore that the transitions between these phases are not of second order. The EPRL/FK model by contrast reveals a far more intricate and complex dynamics. We observe an immediate flow away from the original simplicity constraints; however, with the truncation employed here, the models generically do not converge to a fixed point. The results show that the imposition of simplicity constraints can indeed lead to interesting and also very complex dynamics. Thus we need to further develop coarse graining tools to efficiently study the large scale behavior of spin foam models, in particular for the EPRL/FK model.
Frappier, Vincent; Najmanovich, Rafael J
2014-04-01
Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.
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.
The Theory of Ultra Coarse-graining
NASA Astrophysics Data System (ADS)
Voth, Gregory
2013-03-01
Coarse-grained (CG) models provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms correlated over distance scales of many covalent bond lengths and long time scales. Variational methods based on information from simulations of finer-grained (e.g., all-atom) models, for example the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, provide attractive tools for the systematic development of CG models. However, these methods have important drawbacks when used in the ``ultra coarse-grained'' (UCG) regime, e.g., at a resolution level coarser or much coarser than one amino acid residue per effective CG particle in proteins. This is due to the possible existece of multiple metastable states ``within'' the CG sites for a given UCG model configuration. In this talk I will describe systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain conclusions of this work connect back to single-state force matching and open up new avenues for method development in that area. These results provide a formal statistical mechanical basis for UCG methods related to force matching and relative entropy CG methods and suggest practical algorithms for constructing optimal approximate UCG models from fine-grained simulation data.
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.
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)
Brizuela, Jose; Katchadjian, Pablo; Garcia, Alejandro; Desimone, Carlos
2016-02-01
The aim of this work is to obtain a C-Scan view of an austenitic stainless steel weld from a nuclear use pipe. In order to obtain this result Sectorial Scans (S-Scan) from both sides of the weld are obtained by Ultrasonic Phase Array (UT-PA). Then, spatial image compounding is performed to generate a single image from the S-Scans acquired at the same circumferential position of the transducer. These joints have a coarse grain structure which significantly reduce the transmission of the ultrasonic wave due to attenuation characteristics and backscattered noise from microstructures inside the material. For this reason, phase coherence imaging technique has been also applied to reduce the structural noise and improve the image quality. To verify detected defects, and given the impossibility of cutting the component, gammagraphy were performed with Co60.
Lu, Jibao; Jacobson, Liam C; Perez Sirkin, Yamila A; Molinero, Valeria
2017-01-10
Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution. Here, we develop a high-resolution CG force field for hydrated polyphenylene oxide/trimethylamine chloride (PPO/TMACl) membranes compatible with the mW water model using a hierarchical parametrization approach based on Uncertainty Quantification and reference atomistic simulations modeled with the Generalized Amber Force Field (GAFF) and TIP4P/2005 water. The parametrization weighs multiple properties, including coordination numbers, radial distribution functions (RDFs), self-diffusion coefficients of water and ions, relative vapor pressure of water in the solution, hydration enthalpy of the tetramethylammonium chloride (TMACl) salt, and cohesive energy of its aqueous solutions. We analyze the interdependence between properties and address how to compromise between the accuracies of the properties to achieve an overall best representability. Our optimized CG model FFcomp quantitatively reproduces the diffusivities and RDFs of the reference atomistic model and qualitatively reproduces the experimental relative vapor pressure of water in solutions of tetramethylammonium chloride. These properties are of utmost relevance for the design and operation of fuel cell membranes. To our knowledge, this is the first CG model that includes explicitly each water and ion and accounts for hydrophobic, ionic, and intramolecular interactions explicitly
Coarse-Grained Force field for the Nucleosome from Self-Consistent Multiscaling
Voltz, Karine; Trylska, Joanna; Tozzini, Valentina; Kurkal-Siebert, V; Smith, Jeremy C; Langowski, Jorg
2008-02-01
A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtained from a 5-ns all-atom molecular dynamics (MD) simulation, and were refined to produce agreement with the all-atom MD simulation. This self-consistent multiscale approach yields a coarse-grained model that is capable of reproducing equilibrium structural properties calculated from a 50-ns all-atom MD simulation. This coarse-grained model speeds up nucleosome simulations by a factor of 10{sup 3} and is expected to be useful in examining biologically relevant dynamical nucleosome phenomena on the microsecond timescale and beyond.
Zhang, Yuwei; Cao, Zexing; Zhang, John Zenghui; Xia, Fei
2017-02-27
Construction of coarse-grained (CG) models for large biomolecules used for multiscale simulations demands a rigorous definition of CG sites for them. Several coarse-graining methods such as the simulated annealing and steepest descent (SASD) based on the essential dynamics coarse-graining (ED-CG) or the stepwise local iterative optimization (SLIO) based on the fluctuation maximization coarse-graining (FM-CG), were developed to do it. However, the practical applications of these methods such as SASD based on ED-CG are subject to limitations because they are too expensive. In this work, we extend the applicability of ED-CG by combining it with the SLIO algorithm. A comprehensive comparison of optimized results and accuracy of various algorithms based on ED-CG show that SLIO is the fastest as well as the most accurate algorithm among them. ED-CG combined with SLIO could give converged results as the number of CG sites increases, which demonstrates that it is another efficient method for coarse-graining large biomolecules. The construction of CG sites for Ras protein by using MD fluctuations demonstrates that the CG sites derived from FM-CG can reflect the fluctuation properties of secondary structures in Ras accurately.
Assessing the Quality of the OPEP Coarse-Grained Force Field.
Barducci, Alessandro; Bonomi, Massimiliano; Derreumaux, Philippe
2011-06-14
A coarse-grained potential that could accurately describe the overall conformational landscape of proteins would be extremely valuable not only for structure prediction but also for studying protein dynamics, large conformational motions, and intrinsically disordered systems. Here, we assessed the quality of the OPEP coarse-grained potential by comparing the reconstructed free-energy surfaces (FESs) of two prototypical β-hairpin and α-helix peptides to all-atom calculations in explicit solvent. We found remarkable agreement between the OPEP FES and those obtained using atomistic models, despite a general overstabilization of α- and β-structures by the coarse-grained potential. The use of advanced sampling techniques based on metadynamics and parallel tempering guaranteed a thorough exploration of the conformational space accessible to the two peptides studied.
Coarse-graining with information theory and the relative entropy
NASA Astrophysics Data System (ADS)
Shell, M. Scott
2013-03-01
There remain many both fundamental and practical/methodological questions regarding how coarse-grained models should be developed. Are there theoretically intuitive and numerically robust strategies for turning small-scale all-atom simulations into coarse models suitable for large-scale modeling? How can we identify what atomic details are unnecessary and can be discarded? Are there systematic ways to detect emergent physics? Here we discuss a fundamentally new approach to this problem. We propose that a natural way of viewing the coarse-graining problem is in terms of information theory. A quantity called the relative entropy measures the information lost upon coarse graining and hence the (inverse) fitness of a particular coarse-grained model. Minimization of the relative entropy thus provides a sort-of universal variational principle for coarse-graining, and a way to ``automatically'' discover and generate coarse models of many systems. We show that this new approach enables us to develop very simple but surprisingly accurate models of water, hydrophobic interactions, self-assembling peptides, and proteins that enable new physical insights as well as simulations of large-scale interactions. We discuss both theoretical and numerical aspects of this approach, in particular highlighting a new coarse-graining algorithm that efficiently optimizes coarse-grained models with even thousands of free parameters. We also discuss how the relative entropy approach suggests novel strategies for predicting the errors of coarse models, for identifying relevant degrees of freedom to retain, and for understanding the relationships among other coarse-graining methodologies.
NASA Astrophysics Data System (ADS)
Mognetti, B. M.; Virnau, P.; Yelash, L.; Paul, W.; Binder, K.; Müller, M.; MacDowell, L. G.
2009-01-01
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, and short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on thermodynamic perturbation theory is discussed. Molecules are described by coarse grained models, where either the whole molecule (carbon dioxide, benzene, and methane) or a group of a few successive CH2 groups (in the case of alkanes) are lumped into an effective point particle. Interactions among these point particles are fitted by Lennard-Jones (LJ) potentials such that the vapor-liquid critical point of the fluid is reproduced in agreement with experiment; in the case of quadrupolar molecules a quadrupole-quadrupole interaction is included. These models are shown to provide a satisfactory description of the liquid-vapor phase diagram of these pure fluids. Investigations of mixtures, using the Lorentz-Berthelot (LB) combining rule, also produce satisfactory results if compared with experiment, while in some previous attempts (in which polar solvents were modeled without explicitly taking into account quadrupolar interaction), strong violations of the LB rules were required. For this reason, the present investigation is a step towards predictive modeling of polar mixtures at low computational cost. In many cases Monte Carlo simulations of such models (employing the grand-canonical ensemble together with reweighting techniques, successive umbrella sampling, and finite size scaling) yield accurate results in very good agreement with experimental data. Simulation results are quantitatively compared to an analytical approximation for the equation of state of the same model, which is computationally much more efficient, and some systematic discrepancies are discussed. These very simple coarse-grained models of small molecules developed here should be useful, e.g., for simulations of polymer solutions with such molecules as
Mognetti, B M; Virnau, P; Yelash, L; Paul, W; Binder, K; Müller, M; MacDowell, L G
2009-01-28
The prediction of the equation of state and the phase behavior of simple fluids (noble gases, carbon dioxide, benzene, methane, and short alkane chains) and their mixtures by Monte Carlo computer simulation and analytic approximations based on thermodynamic perturbation theory is discussed. Molecules are described by coarse grained models, where either the whole molecule (carbon dioxide, benzene, and methane) or a group of a few successive CH(2) groups (in the case of alkanes) are lumped into an effective point particle. Interactions among these point particles are fitted by Lennard-Jones (LJ) potentials such that the vapor-liquid critical point of the fluid is reproduced in agreement with experiment; in the case of quadrupolar molecules a quadrupole-quadrupole interaction is included. These models are shown to provide a satisfactory description of the liquid-vapor phase diagram of these pure fluids. Investigations of mixtures, using the Lorentz-Berthelot (LB) combining rule, also produce satisfactory results if compared with experiment, while in some previous attempts (in which polar solvents were modeled without explicitly taking into account quadrupolar interaction), strong violations of the LB rules were required. For this reason, the present investigation is a step towards predictive modeling of polar mixtures at low computational cost. In many cases Monte Carlo simulations of such models (employing the grand-canonical ensemble together with reweighting techniques, successive umbrella sampling, and finite size scaling) yield accurate results in very good agreement with experimental data. Simulation results are quantitatively compared to an analytical approximation for the equation of state of the same model, which is computationally much more efficient, and some systematic discrepancies are discussed. These very simple coarse-grained models of small molecules developed here should be useful, e.g., for simulations of polymer solutions with such molecules as
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
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.
NASA Astrophysics Data System (ADS)
Ogawa, Shizuka; Waide, Sayaka; Takasu, Masako; Miyakawa, Takeshi; Morikawa, Ryota; Sakai, Takamasa; Chung, Ung-il
We study the early process of gelation using our model of 5 particles and 9 particles in a monomer. We compare our models and obtain slower reaction for model of 9 particles. We also study the effect of random force and obtain slower reaction with random force but more extended structure.
