scholarly journals Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation

2016 ◽  
Vol 217 ◽  
pp. 8-19 ◽  
Author(s):  
Cesar Calero-Rubio ◽  
Bradford Paik ◽  
Xinqiao Jia ◽  
Kristi L. Kiick ◽  
Christopher J. Roberts
Keyword(s):  
Molecular Simulation ◽  
Coarse Grained ◽  
Helical Peptides ◽  
Unfolding Thermodynamics

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study

Soft Matter ◽  
2017 ◽  
Vol 13 (38) ◽  
pp. 6770-6783 ◽  
Author(s):  
Joshua E. Condon ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Simulation ◽  
Simulation Study ◽  
Coarse Grained ◽  
Star Polymer ◽  
Backbone Flexibility ◽  
Polymer Architecture ◽  
Polymer Conjugates ◽  
Coarse Grained Simulations

Using coarse-grained simulations, we study the effect of varying oligonucleic acid (ONA) backbone flexibility, ONA charge and star polymer architecture on structure and thermodynamics of ONA–star polymer conjugates assembly.

Molecular simulation of diffusion mechanism of nanorods in cross-linked network

Nanoscale ◽  
2021 ◽  
Author(s):  
Bo-Ran Zhao ◽  
Bin Li ◽  
Xinghua Shi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Simulation ◽  
Diffusion Mechanism ◽  
Coarse Grained ◽  
Aspect Ratios ◽  
Coarse Grained Molecular Dynamics

We study the diffusion of rod-shape nanocarriers with different rigidities and aspect ratios in cross-linked network using coarse-grained molecular dynamics (CGMD) simulations. The diffusivities of nanorods increase as the reduction...

Coarse-Grained Molecular Simulation Model for Gecko Feet Keratin

2018 ◽  
Vol 122 (8) ◽  
pp. 2203-2212 ◽  
Author(s):  
Kenkoh S. Endoh ◽  
Toshihiro Kawakatsu ◽  
Florian Müller-Plathe
Keyword(s):  
Simulation Model ◽  
Molecular Simulation ◽  
Coarse Grained ◽  
Gecko Feet

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

scholarly journals Molecular Simulation of Lipids and Water: Atomistic, Coarse-Grained, and Mixed Resolutions

2016 ◽  
Vol 110 (3) ◽  
pp. 413a
Author(s):  
Mario Orsi ◽  
Wei Ding ◽  
Michail Palaiokostas ◽  
Wen Wang
Keyword(s):  
Molecular Simulation ◽  
Coarse Grained
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