scholarly journals A Coarse-Grained Force Field for Silica–Polybutadiene Interfaces and Nanocomposites

Polymers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1484 ◽  
Author(s):  
Alessio David ◽  
Marta Pasquini ◽  
Ugo Tartaglino ◽  
Guido Raos
Keyword(s):  
Force Field ◽  
Large Scale ◽  
Present Model ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Silica Nanocomposites ◽  
Silica Surfaces ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Large Scale Simulations

We present a coarse-grained force field for modelling silica–polybutadiene interfaces and nanocomposites. The polymer, poly(cis-1,4-butadiene), is treated with a previously published united-atom model. Silica is treated as a rigid body, using one Si-centered superatom for each SiO 2 unit. The parameters for the cross-interaction between silica and the polymer are derived by Boltzmann inversion of the density oscillations at model interfaces, obtained from atomistic simulations of silica surfaces containing both Q 4 (hydrophobic) and Q 3 (silanol-containing, hydrophilic) silicon atoms. The performance of the model is tested in both equilibrium and non-equilibrium molecular dynamics simulations. We expect the present model to be useful for future large-scale simulations of rubber–silica nanocomposites.

LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES

2004 ◽  
Vol 15 (01) ◽  
pp. 193-201 ◽  
Author(s):  
KAI KADAU ◽  
TIMOTHY C. GERMANN ◽  
PETER S. LOMDAHL
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Huge Number ◽  
Physical Problems ◽  
Efficient Data ◽  
Dynamics Simulations ◽  
Large Scale Simulations ◽  
Efficient Data Analysis

We have performed parallel large-scale molecular-dynamics simulations on the QSC-machine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a newly-developed graphics package that renders in a very efficient parallel way a huge number of spheres necessary for the visualization of atomistic simulations. These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the μ-scale.

scholarly journals Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

2021 ◽  
Author(s):  
Mei Zheng ◽  
Andres Jaramillo-Botero ◽  
Xue-hai Ju ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Equation Of State ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Coarse Grained ◽  
Polyacrylamide Gels ◽  
Dynamics Simulations

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

scholarly journals Atomistic potential for graphene and other sp2 carbon systems

2017 ◽  
Author(s):  
Zacharias G. Fthenakis ◽  
George Kalosakas ◽  
Georgios D. Chatzidakis ◽  
Costas Galiotis ◽  
Konstantinos Papagelis ◽  
...  
Keyword(s):  
Force Field ◽  
Large Scale ◽  
Dft Calculation ◽  
Carbon Materials ◽  
Phonon Dispersion ◽  
Significant Loss ◽  
Atomistic Simulations ◽  
Carbon Structures ◽  
Out Of Plane ◽  
Plane Deformations

<div>We introduce a torsional force field for sp<sup>2</sup> carbon to augment an in-plane atomistic potential of a previous work (Kalosakas et al, J. Appl. Phys. 113, 134307 (2013)) so that it is applicable to out-of-plane deformations of graphene and related carbon materials. The introduced force field is fit to reproduce DFT calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp<sup>2</sup> carbon structures without significant loss of accuracy. We show that the complete proposed potential reproduces characteristic properties of fullerenes and carbon nanotubes. In addition, it reproduces very accurately the out-of-plane ZA and ZO modes of graphene’s phonon dispersion as well as all phonons with frequencies up to 1000 cm<sup>−1</sup>.</div>

scholarly journals Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

2015 ◽  
Vol 143 (24) ◽  
pp. 243144 ◽  
Author(s):  
Christopher M. MacDermaid ◽  
Hemant K. Kashyap ◽  
Russell H. DeVane ◽  
Wataru Shinoda ◽  
Jeffery B. Klauda ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cyclic Alkanes ◽  
Dynamics Simulations

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

2020 ◽  
Author(s):  
Alvin Yu ◽  
Alexander J. Pak ◽  
Peng He ◽  
Viviana Monje-Galvan ◽  
Lorenzo Casalino ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Model ◽  
Structural Data ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Current Status ◽  
Multiscale Approach ◽  
X Ray Crystallography ◽  
Coarse Grained Model ◽  
Viral Particles

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely “bottom-up” coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.Significance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.

scholarly journals Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Pieczywek ◽  
W. Płaziński ◽  
A. Zdunek
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Structural Features ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

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