Avitable, Daniele; Wedgwood, Kyle C A
2017-02-01
We study coarse pattern formation in a cellular automaton modelling a spatially-extended stochastic neural network. The model, originally proposed by Gong and Robinson (Phys Rev E 85(5):055,101(R), 2012), is known to support stationary and travelling bumps of localised activity. We pose the model on a ring and study the existence and stability of these patterns in various limits using a combination of analytical and numerical techniques. In a purely deterministic version of the model, posed on a continuum, we construct bumps and travelling waves analytically using standard interface methods from neural field theory. In a stochastic version with Heaviside firing rate, we construct approximate analytical probability mass functions associated with bumps and travelling waves. In the full stochastic model posed on a discrete lattice, where a coarse analytic description is unavailable, we compute patterns and their linear stability using equation-free methods. The lifting procedure used in the coarse time-stepper is informed by the analysis in the deterministic and stochastic limits. In all settings, we identify the synaptic profile as a mesoscopic variable, and the width of the corresponding activity set as a macroscopic variable. Stationary and travelling bumps have similar meso- and macroscopic profiles, but different microscopic structure, hence we propose lifting operators which use microscopic motifs to disambiguate them. We provide numerical evidence that waves are supported by a combination of high synaptic gain and long refractory times, while meandering bumps are elicited by short refractory times.
NASA Astrophysics Data System (ADS)
Franco-Gonzalez, Juan Felipe; Ramos, Javier; Cruz, Victor L.; Martinez-Salazar, Javier
2014-11-01
Coarse grained (CG) modeling has been applied to study the influence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. We will show that the Martini model performs satisfactorily well, giving results well-matched with those obtained by atomistic models as well as with the experimental information existing on homolog receptors. For example, the extra and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting effect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These findings might help to understand the effect of the antibody on the receptor bioactivity.
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.
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.
NASA Astrophysics Data System (ADS)
Chantawansri, T. L.; Sliozberg, Y. R.; Hsieh, A.; Andzelm, J. W.
2012-02-01
Microphase-separated PUU, which consists of 4,4'-dicyclohexylmethane diisocyanate, diethyltoluenediamine and poly[tetramethylene oxide](PTMO), exhibits versatile mechanical properties making them an excellent choice for potential applications in the form of films, adhesives, coatings and matrix materials for composites. To elucidate the effects of composition, including the hard segment content & molecular weight of PTMO, on rate-dependent mechanical deformation in the high strain-rate regime (>> 10^5/s) the stress-strain behavior for PUU at various rates are calculated for four model systems using a coarse-grain model. Pair interactions between topologically non-connected particles are described by the standard truncated Lennard-Jones (LJ) pair potential, where bonded particles interact according to the standard FENE/LJ potential. An angle harmonic potential is also used to enforce the rigidity of the hard segments, and the system is evolved using molecular dynamics. Stress-strain curves are calculated at various strain-rates and qualitatively agree with experimental results when extrapolated to higher rate. Further analysis of the morphology is also performed to characterize the morphology and discern its connection to the calculated mechanical properties.
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
Simulating the Entropic Collapse of Coarse-Grained Chromosomes
NASA Astrophysics Data System (ADS)
Shendruk, Tyler N.; Bertrand, Martin; de Haan, Hendrick W.; Harden, James L.; Slater, Gary W.
2015-02-01
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains 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 continous 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.
Marchiori, Alessandro; Capece, Luciana; Giorgetti, Alejandro; Gasparini, Paolo; Behrens, Maik; Carloni, Paolo; Meyerhof, Wolfgang
2013-01-01
Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs). The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC) and propylthiouracil (PROP). We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG) method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.
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.
Systematic Coarse-graining of Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Voth, Gregory
2015-03-01
Coarse-grained (CG) models can provide a computationally efficient means to study biomolecular and other soft matter processes involving large numbers of atoms that are correlated over distance scales of many covalent bond lengths and at long time scales. Systematic variational coarse-graining methods based on information from molecular dynamics simulations of finer-grained (e.g., all-atom) models provide attractive tools for the systematic development of CG models. Examples include the multiscale coarse-graining (MS-CG) and relative entropy minimization methods, and results from the former theory will be presented in this talk. In addition, a new approach will be presented that is appropriate for the ``ultra coarse-grained'' (UCG) regime, e.g., at a coarse-grained resolution that is much coarser than one amino acid residue per CG particle in a protein. At this level of coarse-graining, one is faced with the possible existence of multiple metastable states ``within'' the CG sites for a given UCG model configuration. I will therefore describe newer systematic variational UCG methods specifically designed to CG entire protein domains and subdomains into single effective CG particles. This is accomplished by augmenting existing effective particle CG schemes to allow for discrete state transitions and configuration-dependent resolution. Additionally, certain aspects of this work connect back to single-state force matching and open up new avenues for method development. This general body of theory and algorithm provides a formal statistical mechanical basis for the coarse-graining of fine-grained molecular dynamics simulation data at various levels of CG resolution. Representative applications will be described as time allows.
Interrogating Nucleosome Positioning Through Coarse-Grain Molecular Simulation
NASA Astrophysics Data System (ADS)
Freeman, Gordon S.; Hinckley, Daniel M.; Ortiz, Vanessa; de Pablo, Juan J.
2012-02-01
Nucleosome positioning plays a crucial role in biology. As the fundamental unit in chromosome structure, the nucleosome core particle (NCP) binds to approximately 147 DNA base pairs. The location of bound NCPs in the genome, therefore, affects gene expression. The specific positioning of NCPs has been experimentally probed and competing viewpoints have been presented in the literature. Models for nucleosome positioning based on sequence-dependent flexibility (a genomic ``code" for nucleosome positioning) have been demonstrated to explain available experimental data. However, so do statistical models with no built-in sequence preference; the driving force for NCP positioning therefore remains an open question. We use a coarse-grain model for the NCP in combination with advanced sampling techniques to probe the sequence preference of NCPs. We present a method for determining the relative affinity of two DNA sequences for the NCP and use this method to compare high- and low-affinity sequences. We discuss several coarse-grain protein models with varying level of detail to examine the impact of model resolution on the agreement of our results with experimental evidence. We also investigate the dynamics of the NCP-DNA complex and their dependence on system characteristics.
Wirth, Brian
2016-01-12
Exposure of metallic structural materials to irradiation environments results in significant microstructural evolution, property changes and performance degradation, which limits the extended operation of current generation light water reactors and restricts the design of advanced fission and fusion reactors [1-8]. This effect of irradiation on materials microstructure and properties is a classic example of an inherently multiscale phenomenon, as schematically illustrated in Figure 1a. Pertinent processes range from the atomic nucleus to structural component length scales, spanning more than 15 orders of magnitude. Time scales bridge more than 22 orders of magnitude, with the shortest being less than a femtosecond [1,8]. Further, the mix of radiation-induced features formed and the corresponding property degradation depend on a wide range of material and irradiation variables. This emphasizes the importance of closely integrating models with high-resolution experimental characterization of the evolving radiation- damaged microstructure, including measurements performed in-situ during irradiation. In this article, we review some recent successes through the use of closely coordinated modeling and experimental studies of the defect cluster evolution in irradiated body-centered cubic materials, followed by a discussion of outstanding challenges still to be addressed, which are necessary for the development of comprehensive models of radiation effects in structural materials.
Electronically coarse-grained molecular dynamics using quantum Drude oscillators
NASA Astrophysics Data System (ADS)
Jones, A. P.; Crain, J.; Cipcigan, F. S.; Sokhan, V. P.; Modani, M.; Martyna, G. J.
2013-12-01
Standard molecular dynamics (MD) simulations generally make use of a basic description of intermolecular forces which consists of fixed, pairwise, atom-centred Coulomb, van der Waals and short-range repulsive terms. Important interactions such as many-body polarisation and many-body dispersion which are sensitive to changes in the environment are usually neglected, and their effects treated effectively within mean-field approximations to reproduce a single thermodynamic state point or physical environment. This leads to difficulties in modelling the complex interfaces of interest today where the behaviour may be quite different from the regime of parameterisation. Here, we describe the construction and properties of a Gaussian coarse-grained electronic structure, which naturally generates many-body polarisation and dispersion interactions. The electronic structure arises from a fully quantum mechanical treatment of a set of distributed quantum Drude oscillators (QDOs), harmonic atoms which interact with each other and other moieties via electrostatic (Coulomb) interactions; this coarse-grained approach is capable of describing many-body polarisation and dispersion but not short-range interactions which must be parametrised. We describe how on-the-fly forces due to this exchange-free Gaussian model may be generated with linear scale in the number of atoms in the system using an adiabatic path integral molecular dynamics for quantum Drude oscillators technique (APIMD-QDO). We demonstrate the applicability of the QDO approach to realistic systems via a study of the liquid-vapour interface of water.
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.
Song, Wei; Wei, Guanghong; Mousseau, Normand; Derreumaux, Philippe
2008-04-10
Although a wide variety of proteins can assemble into amyloid fibrils, the structure of the early oligomeric species on the aggregation pathways remains unknown at an atomic level of detail. In this paper we report, using molecular dynamics simulations with the OPEP coarse-grained force field, the free energy landscape of a tetramer and a heptamer of the beta2-microglobulin NHVTLSQ peptide. On the basis of a total of more than 17 ns trajectories started from various states, we find that both species are in equilibrium between amorphous and well-ordered aggregates with cross-beta-structure, a perpendicular bilayer beta-sheet, and, for the heptamer, six- or seven-stranded closed and open beta-barrels. Moreover, analysis of the heptamer trajectories shows that the perpendicular bilayer beta-sheet is one possible precursor of the beta-barrel, but that this barrel can also be formed from a twisted monolayer beta-sheet with successive addition of chains. Comparison with previous aggregation simulations and the fact that nature constructs transmembrane beta-sheet proteins with pores open the possibility that beta-barrels with small inner diameters may represent a common intermediate during the early steps of aggregation.
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
Quinn, Bonnie; Peyronel, Fernanda; Gordon, Tyler; Marangoni, Alejandro; Hanna, Charles B; Pink, David A
2014-11-19
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 component, 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 ?. 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 < 0.0701 u (b) transition regime, 0.0701 u ≤ Δ ≤ 0.0916 u and (c) thick coating regime, Δ > 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 < Δ < 7.0 nm transition regime, 7.0 < Δ < 9.2 nm and thick coating, Δ > 9.2 nm (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin coatings) and 0.94% (thick coatings). Minority
NASA Astrophysics Data System (ADS)
Posnansky, Oleg; Guo, Jing; Hirsch, Sebastian; Papazoglou, Sebastian; Braun, Jürgen; Sack, Ingolf
2012-06-01
Recent advances in dynamic elastography and biorheology have revealed that the complex shear modulus, G*, of various biological soft tissues obeys a frequency-dependent powerlaw. This viscoelastic powerlaw behavior implies that mechanical properties are communicated in tissue across the continuum of scales from microscopic to macroscopic. For deriving constitutive constants from the dispersion of G* in a biological tissue, a hierarchical fractal model is introduced that accounts for multiscale networks. Effective-media powerlaw constants are derived by a constitutive law based on cross-linked viscoelastic clusters embedded in a rigid environment. The spatial variation of G* is considered at each level of hierarchy by an iterative coarse-graining procedure. The establishment of cross-links in this model network is associated with an increasing fractal dimension and an increasing viscoelastic powerlaw exponent. This fundamental relationship between shear modulus dynamics and fractal dimension of the mechanical network in tissue is experimentally reproduced in phantoms by applying shear oscillatory rheometry to layers of tangled paper strips embedded in agarose gel. Both model and experiments demonstrate the sensitivity of G* to the density of the mechanical network in tissue, corroborating disease-related alterations of the viscoelastic powerlaw exponent in human parenchyma demonstrated by in vivo elastography.
