scholarly journals Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

2008 ◽  
Vol 2 ◽  
pp. BBI.S459 ◽  
Author(s):  
Choon-Peng Chng ◽  
Lee-Wei Yang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Conformation ◽  
Conformational Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Time Step ◽  
Effective Potentials ◽  
Functional Dynamics ◽  
Indispensable Tool ◽  
Selection Of

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 a bsence 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.

scholarly journals Origin and structure of liquid crystalline Blue Phase III

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tanay Paul ◽  
Jayashree Saha
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Liquid Crystalline ◽  
Pair Interaction ◽  
Dynamics Simulation ◽  
Phase Iii ◽  
Coarse Grained ◽  
Anisotropic Liquid ◽  
Blue Phase ◽  
Selection Of

Abstract We report here an off-lattice NVT molecular dynamics simulation study of a system of polar chiral ellipsoidal molecules, which spontaneously exhibits Blue Phase III (BPIII), considering coarse-grained attractive-repulsive pair interaction appropriate for anisotropic liquid crystal mesogens. We have observed that suitable selection of chiral and dipolar strengths not only gives rise to thermodynamically stable BPIII but novel Smectic and Bilayered BPIII as well. Further, we have demonstrated that the occurrence of BPIII and its layered counterparts depend crucially on molecular elongation.

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

2011 ◽  
Vol 39 (1) ◽  
pp. 44-58 ◽  
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.

Sliding Dynamics of Ring on Polymer in Rotaxane: A Coarse-Grained Molecular Dynamics Simulation Study

2019 ◽  
Vol 52 (10) ◽  
pp. 3787-3793 ◽  
Author(s):  
Yusuke Yasuda ◽  
Masatoshi Toda ◽  
Koichi Mayumi ◽  
Hideaki Yokoyama ◽  
Hiroshi Morita ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Sliding Dynamics ◽  
Coarse Grained Molecular Dynamics
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