Molecular Dynamics Study of a MARTINI Coarse-Grained Polystyrene Brush in Good Solvent: Structure and Dynamics

2011 ◽  
Vol 45 (1) ◽  
pp. 563-571 ◽  
Author(s):  
Giulia Rossi ◽  
Ian G. Elliott ◽  
Tapio Ala-Nissila ◽  
Roland Faller
Keyword(s):  
Molecular Dynamics ◽  
Coarse Grained ◽  
Solvent Structure ◽  
Structure And Dynamics

scholarly journals Structure and dynamics of liposomes designed for drug delivery: coarse-grained molecular dynamics simulations to reveal the role of lipopolymer incorporation

RSC Advances ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 3745-3755 ◽  
Author(s):  
Mohammed Lemaalem ◽  
Nourddine Hadrioui ◽  
Abdelali Derouiche ◽  
Hamid Ridouane
Keyword(s):  
Drug Delivery ◽  
Molecular Dynamics ◽  
Polyethylene Glycol ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Structure And Dynamics ◽  
Statistical Ensembles ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

In this work, coarse-grained molecular dynamics simulations are carried out in NPTH and NVTE statistical ensembles in order to study the structure and dynamics properties of liposomes coated with polyethylene glycol (PEG).

Structure and dynamics of ions in dipolar solvent: A coarse-grained simulation study

Soft Matter ◽  
2021 ◽  
Author(s):  
Jicai Liang ◽  
Hao Wei ◽  
Kaifeng Yu ◽  
Chengjiang Lin ◽  
Hongfei Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Electric Field ◽  
Simulation Study ◽  
Dynamic Properties ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Ionic Solution ◽  
Structure And Dynamics ◽  
Coarse Grained Molecular Dynamics

We employ the coarse-grained molecular dynamics simulation to investigate the fundamental structural and dynamic properties of the ionic solution with and without the application of the electric field. Our simulations,...

scholarly journals Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

2016 ◽  
Vol 18 (44) ◽  
pp. 30344-30356 ◽  
Author(s):  
Petr Jeřábek ◽  
Jan Florián ◽  
Václav Martínek
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Cytochrome P450 ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cytochrome P450 1A2 ◽  
Structure And Dynamics ◽  
Human Cytochrome ◽  
Membrane Bound ◽  
Dynamics Simulations

The structure and dynamics of the membrane-bound full-length human cytochrome P450 1A2 (CYP1A2) in aqueous solution determined by coarse-grained and all-atom molecular dynamics simulations.

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.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

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