García Daza, Fabián A; Colville, Alexander J; Mackie, Allan D
2015-03-31
The microscopic modeling of surfactant systems is of the utmost importance in understanding the mechanisms related to the micellization process because it allows for prediction and comparison with experimental data of diverse equilibrium system properties. In this work, we present a coarse-grained model for Pluronics, a trademarked type of triblock copolymer, from simulations based on a single-chain mean-field theory (SCMF). This microscopic model is used to quantify the micellization process of these nonionic surfactants at 37 °C and has been shown to be able to quantitatively reproduce experimental data of the critical micelle concentration (CMC) along with other equilibrium properties. In particular, these results correctly capture the experimental behavior with respect to the lengths of the hydrophobic and hydrophilic moieties of the surfactants for low and medium hydrophobicities. However, for the more highly hydrophobic systems with low CMCs, a deviation is found which has been previously attributed to nonequilibrium effects in the experimental data (Garcı́a Daza, F. A.; Mackie, A. D. Low Critical Micelle Concentration Discrepancy between Theory and Experiment. J. Phys. Chem. Lett. 2014, 5, 2027-2032).
Coarse-grained Simulations of Conformational Changes in Multidrug Resistance Transporters
NASA Astrophysics Data System (ADS)
Jewel, S. M. Yead; Dutta, Prashanta; Liu, Jin
2016-11-01
The overexpression of multidrug resistance (MDR) systems on the gram negative bacteria causes serious problems for treatment of bacterial infectious diseases. The system effectively pumps the antibiotic drugs out of the bacterial cells. During the pumping process one of the MDR components, AcrB undergoes a series of large-scale conformational changes which are responsible for drug recognition, binding and expelling. All-atom simulations are unable to capture those conformational changes because of computational cost. Here, we implement a hybrid coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid, to investigate the proton-dependent conformational changes of AcrB. The simulation results in early stage ( 100 ns) of proton-dependent conformational changes agree with all-atom simulations, validating the coarse-grained model. The coarse-grained force field allows us to explore the process in microsecond simulations. Starting from the crystal structures of Access(A)/Binding(B)/Extrusion(E) monomers in AcrB, we find that deprotonation of Asp407 and Asp408 in monomer E causes a series of large-scale conformational changes from ABE to AAA in absence of drug molecules, which is consistent with experimental findings. This work is supported by NIH Grant: 1R01GM122081-01.
Path-space variational inference for non-equilibrium coarse-grained systems
Harmandaris, Vagelis; 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.
Coarse-graining RNA nanostructures for molecular dynamics simulations
Paliy, Maxim; Melnik, Roderick; Shapiro, Bruce A
2013-01-01
A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in full atomistic modeling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4′ dihedrals taken from a reference structure are included. These findings are discussed in the context of RNA conformation classes. PMID:20577037
NASA Astrophysics Data System (ADS)
Pandey, R. B.; Farmer, B. L.
2008-03-01
In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H) , polar (P) , and electrostatic (E) . A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H , P , and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate attractive (PS) and repulsive (HS) interactions with the solvent and execute their stochastic movement with the Metropolis algorithm. Variations of the root mean square displacements of the center of mass and that of its center node of the protease chain and its gyration radius with the time steps are examined for different solvent strength. The structure of the protease swells on increasing the solvent interaction strength which tends to enhance the relaxation time to reach the diffusive behavior of the chain. Equilibrium radius of gyration increases linearly on increasing the solvent strength: A slow rate of increase in weak solvent regime is followed by a faster swelling in stronger solvent. Variation of the gyration radius with the time steps suggests that the protein chain moves via contraction and expansion in a somewhat quasiperiodic pattern particularly in strong solvent.
NASA Astrophysics Data System (ADS)
Michalowsky, Julian; Schäfer, Lars V.; Holm, Christian; Smiatek, Jens
2017-02-01
We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine bilayer. We additionally verify the model by analyzing the potentials of mean force between different sample pairs in refPOL water and comparing the results to reference data obtained using the original polarizable Martini water model as well as fully atomistic simulations. Based on the results, we suggest to replace the original polarizable Martini water model with the new refPOL model for future applications.
2011-04-01
experiments was performed using an artificial neural network to try to capture the nonlinearities. The radial Gaussian artificial neural network system...Modeling Blast-Wave Propagation using Artificial Neural Network Methods‖, in International Journal of Advanced Engineering Informatics, Elsevier
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
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.
Coarse-grained model for N2-N relaxation in hypersonic shock conditions using two-dimensional bins
NASA Astrophysics Data System (ADS)
Zhu, Tong; Li, Zheng; Levin, Deborah A.
2016-11-01
A high fidelity internal energy relaxation model for N2-N suitable for use in direct simulation Monte Carlo (DSMC) modeling of chemically reacting flows is proposed. A novel two-dimensional binning approach with variable bin energy resolutions in the rotational and vibrational modes is developed for treating the internal mode of N2. Both bin-to-bin and state-specific relaxation cross sections are obtained using the molecular dynamics/quasi-classical trajectory (MD/QCT) method with two potential energy surfaces as well as the state-specific database of Jaffe et al. The 99 bin model is used in homogeneous DSMC relaxation simulations and is found to be able to recover the state-specific master equation results of Panesi et al. when the Jaffe state-specific cross sections are used. Rotational relaxation energy profiles and relaxation times obtained using the ReaxFF and Jaffe potential energy surfaces (PESs) are in general agreement but there are larger differences between the vibrational relaxation times. These differences become smaller as the translational temperature increases because the difference in the PES energy barrier becomes less important.
Collapse transition of a hydrophobic self-avoiding random walk in a coarse-grained model solvent.
Gaudreault, Mathieu; Viñals, Jorge
2009-08-01
In order to study solvation effects on protein folding, we analyze the collapse transition of a self-avoiding random walk composed of hydrophobic segments that is embedded in a lattice model of a solvent. As expected, hydrophobic interactions lead to an attractive potential of mean force among chain segments. As a consequence, the random walk in solvent undergoes a collapse transition at a higher temperature than in its absence. Chain collapse is accompanied by the formation of a region depleted of solvent around the chain. In our simulation, the depleted region at collapse is as large as our computational domain.
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.
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.
NASA Astrophysics Data System (ADS)
García Daza, Fabián A.; Colville, Alexander J.; Mackie, Allan D.
2015-03-01
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.
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.
Chen, Yunjie; Roux, Benoît
2015-08-11
Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up
Coarse-graining approach to quantum cosmology
NASA Astrophysics Data System (ADS)
Calzetta, Esteban; Castagnino, Mario; Scoccimarro, Román
1992-04-01
We consider a Friedmann-Robertson-Walker model with both classical radiation and a massive (conformally coupled) quantum scalar field in the framework of quantum cosmology. We define a density matrix and introduce a notion of ``relevance'' which splits this density matrix into a ``relevant'' and an ``irrelevant'' part. A ``generalized coarse-graining method'' is used to obtain the evolution (in Robertson-Walker a ``time'') of the relevant density matrix, taking into account the back reaction of the irrelevant variables. We discuss the physical basis for the choice of a concept of relevance, and the features of cosmic evolution brought forward by the effective dynamics. In the limit of ``small universes,'' the relevant subdynamics is dissipative.
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
Inferring a weighted elastic network from partial unfolding with coarse-grained simulations.
de Mendonça, Matheus R; Rizzi, Leandro G; Contessoto, Vinicius; Leite, Vitor B P; Alves, Nelson A
2014-01-01
A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental Cα coordinates, and they only take the pairs of Cα atoms within a given cutoff distance rc into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two Cα atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures.
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
2013-03-07
In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement
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 test of systematic coarse-graining of molecular dynamics simulations: Transport properties.
Fu, Chia-Chun; Kulkarni, Pandurang M; Shell, M Scott; Leal, L Gary
2013-09-07
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)], 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. Moreover, we
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
Multiscale coarse graining of diblock copolymer self-assembly: from monomers to ordered micelles.
Pierleoni, Carlo; Addison, Chris; Hansen, Jean-Pierre; Krakoviack, Vincent
2006-03-31
Starting from a microscopic lattice model, we investigate clustering, micellization, and micelle ordering in semidilute solutions of AB diblock copolymers in a selective solvent. To bridge the gap in length scales, from monomers to ordered micellar structures, we implement a two-step coarse-graining strategy, whereby the AB copolymers are mapped onto ultrasoft dumbells with monomer-averaged effective interactions between the centers of mass of the blocks. Monte Carlo simulations of this coarse-grained model yield clear-cut evidence for self-assembly into micelles with a mean aggregation number n approximately 100 beyond a critical concentration. At a slightly higher concentration the micelles spontaneously undergo a disorder-order transition to a cubic phase. We determine the effective potential between these micelles from first principles.
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
Mozolewska, Magdalena A; Krupa, Paweł; Scheraga, Harold A; Liwo, Adam
2015-08-01
The iron-sulfur protein 1 (Isu1) and the J-type co-chaperone Jac1 from yeast are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the Γ-shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105 , L109 , and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J Mol Biol 2012; 417:1-12). These residues were also found, by UNRES/molecular dynamics simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N(95), T(98), P(102), H(112), V(159), L(167), and A(170) of Jac1, not yet tested experimentally, were also found to be important in binding.
Mozolewska, Magdalena A.; Krupa, Paweł; Scheraga, Harold A.; Liwo, Adam
2015-01-01
The Iron sulfur protein 1 (Isu1) from yeast, and the J-type co-chaperone Jac1, are part of a huge ATP-dependent system, and both interact with Hsp70 chaperones. Interaction of Isu1 and Jac1 is a part of the iron-sulfur cluster biogenesis system in mitochondria. In this study, the structure and dynamics of the yeast Isu1-Jac1 complex has been modeled. First, the complete structure of Isu1 was obtained by homology modeling using the I-TASSER server and YASARA software and thereafter tested for stability in the all-atom force field AMBER. Then, the known experimental structure of Jac1 was adopted to obtain initial models of the Isu1-Jac1 complex by using the ZDOCK server for global and local docking and the AutoDock software for local docking. Three most probable models were subsequently subjected to the coarse-grained molecular dynamics simulations with the UNRES force field to obtain the final structures of the complex. In the most probable model, Isu1 binds to the left face of the “Γ” shaped Jac1 molecule by the β-sheet section of Isu1. Residues L105, L109, and Y163 of Jac1 have been assessed by mutation studies to be essential for binding (Ciesielski et al., J. Mol. Biol. 2012, 417, 1–12). These residues were also found, by UNRES/MD simulations, to be involved in strong interactions between Isu1 and Jac1 in the complex. Moreover, N95, T98, P102, H112, V159, L167 and A170 of Jac1, not yet tested experimentally, were also found important in binding. PMID:25973573
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.
Curvature function and coarse graining
Diaz-Marin, Homero; Zapata, Jose A.
2010-12-15
A classic theorem in the theory of connections on principal fiber bundles states that the evaluation of all holonomy functions gives enough information to characterize the bundle structure (among those sharing the same structure group and base manifold) and the connection up to a bundle equivalence map. This result and other important properties of holonomy functions have encouraged their use as the primary ingredient for the construction of families of quantum gauge theories. However, in these applications often the set of holonomy functions used is a discrete proper subset of the set of holonomy functions needed for the characterization theorem to hold. We show that the evaluation of a discrete set of holonomy functions does not characterize the bundle and does not constrain the connection modulo gauge appropriately. We exhibit a discrete set of functions of the connection and prove that in the abelian case their evaluation characterizes the bundle structure (up to equivalence), and constrains the connection modulo gauge up to ''local details'' ignored when working at a given scale. The main ingredient is the Lie algebra valued curvature function F{sub S}(A) defined below. It covers the holonomy function in the sense that expF{sub S}(A)=Hol(l={partial_derivative}S,A).
Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.
Zhou, Lei; Siegelbaum, Steven A
2008-05-01
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.
Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems
NASA Astrophysics Data System (ADS)
Katsoulakis, Markos A.; Plecháč, Petr
2013-08-01
In this paper, we focus on the development of new methods suitable for efficient and reliable coarse-graining of non-equilibrium molecular systems. In this context, we propose error estimation and controlled-fidelity model reduction methods based on Path-Space Information Theory, combined with statistical parametric estimation of rates for non-equilibrium stationary processes. The approach we propose extends the applicability of existing information-based methods for deriving parametrized coarse-grained models to Non-Equilibrium systems with Stationary States. In the context of coarse-graining it allows for constructing optimal parametrized Markovian coarse-grained dynamics within a parametric family, by minimizing information loss (due to coarse-graining) on the path space. Furthermore, we propose an asymptotically equivalent method—related to maximum likelihood estimators for stochastic processes—where the coarse-graining is obtained by optimizing the information content in path space of the coarse variables, with respect to the projected computational data from a fine-scale simulation. Finally, the associated path-space Fisher Information Matrix can provide confidence intervals for the corresponding parameter estimators. We demonstrate the proposed coarse-graining method in (a) non-equilibrium systems with diffusing interacting particles, driven by out-of-equilibrium boundary conditions, as well as (b) multi-scale diffusions and the corresponding stochastic averaging limits, comparing them to our proposed methodologies.
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.
Coarse-graining two-dimensional turbulence via dynamical optimization
NASA Astrophysics Data System (ADS)
Turkington, Bruce; Chen, Qian-Yong; Thalabard, Simon
2016-10-01
A model reduction technique based on an optimization principle is employed to coarse-grain inviscid, incompressible fluid dynamics in two dimensions. In this reduction the spectrally-truncated vorticity equation defines the microdynamics, while the macroscopic state space consists of quasi-equilibrium trial probability densities on the microscopic phase space, which are parameterized by the means and variances of the low modes of the vorticity. A macroscopic path therefore represents a coarse-grained approximation to the evolution of a nonequilibrium ensemble of microscopic solutions. Closure in terms of the vector of resolved variables, namely, the means and variances of the low modes, is achieved by minimizing over all feasible paths the time integral of their mean-squared residual with respect to the Liouville equation. The equations governing the optimal path are deduced from Hamilton-Jacobi theory. The coarse-grained dynamics derived by this optimization technique contains a scale-dependent eddy viscosity, modified nonlinear interactions between the low mode means, and a nonlinear coupling between the mean and variance of each low mode. The predictive skill of this optimal closure is validated quantitatively by comparing it against direct numerical simulations. These tests show that good agreement is achieved without adjusting any closure parameters.
Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.
McCullagh, Peter; Lake, Peter T; McCullagh, Martin
2016-09-13
An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.
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).
Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.
Li, Min; Zhang, John Zenghui; Xia, Fei
2016-04-12
Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.
Krishna, Vinod; Ayton, Gary S; Voth, Gregory A
2010-01-06
Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of approximately 1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to generate the curvature of the capsid shell. It is demonstrated that variation of the strength of this interaction for different subunits in the lattice can cause formation of asymmetric, conical-shaped closed capsid shells, and it is proposed that variations, in the structure of the additional carboxyl-amino terminal binding interface during self-assembly, are important aspects of capsid cone formation. These results are in agreement with recent structural studies of the capsid hexamer subunit, which suggest that variability in the binding interface is a cause of the differences in subunit environments that exist in a conical structure.
Krishna, Vinod; Ayton, Gary S.; Voth, Gregory A.
2010-01-01
Abstract Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of ∼1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to generate the curvature of the capsid shell. It is demonstrated that variation of the strength of this interaction for different subunits in the lattice can cause formation of asymmetric, conical-shaped closed capsid shells, and it is proposed that variations, in the structure of the additional carboxyl-amino terminal binding interface during self-assembly, are important aspects of capsid cone formation. These results are in agreement with recent structural studies of the capsid hexamer subunit, which suggest that variability in the binding interface is a cause of the differences in subunit environments that exist in a conical structure. PMID:20085716
Strom, Alexander M; Fehling, Samuel C; Bhattacharyya, Sudeep; Hati, Sanchita
2014-05-01
Coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. To evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-tRNA synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-tRNA synthetases--Escherichia coli methionyl-tRNA synthetase, Thermus thermophilus leucyl-tRNA synthetase, and Enterococcus faecium prolyl-tRNA synthetase. In the present study, comparison of predicted dynamics based on B-factor and overlap calculations revealed that coarse-grained methods are comparable to the all-atom simulations in depicting the intrinsic global dynamics of the three enzymes. However, the principal component analyses of the motions obtained from the all-atom molecular dynamics simulations provide a superior description of the local fluctuations of these enzymes. In particular, the all-atom model was able to capture the functionally relevant substrate-induced dynamical changes in prolyl-tRNA synthetase. The alteration in the coupled dynamics between the catalytically important proline-binding loop and its neighboring structural elements due to substrate binding has been characterized and reported for the first time. Taken together, the study portrays comparable and contrasting situations in studying the functional dynamics of large multi-domain aminoacyl-tRNA synthetases using coarse-grained and all-atom simulation methods.
PRIMO: A Transferable Coarse-grained Force Field for Proteins
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael
2013-01-01
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36–155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides. PMID:23997693
PRIMO: A Transferable Coarse-grained Force Field for Proteins.
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael
2013-08-13
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36-155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides.
The coarse-grained OPEP force field for non-amyloid and amyloid proteins.
Chebaro, Yassmine; Pasquali, Samuela; Derreumaux, Philippe
2012-08-02
Coarse-grained protein models with various levels of granularity and degrees of freedom offer the possibility to explore many phenomena including folding, assembly, and recognition in terms of dynamics and thermodynamics that are inaccessible to all-atom representations in explicit aqueous solution. Here, we present a refined version of the coarse-grained optimized potential for efficient protein structure prediction (OPEP) based on a six-bead representation. The OPEP version 4.0 parameter set, which uses a new analytical formulation for the nonbonded interactions and adds specific side-chain-side-chain interactions for α-helix, is subjected to three tests. First, we show that molecular dynamics simulations at 300 K preserve the experimental rigid conformations of 17 proteins with 37-152 amino acids within a root-mean-square deviation (RMSD) of 3.1 Å after 30 ns. Extending the simulation time to 100 ns for five proteins does not change the RMSDs. Second, replica exchange molecular dynamics (REMD) simulations recover the NMR structures of three prototypical β-hairpin and α-helix peptides and the NMR three-stranded β-sheet topology of a 37-residue WW domain, starting from randomly chosen states. Third, REMD simulations on the ccβ peptide show a temperature transition from a three-stranded coiled coil to amyloid-like aggregates consistent with experiments, while simulations on low molecular weight aggregates of the prion protein helix 1 do not. Overall, these studies indicate the effectiveness of our OPEP4 coarse-grained model for protein folding and aggregation, and report two future directions for improvement.
Transferability of coarse-grained force fields: The polymer case
NASA Astrophysics Data System (ADS)
Carbone, Paola; Varzaneh, Hossein Ali Karimi; Chen, Xiaoyu; Müller-Plathe, Florian
2008-02-01
A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at
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.
Das, Avisek; Lu, Lanyuan; Andersen, Hans C; Voth, Gregory A
2012-05-21
The multiscale coarse-graining (MS-CG) method uses simulation data for an atomistic model of a system to construct a coarse-grained (CG) potential for a coarse-grained model of the system. The CG potential is a variational approximation for the true potential of mean force of the degrees of freedom retained in the CG model. The variational calculation uses information about the atomistic positions and forces in the simulation data. In principle, the resulting MS-CG potential will be an accurate representation of the true CG potential if the basis set for the variational calculation is complete enough and the canonical distribution of atomistic states is well sampled by the data set. In practice, atomistic configurations that have very high potential energy are not sampled. As a result there usually is a region of CG configuration space that is not sampled and about which the data set contains no information regarding the gradient of the true potential. The MS-CG potential obtained from a variational calculation will not necessarily be accurate in this unsampled region. A priori considerations make it clear that the true CG potential of mean force must be very large and positive in that region. To obtain an MS-CG potential whose behavior in the sampled region is determined by the atomistic data set, and whose behavior in the unsampled region is large and positive, it is necessary to intervene in the variational calculation in some way. In this paper, we discuss and compare two such methods of intervention, which have been used in previous MS-CG calculations for dealing with nonbonded interactions. For the test systems studied, the two methods give similar results and yield MS-CG potentials that are limited in accuracy only by the incompleteness of the basis set and the statistical error of associated with the set of atomistic configurations used. The use of such methods is important for obtaining accurate CG potentials.
Application of phased array techniques to coarse grain components inspection.
Mahaut, Steve; Godefroit, Jean-Louis; Roy, Olivier; Cattiaux, Gérard
2004-04-01
Ultrasonic inspection of cast stainless steel components from primary and auxiliary cooling circuits of French Nuclear Power Plant has to face with major difficulties due to the coarse grained structure of these materials. Attenuation losses and structural noise are encountered, which limits the performances of defect detection ability, mostly in terms of degraded signal-to-noise ratio and poor sensitivity. To overcome such problems, theoretical and experimental studies have been achieved at the French Atomic Energy Commission, with support from the French Institute for Radiological Protection and Nuclear Safety. Experimental studies have been performed over stainless steel specimen of known coarse structure (equiaxial grains and/or elongated grains), containing artificial reflectors (cylindrical holes and electro-eroded surface breaking notches). Those mock-ups have been inspected using contact probes of different array designs (linear or matrix splitting), and using pulse echo or dual-element techniques. Such arrays allow to control the ultrasonic beam so as to investigate different inspection angles and focusing depths. Experiments were carried out using oblique longitudinal waves, using delay laws computed by a specific model, taking account of acoustical and geometrical properties of the probes and the inspected component. In addition, specific reconstruction techniques have been investigated to enhance the signal-to-noise ratio as well as spatial resolution. These techniques are based on beam-forming summation and multi-angle inspections. Experimental results show that such techniques allow to reduce the speckle noise and to optimise the beam resolution. Those increased performances allow to detect and to size small planar defects located at the inner wall of a thick specimen, using corner and tip diffraction echoes.
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.
Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.
Chebaro, Yassmine; Dong, Xiao; Laghaei, Rozita; Derreumaux, Philippe; Mousseau, Normand
2009-01-08
Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.
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.
Franklin, Joel; Koehl, Patrice; Doniach, Sebastian; Delarue, Marc
2007-07-01
The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an approximate way using 'morphing' techniques, which are linear interpolations of either the Cartesian or the internal coordinates between the initial and end states, followed by energy minimization. Here we describe a web tool that implements a new method to calculate the most probable trajectory that is exact for harmonic potentials; as an illustration of the method, the classical Calpha-based Elastic Network Model (ENM) is used both for the initial and the final states but other variants of the ENM are also possible. The Langevin equation under this potential is solved analytically using the Onsager and Machlup action minimization formalism on each side of the transition, thus replacing the original non-linear problem by a pair of linear differential equations joined by a non-linear boundary matching condition. The crossover between the two multidimensional energy curves around each state is found numerically using an iterative approach, producing the most probable trajectory and fully characterizing the transition state and its energy. Jobs calculating such trajectories can be submitted on-line at: http://lorentz.dynstr.pasteur.fr/joel/index.php.
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.
Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease
NASA Astrophysics Data System (ADS)
Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta
2016-11-01
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.
Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S; Blood, Philip; Scheraga, Harold A
2010-03-09
We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.
NASA Astrophysics Data System (ADS)
Majumder, Manoj K.; Ramkumar, S.; Mahajan, Dhiraj K.; Basu, Sumit
2010-01-01
Simulation of the deformation of polymers below their glass transition through molecular dynamics provides an useful route to correlate their molecular architecture to deformation behavior. However, present computational capabilities severely restrict the time and length scales that can be simulated when detailed models of these macromolecules are used. Coarse-graining techniques for macromolecular structures intend to make bigger and longer simulations possible by grouping atoms into superatoms and devising ways of determining reasonable force fields for the superatoms in a manner that retains essential macromolecular features relevant to the process under study but jettisons unnecessary details. In this work we systematically develop a coarse-graining scheme aimed at simulating uniaxial stress-strain behavior of polymers below their glass transition. The scheme involves a two step process of obtaining the coarse grained force field parameters above glass transition. This seems to be enough to obtain “faithful” stress-strain responses after quenching to below the glass transition temperature. We apply the scheme developed to a commercially important polymer polystyrene, derive its complete force field parameters and thus demonstrate the effectiveness of the technique.
Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies
Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.
2016-02-05
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion is used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase.
Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L
2015-11-07
In this article, we present and compare two different, coarse-grained approaches to model electrostatic interactions of disc-shaped aromatic molecules, specifically coronene. Our study builds on our previous work [T. Heinemann et al., J. Chem. Phys. 141, 214110 (2014)], where we proposed, based on a systematic coarse-graining procedure starting from the atomistic level, an anisotropic effective (Gay-Berne-like) potential capable of describing van der Waals contributions to the interaction energy. To take into account electrostatics, we introduce, first, a linear quadrupole moment along the symmetry axis of the coronene disc. The second approach takes into account the fact that the partial charges within the molecules are distributed in a ring-like fashion. We then reparametrize the effective Gay-Berne-like potential such that it matches, at short distances, the ring-ring potential. To investigate the validity of these two approaches, we perform many-particle molecular dynamics simulations, focusing on the crystalline phase (karpatite) where electrostatic interaction effects are expected to be particularly relevant for the formation of tilted stacked columns. Specifically, we investigate various structural parameters as well as the melting transition. We find that the second approach yields consistent results with those from experiments despite the fact that the underlying potential decays with the wrong distance dependence at large molecule separations. Our strategy can be transferred to a broader class of molecules, such as benzene or hexabenzocoronene.
Coarse-grained electrostatic interactions of coronene: Towards the crystalline phase
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.
Coarse-grained simulation of lipid vesicles with ``n-atic'' orientational order
NASA Astrophysics Data System (ADS)
Geng, Jun; Selinger, Jonathan; Selinger, Robin
2012-02-01
We perform coarse-grained simulation studies of fluid lipid vesicles with in-plane ``n-atic'' orientational order associated with the shape of lipid head group, to test the theoretical predictions of Park, Lubensky and MacKintosh [1] for resulting vesicle shape and defect structures. Our simulation model uses a single layer coarse-grained implicit-solvent approach proposed by Yuan et al [2], with addition of an extra vector degree of freedom representing in-plane orientational order. We carry out simulation studies for n=1 to 6, examining in each case the spatial distribution of defects and resulting deformation of the vesicle. An initially spherical vesicle (genus zero) with n-atic order has a ground state with 2n vortices of strength 1/n, as expected, but the observed equilibrium shapes are sometimes quite different from those predicted theoretically. For the n=1 case, we find that the vesicle may become trapped in a disordered, long-lived metastable state with extra +/- defects whose pair-annihilation is inhibited by local changes in membrane curvature, and thus may never reach its predicted ground state. [4pt] [1] J. Park, T. C. Lubensky, and F. C. MacKintosh, Europhys. Lett. 20, 279 (1992)[0pt] [2] H. Yuan, C. Huang, Ju Li, G. Lykotrafitis, and S. Zhang, Phys. Rev. E 82, 011905 (2010)
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.
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.
Hori-Tanaka, Yasuha; Yura, Kei; Takai-Igarashi, Takako; Tanaka, Hiroshi
2015-04-01
Steroid hormone is extensively used for transmitting variety of biological signals in organisms. Natural steroid hormone is synthesized from cholesterol in adrenal cortex and in sexual gland in vertebrates. Appropriately dosed synthetic steroid hormones can be used for medication. Despite their positive effects as medicine, they sometimes cause significant side effects due to their wide range of actions, and the studies for discovering the mechanisms of side effects were carried out aiming to reduce the side effects. The fundamental cause of the side effects seems to be interactions between the steroid and a non-target protein. To understand the possible range of interaction of steroid molecule, we gathered all the three-dimensional structures of protein-steroid complex determined by X-ray crystallography, compared the atomic environments of the steroid-binding sites in proteins and classified the pattern of steroid binding. Protein Data Bank contained 871 structures of steroid-protein complexes in 382 entries. For this study, we selected 832 steroid binding proteins. Using a newly developed method to describe the atomic environments of these steroid molecules and their function, we were able to separate the environments into six patterns. This classification had a potential to predict the function of function-unknown proteins with a co-crystallized steroid molecule. We speculated that the proteins grouped into the same pattern of nuclear receptors were the candidates of non-targeted proteins causing a side effect by a therapeutic prescription of steroid hormone.
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.
A unified data representation theory for network visualization, ordering and coarse-graining.
Kovács, István A; Mizsei, Réka; Csermely, Péter
2015-09-08
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.
From time series to complex networks: The phase space coarse graining
NASA Astrophysics Data System (ADS)
Wang, Minggang; Tian, Lixin
2016-11-01
In this paper, we present a simple and fast computational method, the phase space coarse graining algorithm that converts a time series into a directed and weighted complex network. The constructed directed and weighted complex network inherits several properties of the series in its structure. Thereby, periodic series convert into regular networks, and random series do so into random networks. Moreover, chaotic series convert into scale-free networks. It is shown that the phase space coarse graining algorithm allows us to distinguish, identify and describe in detail various time series. Finally, we apply the phase space coarse graining algorithm to the practical observations series, international gasoline regular spot price series and identify its dynamic characteristics.
Tension dynamics in semiflexible polymers. I. Coarse-grained equations of motion.
Hallatschek, Oskar; Frey, Erwin; Kroy, Klaus
2007-03-01
Based on the wormlike chain model, a coarse-grained description of the nonlinear dynamics of a weakly bending semiflexible polymer is developed. By means of a multiple-scale perturbation analysis, a length-scale separation inherent to the weakly bending limit is exploited to reveal the deterministic nature of the spatio temporal relaxation of the backbone tension and to deduce the corresponding coarse-grained equation of motion. From this partial integro-differential equation, some detailed analytical predictions for the nonlinear response of a weakly bending polymer are derived in an accompanying paper [O. Hallatschek, following paper, Phys. Rev. E 75, 031906 (2007)].
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.
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.
A coarse-grain force-field for xylan and its interaction with cellulose.
Li, Liang; Pérré, Patrick; Frank, Xavier; Mazeau, Karim
2015-01-01
We have built a coarse-grain (CG) model describing xylan and its interaction with crystalline cellulose surfaces. Each xylosyl or glucosyl unit was represented by a single grain. Our calculations rely on force-field parameters adapted from the atomistic description of short xylan fragments and their adsorption on cellulose. This CG model was first validated for xylan chains both isolated and in the bulk where a good match was found with its atomistic counterpart as well as with experimental measurements. A similar agreement was also found when short xylan fragments were adsorbed on the (110) surface of crystalline cellulose. The CG model, which was extended to the (100) and (1-10) surfaces, revealed that the adsorbed xylan, which was essentially extended in the atomistic situation, could also adopt coiled structures, especially when laying on the hydrophobic cellulose surfaces.
Srinivas, Goundla; Mohan, Ram V; Kelkar, Ajit D
2013-10-10
Understanding drug transportation and delivery mechanism from a molecular viewpoint is essential to find better treatment pathways. Despite the fact that many significant drugs such as anticancer doxorubicin and mitoxantrone are predominantly hydrophilic, an efficient methodology to deliver hydrophilic drug components is not well established. Here we explore this problem by studying "patchy" polymeric micelle assisted hydrophilic component transportation across a lipid membrane and delivery inside a biological lipid vesicle. Using the MARTINI force field as the basis, we study the interaction of polymeric micelle with DPPC lipid vesicles in detail. In order to facilitate hydrophilic drug transportation study, a primitive CG model for hydrophilic drug component is used. Extensive simulations carried out over hundreds of nanoseconds demonstrate successful encapsulation, transportation of hydrophilic components by patchy polymeric micelles. Results show the polymeric micelle releases a significant portion of hydrophilic contents inside the lipid vesicle. The present simulation study also reveals a possible mechanism for efficient hydrophilic component transportation and delivery. Insights from this study could potentially help the experimental community to design better delivery vehicles, especially for hydrophilic drug molecules.
NASA Astrophysics Data System (ADS)
Wei, Dongshan; Wang, Feng
2010-08-01
The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are 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.
Ultrasonic imaging in coarse-grained stainless steels by total focusing method
NASA Astrophysics Data System (ADS)
Villaverde, E. Lopez; Robert, S.; Prada, C.
2016-02-01
In the present work, the Total Focusing Method (TFM) is used to image flaws in coarse-grained steels with a contact phased-array probe. In order to reduce the noise introduced by the heterogeneous structure, as well as artifacts due to surface guided waves, the Decomposition of the Time Reversal Operator method is performed before calculating TFM images.
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
2013-04-04
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 Physics-Based Approach of Coarse-Graining the Cytoplasm of Escherichia coli (CGCYTO)
Wang, Qian; Cheung, Margaret S.
2012-01-01
We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λc = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature Tf of a test protein (apoazurin) in a PD model is ∼5° greater than that in a F70 model. In addition, the deviation of Tf in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models. PMID:22677389
Spiriti, Justin; Zuckerman, Daniel M
2014-11-11
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 (Lettieri S.; Zuckerman D. M.J. Comput. Chem.2012, 33, 268-275) 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 (Lyman E.; Zuckerman D
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.
Cieplak, Marek; Thompson, Damien
2008-06-21
A coarse-grained molecular dynamics (MD) model is developed to study the multivalent, or multisite, binding of small functionalized dendrimer molecules to beta-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.
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.
From rigid base pairs to semiflexible polymers: coarse-graining DNA.
Becker, Nils B; Everaers, Ralf
2007-08-01
The elasticity of double-helical DNA on a nm length scale is captured in detail by the rigid base-pair model, whose conformation variables are the relative positions and orientations of adjacent base pairs. Corresponding sequence-dependent elastic potentials have been obtained from all-atom MD simulation and from high-resolution structural data. On the scale of 100 nm, DNA is successfully described by a continuous wormlike chain model with homogeneous elastic properties, characterized by a set of four elastic constants which have been measured in single-molecule experiments. We present here a theory that links these experiments on different scales, by systematically coarse-graining the rigid base-pair model to an effective wormlike chain description. The average helical geometry of the molecule is accounted for exactly, and repetitive as well as random sequences are considered. Structural disorder is shown to produce a small, additive and short-range correction to thermal conformation fluctuations as well as to entropic elasticity. We also discuss the limits of applicability of the homogeneous wormlike chain on short scales, quantifying the anisotropy of bending stiffness, the non-Gaussian bend angle distribution and the variability of stiffness, all of which are noticeable below a helical turn. The coarse-grained elastic parameters show remarkable overall agreement with experimental wormlike chain stiffness. For the best-matching potential, bending persistence lengths of dinucleotide repeats span a range of 37-53 nm, with a random DNA value of 43 nm. While twist stiffness is somewhat underestimated and stretch stiffness is overestimated, the counterintuitive negative sign and the magnitude of the twist-stretch coupling agree with recent experimental findings.
