Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation, that is, the target distribution function, the PMF potential energy is extracted, and then the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have gone through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.

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Is Preservation of Symmetry Necessary for Coarse-Graining?

10.26434/chemrxiv.10728128.v1 ◽

2019 ◽

Author(s):

Maghesree Chakraborty ◽

Jinyu Xu ◽

Andrew White

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Coarse Graining ◽

Dynamics Simulation ◽

Coarse Grained ◽

Molecular Symmetry

This work investigates how preservation of molecular symmetry affects accuracy of coarse-grained (CG) molecular dynamics simulation. We studied 26 mapping operators for 7 molecules to find that it has little effect on accuracy of CG simulations.

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Molecular Dynamics Simulation of the Mechanical Properties of NR/TPI

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.560-561.1114 ◽

2012 ◽

Vol 560-561 ◽

pp. 1114-1118 ◽

Cited By ~ 3

Author(s):

Hao Jiang ◽

Hong Yue ◽

Jian Yong Zhao ◽

Qing E Sha

Keyword(s):

Mechanical Properties ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Pair Correlation ◽

Simulation Method ◽

Dynamics Simulation ◽

Structure Property ◽

Rubber Blends ◽

Multi Scale ◽

Gutta Percha

This paper addresses the potential of molecular dynamics simulation for structure–property correlations in rubber. This is an important topic within a multi-scale framework to rubber blends. For that purpose, the Mechanical Properties of NR(Natural rubber)/TPI(Gutta percha) are studied by Molecular dynamics simulation method. The result indicates that the NR/TPI’s properties have been improved significantly. Compared to the pure TPI, the rubber blends’ Modulus and rigidity decrease while flexibility and strength are enhanced. Based on these, the pair correlation functions are discussed, the best simulation technique identified in this study reveal the nature of interactions between the components of the blends.

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Multi-scale coarse-grained molecular dynamics simulation to investigate the thermo-mechanical behavior of shape-memory polyurethane copolymers

Polymer ◽

10.1016/j.polymer.2020.123228 ◽

2020 ◽

pp. 123228

Author(s):

Sungwoo Park ◽

Junghwan Moon ◽

Byungjo Kim ◽

Maenghyo Cho

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Mechanical Behavior ◽

Shape Memory ◽

Dynamics Simulation ◽

Coarse Grained ◽

Multi Scale ◽

Shape Memory Polyurethane ◽

Coarse Grained Molecular Dynamics

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Molecular Dynamics Simulation on Dynamic Properties of Bubble

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.705.150 ◽

2013 ◽

Vol 705 ◽

pp. 150-156

Author(s):

Chao Qiu ◽

Hui Сhen Zhang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Potential Energy ◽

Canonical Ensemble ◽

Dynamic Properties ◽

Simulation Method ◽

Dynamics Simulation ◽

Final State ◽

Balance State ◽

Three Stages

Development of a single bubble in free space under the canonical ensemble was studied by using molecular dynamics simulation method. The detailed dynamic characteristics in the evolution process were analyzed by calculating the displacement of molecules, density, diffusion coefficient, pressure and potential energy of bubble. The results indicate that the evolution is divided into three stages according to the change of bubble potential energy, which are expansion, compression and balance state respectively. The temperature and density have significant influences on the final state of bubbles. The bubble in the liquid with larger density has a higher transition rate. The collapsing speed of bubble becomes faster with temperature increasing.

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The Improvement of Generalized Particle Method for Nano-Materials Molecular Dynamics Simulation

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.97-101.2159 ◽

2010 ◽

Vol 97-101 ◽

pp. 2159-2162 ◽

Cited By ~ 1

Author(s):

Zhen Qing Wang ◽

Zeng Jie Yang ◽

Yong Jun Wang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Potential Energy ◽

Particle Method ◽

Potential Energy Function ◽

Simulation Software ◽

Dynamics Simulation ◽

Nano Materials ◽

Multi Scale ◽

Structural Details

A generalized particle molecular dynamics simulation (GP) method has been proposed by J. Fan to solve the multi-scale problems in nano-materials. Although the method has attractive features, its acceleration equivalency hypothesis doesn’t meet the actual situation. In this paper an improved GP method is proposed. It assumes that the potential energy of generalized particles is equal to the potential energy of corresponding atomic groups in nano-materials. The parameters of improved GP method rest with the atomic structural details and corresponding atomic potential energy function. And by using open-source molecular simulation software DL-POLY, an example to compare the MD and the improved GP methods has been proposed, in which the Improved GP method presents sufficient accuracy

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Investigation of the Microscopic Viscoelastic Property for Cross-linked Polymer Network by Molecular Dynamics Simulation

Tire Science and Technology ◽

10.2346/1.3555178 ◽

2011 ◽

Vol 39 (1) ◽

pp. 44-58 ◽

Cited By ~ 3

Author(s):

Y. Masumoto ◽

Y. Iida

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Analytical Method ◽

Viscoelastic Properties ◽

Polymer Network ◽

Dynamics Simulation ◽

Coarse Grained ◽

The Cross ◽

Microscopic Dynamic ◽

Coarse Grained Molecular Dynamics

Abstract The purpose of this work is to develop a new analytical method for simulating the microscopic mechanical property of the cross-linked polymer system using the coarse-grained molecular dynamics simulation. This new analytical method will be utilized for the molecular designing of the tire rubber compound to improve the tire performances such as rolling resistance and wet traction. First, we evaluate the microscopic dynamic viscoelastic properties of the cross-linked polymer using coarse-grained molecular dynamics simulation. This simulation has been conducted by the coarse-grained molecular dynamics program in the OCTA) (http://octa.jp/). To simplify the problem, we employ the bead-spring model, in which a sequence of beads connected by springs denotes a polymer chain. The linear polymer chains that are cross-linked by the cross-linking agents express the three-dimensional cross-linked polymer network. In order to obtain the microscopic dynamic viscoelastic properties, oscillatory deformation is applied to the simulation cell. By applying the time-temperature reduction law to this simulation result, we can evaluate the dynamic viscoelastic properties in the wide deformational frequency range including the rubbery state. Then, the stress is separated into the nonbonding stress and the bonding stress. We confirm that the contribution of the nonbonding stress is larger at lower temperatures. On the other hand, the contribution of the bonding stress is larger at higher temperatures. Finally, analyzing a change of microscopic structure in dynamic oscillatory deformation, we determine that the temperature/frequency dependence of bond stress response to a dynamic oscillatory deformation depends on the temperature dependence of the average bond length in the equilibrium structure and the temperature/frequency dependence of bond orientation. We show that our simulation is a useful tool for studying the microscopic properties of a cross-linked polymer.

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Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

Physical Chemistry Chemical Physics ◽

10.1039/d0cp06104b ◽

2021 ◽

Vol 23 (9) ◽

pp. 5236-5243

Author(s):

Ying Hu ◽

Chao Xu ◽

Linfeng Ye ◽

Feng Long Gu ◽

Chaoyuan Zhu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Potential Energy ◽

Potential Energy Surfaces ◽

Dynamics Simulation ◽

Surface Hopping ◽

Nonadiabatic Molecular Dynamics ◽

Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

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