coarse grain models and the computer simulation of soft

Coarse grain models and the computer simulation of soft materials

2020/5/18Coarse grain models and the computer simulation of soft materials To cite this article: Steve O Nielsen et al 2004 J. Phys.: Condens. Matter 16 R481 View the article online for updates and enhancements. Related content Self-assembly of a phospholipid

On

PHYSICAL REVIEW E 85, 036709 (2012) On-the-fly coarse-graining methodology for the simulation of chain formation of superparamagnetic colloids in strong magnetic fields Jordi S. Andreu,1,* Carles Calero, 2Juan Camacho, and Jordi Faraudo1 1Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193 Bellaterra, Spain`

On

Within this approach, the coarse-grain objects of the simulation and their dynamic behavior are not fixed a priori at the beginning of the simulation but rather redefined on the fly. The motion of the CG objects (single particles or aggregates) is described by an anisotropic diffusion model and the magnetic dipole-dipole interaction is replaced by an effective short-range interaction between

Computer simulation studies of soft materials: the

The talk will review efforts to use computer simulation methodologies to study self-assembling systems. It will highlight the topical theme of ``bridging length and time-scales using so-called coarse grain models and also stress the continuing need for high performance computing. Examples will include the spontaneous formation of various (lamellar, cylindrical) phases exhibited by membrance

Simulation of polymer melts. I. Coarse‐graining procedure

The paper introduces a systematic procedure to coarse grain atomistic polymer models into a mesoscopic model, which then allows an effective and fast simulation of melts. The method, which provides information on both static and dynamic properties, is tested for

On

Within this approach, the coarse-grain objects of the simulation and their dynamic behavior are not fixed a priori at the beginning of the simulation but rather redefined on the fly. The motion of the CG objects (single particles or aggregates) is described by an anisotropic diffusion model and the magnetic dipole-dipole interaction is replaced by an effective short-range interaction between

Magic v.3: An integrated software package for

2019/4/1Molecular computer simulations using coarse-grained (CG) models have received widespread popularity as a practical way to overcome problems related to large system sizes and long simulation times . By reducing the number of degrees of freedom, CG models allow speed up simulations by several orders of magnitude and address to problems which are impossible to model

[PDF] Monte Carlo Simulation of Polymers: Coarse

A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific polymer and reflect the underlying atomistic details to some extent, and those which retain only the most basic features of a polymer chain (chain connectivity

Coarse grain models and the computer simulation of soft

2004/4/2Coarse grain models and the computer simulation of soft materials Steve O Nielsen, Carlos F Lopez, Goundla Srinivas and Michael L Klein 1 Published 2 April 2004 • IOP Publishing Ltd Journal of Physics: Condensed Matter, Volume 16, Number 15

Coarse graining page on SklogWiki

Steve O Nielsen, Carlos F Lopez, Goundla Srinivas and Michael L Klein Coarse grain models and the computer simulation of soft materials, Journal of Physics: Condensed Matter 16 pp. R481-R512 (2004) J. -W. Chu; G. S. Ayton; S. Izvekov; G. A. Voth Emerging methods for multiscale simulation of biomolecular systems, Molecular Physics 105 pp. 167-175 (2007)

Coarse

In this work, we study the influence of polymer chain length (m), based on Lennard-Jones potential, and nanoparticle (NP)-polymer interaction strength (∊SUBnp/SUB) on aggregation and dispersion of soft repulsive spherically structured NPs in polymer melt using coarse-grain molecular dynamics simulations. A phase diagram is proposed where transitions between different structures in the NP

Computer simulation of surfactant solutions

2000/3/1Many of the non-lattice coarse grain models are similar to those adopted by Smit and coworkers,, as a variation on a models developed earlier by Telo de Gamma and Gubbins, . Most of these models employ non-bonded potentials which consist of a Lennard–Jones potential that is truncated and shifted in energy so that the potential is 0 at the point of truncation.

ESPResSo Extensible Simulation Package for the

Nature Cover Issue from 2007. The data in this article was produced with ESPResSo. is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft matter research in physics, chemistry and molecular biology. It can be used to simulate

Coarse graining page on SklogWiki

Steve O Nielsen, Carlos F Lopez, Goundla Srinivas and Michael L Klein Coarse grain models and the computer simulation of soft materials, Journal of Physics: Condensed Matter 16 pp. R481-R512 (2004) J. -W. Chu; G. S. Ayton; S. Izvekov; G. A. Voth Emerging methods for multiscale simulation of biomolecular systems, Molecular Physics 105 pp. 167-175 (2007)

Adaptive resolution simulation of an atomistic protein in

We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained

Computer Simulation Studies of Model Biological Membranes

In coarse grain models, solute and solvent sites are usually represented as a group of atoms that interact in an effective way, reducing in this way the computer time needed for the calculations. Coarse grain models can be adjusted to mimic a specific system 22

Coarse grain forces in star polymer melts

All functions and parameters in a coarse grain model based on these concepts are obtained from the underlying small scale simulation. The coarse model reproduces both the diffusion coefficient and the shear relaxation modulus. Ways to improve the model

Comparative atomistic and coarse

2009/1/14We employ the inverse Boltzmann method to coarse-grain three commonly used three-site water models (TIP3P, SPC and SPC/E) where one molecule is replaced with one coarse-grained particle with isotropic two-body interactions only. The shape of the coarse-grained potentials is dominated by the ratio of two lengths, which can be rationalized by the geometric constraints of the

Prediction of Partition Coefficients by Multiscale Hybrid Atomic

Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level.

Coarse

Another major challenge in the simulation with coarse-grained models is the reproduction of dynamic properties in accordance with fine-grained reference models. In general, the time scales of relaxation are smaller in coarser models and this leads to an effective 'speed-up' of these simulations, a behavior which is related to a loss of dissipative degrees of freedom in the coarser model.

Figure 1 from Monte Carlo Simulation of Polymers: Coarse

Corpus ID: 6113122 Monte Carlo Simulation of Polymers: Coarse-Grained Models article{Baschnagel2004MonteCS, title={Monte Carlo Simulation of Polymers: Coarse-Grained Models}, author={J. Baschnagel and J. Wittmer and H. Meyer}, journal={arXiv: Soft

Monte Carlo Simulation of Polymers: Coarse

coarse-grained models is only touched upon briey . Generic models are suited to explore gen-eral and universal properties of polymer systems, which occur particularly in the limit of long chains. The simulation of long chains represents a challenging problem due

Coarse

Steve O. Nielsen, Carlos F. Lopez, Goundla Srinivas, Michael L. Klein, Coarse grain models and the computer simulation of soft materials, Journal of Physics: Condensed Matter 16 (15), R481 (2004). Goundla Srinivas, Dennis E. Discher, Michael L. Klein, Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics, Nature Materials 3 (9), 638-644 (2004).

Coarse

2008/9/22Coarse-Grain Models for Nucleic Acids and Large Nucleoprotein Assemblies Robert K.-Z. Tan, Anton S. Petrov, Batsal Devkota, and Stephen C. Harvey Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics

Adaptive resolution simulation of an atomistic protein in

We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained

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