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.
Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach
NASA Astrophysics Data System (ADS)
Lemarchand, Claire A.; Couty, Marc; Rousseau, Bernard
2017-02-01
We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations. We suggest two reasons for this behavior: the Markovian approximation is better satisfied as the level of coarse-graining increases, while the pair-wise approximation neglects important contributions due to the relative orientation of the beads at large levels of coarse-graining. Finally, we highlight a possible limit of the Markovian approximation: the fact that in constrained simulations, in which the centers-of-mass of the beads are kept constant, the bead rotational dynamics become extremely slow.
Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach.
Lemarchand, Claire A; Couty, Marc; Rousseau, Bernard
2017-02-21
We apply the dissipative particle dynamics strategy proposed by Hijón et al. [Faraday Discuss. 144, 301-322 (2010)] and based on an exact derivation of the generalized Langevin equation to cis- and trans-1,4-polybutadiene. We prove that it is able to reproduce not only the structural but also the dynamical properties of these polymers without any fitting parameter. A systematic study of the effect of the level of coarse-graining is done on cis-1,4-polybutadiene. We show that as the level of coarse-graining increases, the dynamical properties are better and better reproduced while the structural properties deviate more and more from those calculated in molecular dynamics (MD) simulations. We suggest two reasons for this behavior: the Markovian approximation is better satisfied as the level of coarse-graining increases, while the pair-wise approximation neglects important contributions due to the relative orientation of the beads at large levels of coarse-graining. Finally, we highlight a possible limit of the Markovian approximation: the fact that in constrained simulations, in which the centers-of-mass of the beads are kept constant, the bead rotational dynamics become extremely slow.
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.
Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N
2011-09-06
Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.
All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
Perlmutter, Jason D.; Drasler, William J.; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N.
2011-01-01
Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native and functional state for longer periods than detergents do. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles, with a mass of ~40 kDa and a Rg of ~2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. While AAMD simulations result in cohesive and stable particles over a 45-ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond timescale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations, and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows higher-resolution characterization of a configuration determined by a long-timescale simulation. An excellent agreement is observed between MD models and experimental, small angle neutron scattering data. The MD data provides new insights into the structure and dynamics of A8-35 particles, possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes. PMID:21806035
Tillack, Andreas F; Johnson, Lewis E; Eichinger, Bruce E; Robinson, Bruce H
2016-09-13
We have developed an approach to coarse-grained (CG) modeling of the van der Waals (vdW) type of interactions among molecules by representing groups of atoms within those molecules in terms of ellipsoids (rather than spheres). Our approach systematically translates an arbitrary underlying all-atom (AA) representation of a molecular system to a multisite ellipsoidal potential within the family of Gay-Berne type potentials. As the method enables arbitrary levels of coarse-graining, or even multiple levels of coarse-graining within a single simulation, we describe the method as a Level of Detail (LoD) model. The LoD model, as integrated into our group's Metropolis Monte Carlo computational package, is also capable of reducing the complexity of the molecular electrostatics by means of a multipole expansion of charges obtained from an AA force field (or directly from electronic structure calculations) of the charges within each ellipsoid. Electronic polarizability may additionally be included. The present CG representation does not include transformation of bonded interactions; ellipsoids are connected at the fully atomistic bond sites by freely rotating links that are constrained to maintain a constant distance. The accuracy of the method is demonstrated for three distinct types of self-assembling or self-organizing molecular systems: (1) the interaction between benzene and perfluorobenzene (dispersion interactions), (2) linear hydrocarbon chains (a system with large conformational flexibility), and (3) the self-organization of ethylene carbonate (a highly polar liquid). Lastly, the method is applied to the interaction of large (∼100 atom) molecules, which are typical of organic nonlinear optical chromophores, to demonstrate the effect of different CG models on molecular assembly.
Coarse-grained Molecular-level Analysis of Polyurea Properties and Shock-mitigation Potential
NASA Astrophysics Data System (ADS)
Grujicic, M.; Snipes, J. S.; Ramaswami, S.; Yavari, R.; Runt, J.; Tarter, J.; Dillon, G.
2013-07-01
Several experimental investigations reported in the open literature clearly established that polyurea (PU), an elastic copolymer, has an unusually high ability to attenuate and disperse shock waves. This behavior of PU is normally attributed to its unique nanometer-scale two-phase microstructure consisting of (high glass-transition temperature, T g) hydrogen-bonded discrete, hard domains dispersed within a (low T g) contiguous soft matrix. However, details regarding the mechanism(s) responsible for the superior shock-wave mitigation capacity of PU are still elusive. In the present study, molecular-level computational methods and tools are used to help us identify and characterize these mechanism(s). Because the shock-wave front structure and propagation involve coordinated motion of a large number of atoms and nano-second to micro-second characteristic times, these phenomena cannot be readily analyzed using all-atom molecular-level modeling and simulation techniques. To overcome this problem, all-atom PU microstructure is coarse-grained by introducing larger particles (beads), which account for the collective degrees of freedom of the constituent atoms, the associated force-field functions determined and parameterized using all-atom computational results, and the resulting coarse-grained model analyzed using conventional molecular-level computational methods and tools. The results thus obtained revealed that a combination of different deformation mechanisms (primarily shock-induced ordering and crystallization of hard domains and coordinated shuffle-like lateral motion of the soft-matrix segments) is most likely responsible for the superior ability of PU to attenuate/disperse shock waves.
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.
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
2016-09-08
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.
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.
Comparison of iterative inverse coarse-graining methods
NASA Astrophysics Data System (ADS)
Rosenberger, David; Hanke, Martin; van der Vegt, Nico F. A.
2016-10-01
Deriving potentials for coarse-grained Molecular Dynamics (MD) simulations is frequently done by solving an inverse problem. Methods like Iterative Boltzmann Inversion (IBI) or Inverse Monte Carlo (IMC) have been widely used to solve this problem. The solution obtained by application of these methods guarantees a match in the radial distribution function (RDF) between the underlying fine-grained system and the derived coarse-grained system. However, these methods often fail in reproducing thermodynamic properties. To overcome this deficiency, additional thermodynamic constraints such as pressure or Kirkwood-Buff integrals (KBI) may be added to these methods. In this communication we test the ability of these methods to converge to a known solution of the inverse problem. With this goal in mind we have studied a binary mixture of two simple Lennard-Jones (LJ) fluids, in which no actual coarse-graining is performed. We further discuss whether full convergence is actually needed to achieve thermodynamic representability.
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.
Coarse graining of star-polymer - colloid nanocomposites
NASA Astrophysics Data System (ADS)
Marzi, Daniela; Likos, Christos N.; Capone, Barbara
2012-07-01
We consider mixtures of self-avoiding multiarm star polymers with hard colloids that are smaller than the star polymer size. By employing computer simulations, and by extending previous theoretical approaches, developed for the opposite limit of small star polymers [A. Jusufi et al., J. Phys.: Condens. Matter 13, 6177 (2001), 10.1088/0953-8984/13/28/303], we coarse-grain the mixture by deriving an effective cross-interaction between the unlike species. The excellent agreement between theory and simulation for all size ratios examined demonstrates that the theoretical approaches developed for the colloidal limit can be successfully modified to maintain their validity also for the present case of the protein limit, in contrast to the situation for mixtures of colloids and linear polymers. We further analyze, on the basis of the derived interactions, the non-additivity parameter of the mixture as a function of size ratio and star functionality and delineate the regions in which we expect mixing as opposed to demixing behavior. Our results are relevant for the study of star-colloid nanocomposites and pave the way for further investigations of the structure and thermodynamics of the same.
TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.
Li, Min; Liu, Fengjiao; Zhang, John Z H
2016-12-13
Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.
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.
Español, Pep; Donev, Aleksandar
2015-12-21
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables, we select the position of the nanoparticle and the total mass and momentum density field of the fluid, which are locally conserved slow variables because they are defined to include the contribution of the nanoparticle. The theory of coarse graining based on the Zwanzing projection operator leads us to a system of stochastic ordinary differential equations that are closed in the relevant variables. We demonstrate that our discrete coarse-grained equations are consistent with a Petrov-Galerkin finite-element discretization of a system of formal stochastic partial differential equations which resemble previously used phenomenological models based on fluctuating hydrodynamics. Key to this connection between our "bottom-up" and previous "top-down" approaches is the use of the same dual orthogonal set of linear basis functions familiar from finite element methods (FEMs), both as a way to coarse-grain the microscopic degrees of freedom and as a way to discretize the equations of fluctuating hydrodynamics. Another key ingredient is the use of a "linear for spiky" weak approximation which replaces microscopic "fields" with a linear FE interpolant inside expectation values. For the irreversible or dissipative dynamics, we approximate the constrained Green-Kubo expressions for the dissipation coefficients with their equilibrium averages. Under suitable approximations, we obtain closed approximations of the coarse-grained dynamics in a manner which gives them a clear physical interpretation and provides explicit microscopic expressions for all of the coefficients appearing in the closure. Our work leads to a model for dilute nanocolloidal suspensions that can be simulated effectively using feasibly short molecular dynamics simulations as input
Español, Pep; 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
Subsurface Optical Microscopy of Coarse Grain Spinels. Phase 1
2013-12-01
A 456 nm LED line bar illuminated in figure 15 and a Xenon fiber optic bar illuminator is shown for figure 16. The optical in situ or subsurface ... imaging of coarse grain spinels and AlONs is optically more complex than expected. An overhead view of the side illumination field is shown in figure 20
NASA Astrophysics Data System (ADS)
Ito, Hiroaki; Higuchi, Yuji; Shimokawa, Naofumi
2016-10-01
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and morphological dynamics in charged lipid bilayer vesicles. The screened long-range electrostatic repulsion among charged head groups delays or inhibits the lateral phase separation in charged vesicles compared with neutral vesicles, suggesting the transition of the phase-separation mechanism from spinodal decomposition to nucleation or homogeneous dispersion. Moreover, the electrostatic repulsion causes morphological changes, such as pore formation, and further transformations into disk, string, and bicelle structures, which are spatiotemporally coupled to the lateral segregation of charged lipids. Based on our coarse-grained MD simulation, we propose a plausible mechanism of pore formation at the molecular level. The pore formation in a charged-lipid-rich domain is initiated by the prior disturbance of the local molecular orientation in the domain.
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.
Steric exclusion and constraint satisfaction in multi-scale coarse-grained simulations.
Taylor, William R
2016-10-01
An algorithm is described for the interaction of a hierarchy of objects that seeks to circumvent a fundamental problem in coarse-grained modelling which is the loss of fine detail when components become bundled together. A "currants-in-jelly" model is developed that provides a flexible approach in which the contribution of the soft high-level objects (jelly-like) are employed to protect the underlying atomic structure (currants), while still allowing them to interact. Idealised chains were used to establish the parameters to achieve this degree of interaction over a hierarchy spanning four levels and in a more realistic example, the distortion experienced by a protein domain structure during collision was measured and the parameters refined. This model of steric repulsion was then combined with sets of predicted distance constraints, derived from correlated mutation analysis. Firstly, an integral trans-membrane protein was modelled in which the packing of the seven helices was refined but without topological rearrangement. Secondly, an RNA structure was 'folded' under the predicted constraints, starting only from its 2-dimensional secondary structure prediction.
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.
NASA Astrophysics Data System (ADS)
Rudzinski, J. F.; Bereau, T.
2016-10-01
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.
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.
Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.
Eichenberger, Andreas P; Huang, Wei; Riniker, Sereina; van Gunsteren, Wilfred F
2015-07-14
A supra-atomic coarse-grained (CG) force field for liquid n-alkanes is presented. The model was calibrated using experimental thermodynamic data and structural as well as energetic properties for 14 n-alkanes as obtained from atomistic fine-grained (FG) simulations of the corresponding hydrocarbons using the GROMOS 45A3 biomolecular force field. A variation of the nonbonded force-field parameters obtained from mapping the FG interactions onto the CG degrees of freedom to fit the density and heat of vaporization to experimental values turned out to be mandatory for a correct reproduction of these data by the CG model, while the bonded force-field parameters for the CG model could be obtained from a Boltzmann-weighted fit with some variations with respect to the corresponding properties from the FG simulations mapped onto the CG degrees of freedom. The model presents 6 different CG bead types, for bead sizes from 2 to 4 distinguishing between terminal and nonterminal beads within an alkane chain (end or middle). It contains different nonbonded Lennard-Jones parameters for the interaction of CG alkanes with CG water. The CG alkane model was further tested by comparing predictions of the excess free energy, the self-diffusion constant, surface tension, isothermal compressibility, heat capacity, thermal expansion coefficient, and shear viscosity for n-alkanes to experimental values. The CG model offers a thermodynamically calibrated basis for the development of CG models of lipids.
Mechanism of Nucleation and Growth of Aβ40 Fibrils from All-Atom and Coarse-Grained Simulations.
Sasmal, Sukanya; Schwierz, Nadine; Head-Gordon, Teresa
2016-12-01
In this work, we characterize the nucleation and elongation mechanisms of the "diseased" polymorph of the amyloid-β 40 (Aβ40) fibril using an off-lattice coarse-grained (CG) protein model. After determining the nucleation size and subsequent stable protofibrillar structure from the CG model, validated with all-atom simulations, we consider the "lock and dock" and "activated monomer" fibril elongation mechanisms for the protofibril by statistical additions of a monomer drawn from four different ensembles of the free Aβ40 peptide to grow the fibril. Our CG model shows that the dominant mechanism for fibril elongation is the lock and dock mechanism across all monomer ensembles, even when the monomer is in the activated form. Although our CG model finds no thermodynamic difference between the two fibril elongation mechanisms, the activated monomer is found to be kinetically faster by a factor of 2 for the "locking" step compared with all other structured or unstructured monomer ensembles.
The attachment of α -synuclein to a fiber: A coarse-grain approach
NASA Astrophysics Data System (ADS)
Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.
2017-03-01
We present simulations of the amyloidogenic core of α-synuclein, the protein causing Parkinson's disease, as a short chain of coarse-grain patchy particles. Each particle represents a sequence of about a dozen amino acids. The fluctuating secondary structure of this intrinsically disordered protein is modelled by dynamic variations of the shape and interaction characteristics of the patchy particles, ranging from spherical with weak isotropic attractions for the disordered state to spherocylindrical with strong directional interactions for a β-sheet. Flexible linkers between the particles enable sampling of the tertiary structure. This novel model is applied here to study the growth of an amyloid fibril, by calculating the free energy profile of a protein attaching to the end of a fibril. The simulation results suggest that the attaching protein readily becomes trapped in a mis-folded state, thereby inhibiting further growth of the fibril until the protein has readjusted to conform to the fibril structure, in line with experimental findings and previous simulations on small fragments of other proteins.
Systematic methods for defining coarse-grained maps in large biomolecules.
Zhang, Zhiyong
2015-01-01
Large biomolecules are involved in many important biological processes. It would be difficult to use large-scale atomistic molecular dynamics (MD) simulations to study the functional motions of these systems because of the computational expense. Therefore various coarse-grained (CG) approaches have attracted rapidly growing interest, which enable simulations of large biomolecules over longer effective timescales than all-atom MD simulations. The first issue in CG modeling is to construct CG maps from atomic structures. In this chapter, we review the recent development of a novel and systematic method for constructing CG representations of arbitrarily complex biomolecules, in order to preserve large-scale and functionally relevant essential dynamics (ED) at the CG level. In this ED-CG scheme, the essential dynamics can be characterized by principal component analysis (PCA) on a structural ensemble, or elastic network model (ENM) of a single atomic structure. Validation and applications of the method cover various biological systems, such as multi-domain proteins, protein complexes, and even biomolecular machines. The results demonstrate that the ED-CG method may serve as a very useful tool for identifying functional dynamics of large biomolecules at the CG level.
Treptow, Werner; Marrink, Siewert-J; Tarek, Mounir
2008-03-20
Voltage-gated potassium (Kv) channels are ubiquitous transmembrane proteins involved in electric signaling of excitable tissues. A fundamental property of these channels is the ability to open or close in response to changes in the membrane potential. To date, their structure-based activation mechanism remains unclear, and there is a large controversy on how these gates function at the molecular level, in particular, how movements of the voltage sensor domain are coupled to channel gating. So far, all mechanisms proposed for this coupling are based on the crystal structure of the open voltage-gated Kv1.2 channel and structural models of the closed form based on electrophysiology experiments. Here, we use coarse-grain (CG) molecular dynamics simulations that allow conformational changes from the open to the closed form of the channel (embedded in its membrane environment) to be followed. Despite the low specificity of the CG force field, the obtained closed structure satisfies several experimental constraints. The overall results suggest a gating mechanism in which a lateral displacement the S4-S5 linker leads to a closing of the gate. Only a small up-down movement of the S4 helices is noticed. Additionally, the study suggests a peculiar upward motion of the intracellular tetramerization domain of the channel, hence providing a molecular view on how this domain may further regulate conduction in Kv channels.
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.
Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.
2015-01-01
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. PMID:26723608
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.
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
Dyatkin, Boris; Gogotsi, Oleksiy; Malinovskiy, Bohdan; ...
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.
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.
Coarse-grained simulations of poly(propylene imine) dendrimers in solution
NASA Astrophysics Data System (ADS)
Smeijers, A. F.; Markvoort, A. J.; Pieterse, K.; Hilbers, P. A. J.
2016-02-01
The behavior of poly(propylene imine) (PPI) dendrimers in concentrated solutions has been investigated using molecular dynamics simulations containing up to a thousand PPI dendrimers of generation 4 or 5 in explicit water. To deal with large system sizes and time scales required to study the solutions over a wide range of dendrimer concentrations, a previously published coarse-grained model was applied. Simulation results on the radius of gyration, structure factor, intermolecular spacing, dendrimer interpenetration, and water penetration are compared with available experimental data, providing a clear concentration dependent molecular picture of PPI dendrimers. It is shown that with increasing concentration the dendrimer volume diminishes accompanied by a reduction of internalized water, ultimately resulting in solvent filled cavities between stacked dendrimers. Concurrently dendrimer interpenetration increases only slightly, leaving each dendrimer a separate entity also at high concentrations. Moreover, we compare apparent structure factors, as calculated in experimental studies relying on the decoupling approximation and the constant atomic form factor assumption, with directly computed structure factors. We demonstrate that these already diverge at rather low concentrations, not because of small changes in form factor, but rather because the decoupling approximation fails as monomer positions of separate dendrimers become correlated at concentrations well below the overlap concentration.
Conformational response of a clay binding protein (EGF) by a coarse-grained Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Farmer, Barry; Drummy, Lawrence; Naik, Rajesh; Kadakia, Madhavi; Pandey, Ras
2012-02-01
Biofunctionalization of montmorillonite (MMT) clay platelets with epidermal growth factor (EGF) appears to play a critical role in tissue regeneration (cell growth and migration) [1]. How the protein (EGF) binds to clay platelet and conforms is very important in its ability to activate the epidermal growth factor receptor. It is however difficult to monitor such structural response systematically in a current laboratory setting. We investigate the structural response of the protein EGF as it binds to the clay platelet with a coarse-grained model already used to investigate binding of short peptides. Both the EGF protein and the clay platelets are described by nodes tethered together by fluctuating covalent bonds. Each residue interacts with a phenomenological interaction (based on its hydropathy index). Protein and platelet perform their stochastic motion with the Metropolis algorithm. A number of local (e.g. mobility and structural profiles) and global physical quantities such as gyration radius are examined as a function of temperature. We are able to identify the immobilized segments of protein and the variation of its size as a function of temperature. [1] C.A. Vaiana et al Biomacromolecules xxx (2011)
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
Brandt, Erik G
2013-07-01
The stochastic Eulerian-Lagrangian method (SELM) is used to simulate coarse-grained lipid membrane models under steady-state conditions and in shear flow. SELM is an immersed boundary method which combines the efficiency of particle-based simulations with the realistic solvent dynamics provided by fluctuating hydrodynamics. Membrane simulations in SELM are shown to give structural properties in accordance with equilibrium statistical mechanics and dynamic properties in agreement with previous simulations of highly detailed membrane models in explicit solvent. Simulations of sheared membranes are used to calculate surface shear viscosities and inter-monolayer friction coefficients. The membrane models are shown to be shear thinning under a wide range of applied shear rates.
PSII-LHCII supercomplex organizations in photosynthetic membrane by coarse-grained simulation.
Lee, Cheng-Kuang; Pao, Chun-Wei; Smit, Berend
2015-03-12
Green plant photosystem II (PSII) and light-harvesting complex II (LHCII) in the stacked grana regions of thylakoid membranes can self-organize into various PSII-LHCII supercomplexes with crystalline or fluid-like supramolecular structures to adjust themselves with external stimuli such as high/low light and temperatures, rendering tunable solar light absorption spectrum and photosynthesis efficiencies. However, the mechanisms controlling the PSII-LHCII supercomplex organizations remain elusive. In this work, we constructed a coarse-grained (CG) model of the thylakoid membrane including lipid molecules and a PSII-LHCII supercomplex considering association/dissociation of moderately bound-LHCIIs. The CG interaction between CG beads were constructed based on electron microscope (EM) experimental results, and we were able to simulate the PSII-LHCII supramolecular organization of a 500 × 500 nm(2) thylakoid membrane, which is compatible with experiments. Our CGMD simulations can successfully reproduce order structures of PSII-LHCII supercomplexes under various protein packing fractions, free-LHCII:PSII ratios, and temperatures, thereby providing insights into mechanisms leading to PSII-LHCII supercomplex organizations in photosynthetic membranes.
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.
Bell, David R; Cheng, Sara Y; Salazar, Heber; Ren, Pengyu
2017-04-10
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R(2) = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3-4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes).
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.
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
Bell, David R.; Cheng, Sara Y.; Salazar, Heber; Ren, Pengyu
2017-01-01
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3–4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes). PMID:28393861
Protein simulations in fluids: coupling the OPEP coarse-grained force field with hydrodynamics
Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone
2017-01-01
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 modelling systems made up to thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multi-scale approach are also discussed. PMID:26574390
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.
Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe
2013-10-08
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.
Sterpone, Fabio; Nguyen, Phuong H.; Kalimeri, Maria; Derreumaux, Philippe
2014-01-01
We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions. PMID:25419192
NASA Astrophysics Data System (ADS)
McLeland, Anna; Johnson, Daniel; Jayaraman, Arthi
2014-03-01
Gene therapy is a method involving transfection or delivery of therapeutic DNA to target cells for expression of proteins that can cure diseases. Polycations have shown tremendous potential as DNA delivery vectors because the positive charges along the polycation interact with the negatively charged DNA backbone to form a polyplex that protects and transfects the DNA. Past work has shown that the structure and chemistry of the polycation affects DNA transfection efficiency. In this work, we use coarse grained models that are mapped from atomistic simulations, along with molecular dynamics simulations to study the binding of polycations and polyanions into polyplexes. We characterize the structure, surface composition and shape of the polyplex, features that impact DNA delivery, as a function of polycation chemistry, architecture (linear versus grafted), and molecular weight. The results from these simulations serve as valuable guidelines for experimentalists on what molecular characteristics they need to incorporate in the polycations to achieve higher transfection efficiency.
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
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.
Coarse-grained incompressible magnetohydrodynamics: analyzing the turbulent cascades
NASA Astrophysics Data System (ADS)
Aluie, Hussein
2017-02-01
We formulate a coarse-graining approach to the dynamics of magnetohydrodynamic (MHD) fluids at a continuum of length-scales ℓ. In this methodology, effective equations are derived for the observable velocity and magnetic fields spatially-averaged at an arbitrary scale of resolution. The microscopic equations for the ‘bare’ velocity and magnetic fields are ‘renormalized’ by coarse-graining to yield macroscopic effective equations that contain both a subscale stress and a subscale electromotive force (EMF) generated by nonlinear interaction of eliminated fields and plasma motions. Particular attention is given to the effects of these subscale terms on the balances of the quadratic invariants of ideal incompressible MHD—energy, cross-helicity and magnetic helicity. At large coarse-graining length-scales, the direct dissipation of the invariants by microscopic mechanisms (such as molecular viscosity and Spitzer resistivity) is shown to be negligible. The balance at large scales is dominated instead by the subscale nonlinear terms, which can transfer invariants across scales, and are interpreted in terms of work concepts for energy and in terms of topological flux-linkage for the two helicities. An important application of this approach is to MHD turbulence, where the coarse-graining length ℓ lies in the inertial cascade range. We show that in the case of sufficiently rough velocity and/or magnetic fields, the nonlinear inter-scale transfer need not vanish and can persist to arbitrarily small scales. Although closed expressions are not available for subscale stress and subscale EMF, we derive rigorous upper bounds on the effective dissipation they produce in terms of scaling exponents of the velocity and magnetic fields. These bounds provide exact constraints on phenomenological theories of MHD turbulence in order to allow the nonlinear cascade of energy and cross-helicity. On the other hand, we prove a very strong version of the Woltjer-Taylor conjecture
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.
Bochicchio, Davide; Pavan, Giovanni M
2017-01-24
Supramolecular polymers, formed via noncovalent self-assembly of elementary monomers, are extremely interesting for their dynamic bioinspired properties. In order to understand their behavior, it is necessary to access their dynamics while maintaining high resolution in the treatment of the monomer structure and monomer-monomer interactions, which is typically a difficult task, especially in aqueous solution. Focusing on 1,3,5-benzenetricarboxamide (BTA) water-soluble supramolecular polymers, we have developed a transferable coarse-grained model that allows studying BTA supramolecular polymerization in water, while preserving remarkable consistency with the atomistic models in the description of the key interactions between the monomers (hydrophobic, H-bonding, etc.), self-assembly cooperativity, and amplification of order into the growing fibers. This permitted us to monitor the amplification of the key interactions between the monomers (including H-bonding) in the BTA fibers during the dynamic polymerization process. Our molecular dynamics simulations provide a picture of a stepwise cooperative polymerization mechanism, where initial fast hydrophobic aggregation of the BTA monomers in water is followed by the slower reorganization of these disordered aggregates into ordered directional oligomers. Supramolecular polymer growth then proceeds on a slower time scale. We challenged our models via comparison with the experimental evidence, capturing the effect of temperature variations and subtle changes in the monomer structure on the polymerization and on the properties of the fibers seen in the real systems. This work provides a multiscale spatiotemporal characterization of BTA self-assembly in water and a useful platform to study a variety of BTA-based supramolecular polymers toward structure-property relationships.
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
Májek, Peter; Elber, Ron
2009-01-01
A coarse grained potential for protein simulations and fold ranking is presented. The potential is based on a two-point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and re-sampling are in the spirit of the generalized ensemble approach. No native structure information (e.g. secondary structure) is used in the calculation of the potential, or in the simulation of a particular protein. The potential is subject to two tests: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set), and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys, and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than twenty nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. PMID:19291741
Synchronization of coupled noisy oscillators: Coarse graining from continuous to discrete phases
NASA Astrophysics Data System (ADS)
Escaff, Daniel; Rosas, Alexandre; Toral, Raúl; Lindenberg, Katja
2016-11-01
The theoretical description of synchronization phenomena often relies on coupled units of continuous time noisy Markov chains with a small number of states in each unit. It is frequently assumed, either explicitly or implicitly, that coupled discrete-state noisy Markov units can be used to model mathematically more complex coupled noisy continuous phase oscillators. In this work we explore conditions that justify this assumption by coarse graining continuous phase units. In particular, we determine the minimum number of states necessary to justify this correspondence for Kuramoto-like oscillators.
Synchronization of coupled noisy oscillators: Coarse graining from continuous to discrete phases.
Escaff, Daniel; Rosas, Alexandre; Toral, Raúl; Lindenberg, Katja
2016-11-01
The theoretical description of synchronization phenomena often relies on coupled units of continuous time noisy Markov chains with a small number of states in each unit. It is frequently assumed, either explicitly or implicitly, that coupled discrete-state noisy Markov units can be used to model mathematically more complex coupled noisy continuous phase oscillators. In this work we explore conditions that justify this assumption by coarse graining continuous phase units. In particular, we determine the minimum number of states necessary to justify this correspondence for Kuramoto-like oscillators.
Ginzburg-Landau free energy for molecular fluids: Determination and coarse-graining
NASA Astrophysics Data System (ADS)
Desgranges, Caroline; Delhommelle, Jerome
2017-02-01
Using molecular simulation, we determine Ginzburg-Landau free energy functions for molecular fluids. To this aim, we extend the Expanded Wang-Landau method to calculate the partition functions, number distributions and Landau free energies for Ar,CO2 and H2O . We then parametrize a coarse-grained free energy function of the density order parameter and assess the performance of this free energy function on its ability to model the onset of criticality in these systems. The resulting parameters can be readily used in hybrid atomistic/continuum simulations that connect the microscopic and mesoscopic length scales.
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
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.
Mean-Field Models of Structure and Dispersion of Polymer-nanoparticle Mixtures
2010-07-29
bare polymer matrix by as much as an order of magnitude.2,3,12–14 Gas barrier properties of butyl rubber latexes was shown to be reduced by almost 2...research developments in coarse-grained modeling based on mean-field approaches of the equilibrium dispersion and structure of polymer nanoparticle...polymernanoparticle mixtures Report Title ABSTRACT We review some recent research developments in coarse-grained modeling based on mean-field approaches of the
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 atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.
Role of Ionic Clusters in Dynamics of Ionomer Melts: From Atomistic to Coarse Grained Simulations
NASA Astrophysics Data System (ADS)
Agrawal, Anupriya
Ionomers, polymers decorated with ionizable groups, have found application in numerous technologies where ionic transport is required. The ionic groups associate into random clusters resulting in substantial effect on structure, dynamics and transport of these materials. The effects of topology, size and dynamics of these aggregates however remain an open question. Here we probe cluster formation correlated with polymer dynamics through a model system of randomly sulfonated polystyrene (SPS) melts with molecular dynamics (MD) simulations over a broad time and length scales ranging from that within the ionic clusters through polymer segmental dynamics to the motion of the entire molecules. The cluster evolution was probed by fully atomistic studies. We find ladder-like aggregates that transform to globule-like with increasing the dielectric constant of media for sodium neutralized SPS. With increasing dielectric constant, the size of the aggregates decrease and their number increases. Concurrently, the mobility of the polymer increases. The counterion radius and valency affect both morphology and dynamics as is evident in the calculated static and dynamic structure factors. It is further manifested in the results of viscosity obtained through non-equilibrium molecular dynamics technique. Finally, to access larger length scales a three bead coarse-grained model to describe sulfonated styrene that we have developed will be discussed in view of the outstanding challenges in ionic polymers. Supported in part by DOE Grant No. DE-SC007908. This work was carried out in collaboration with Dvora Perahia and Gary Grest while I was a postdoc at Clemson University. I gratefully acknowledge both of them for their support and encouragement.
Coarse-grained kinetic equations for quantum systems
NASA Astrophysics Data System (ADS)
Petrov, E. G.
2013-01-01
The nonequilibrium density matrix method is employed to derive a master equation for the averaged state populations of an open quantum system subjected to an external high frequency stochastic field. It is shown that if the characteristic time τstoch of the stochastic process is much lower than the characteristic time τsteady of the establishment of the system steady state populations, then on the time scale Δ t ˜ τsteady, the evolution of the system populations can be described by the coarse-grained kinetic equations with the averaged transition rates. As an example, the exact averaging is carried out for the dichotomous Markov process of the kangaroo type.
Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A
2014-12-01
Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure.
All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5
NASA Astrophysics Data System (ADS)
Genheden, Samuel; Essex, Jonathan W.
2016-11-01
We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.
Path statistics, memory, and coarse-graining of continuous-time random walks on networks.
Manhart, Michael; Kion-Crosby, Willow; Morozov, Alexandre V
2015-12-07
Continuous-time random walks (CTRWs) on discrete state spaces, ranging from regular lattices to complex networks, are ubiquitous across physics, chemistry, and biology. Models with coarse-grained states (for example, those employed in studies of molecular kinetics) or spatial disorder can give rise to memory and non-exponential distributions of waiting times and first-passage statistics. However, existing methods for analyzing CTRWs on complex energy landscapes do not address these effects. Here we use statistical mechanics of the nonequilibrium path ensemble to characterize first-passage CTRWs on networks with arbitrary connectivity, energy landscape, and waiting time distributions. Our approach can be applied to calculating higher moments (beyond the mean) of path length, time, and action, as well as statistics of any conservative or non-conservative force along a path. For homogeneous networks, we derive exact relations between length and time moments, quantifying the validity of approximating a continuous-time process with its discrete-time projection. For more general models, we obtain recursion relations, reminiscent of transfer matrix and exact enumeration techniques, to efficiently calculate path statistics numerically. We have implemented our algorithm in PathMAN (Path Matrix Algorithm for Networks), a Python script that users can apply to their model of choice. We demonstrate the algorithm on a few representative examples which underscore the importance of non-exponential distributions, memory, and coarse-graining in CTRWs.
Correlations in polymer blends: Simulations, perturbation theory, and coarse-grained theory
NASA Astrophysics Data System (ADS)
Chung, Jun Kyung
A thermodynamic perturbation theory of symmetric polymer blends is developed that properly accounts for the correlation in the spatial arrangement of monomers. By expanding the free energy of mixing in powers of a small parameter alpha which controls the incompatibility of two monomer species, we show that the perturbation theory has the form of the original Flory-Huggins theory, to first order in alpha. However, the lattice coordination number in the original theory is replaced by an effective coordination number. A random walk model for the effective coordination number is found to describe Monte Carlo simulation data very well. We also propose a way to estimate Flory-Huggins chi parameter by extrapolating the perturbation theory to the limit of a hypothetical system of infinitely long chains. The first order perturbation theory yields an accurate estimation of chi to first order in alpha. Going to second order, however, turns out to be more involved and an unambiguous determination of the coefficient of alpha2 term is not possible at the moment. Lastly, we test the predictions of