scholarly journals Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries

2017 ◽  
Vol 15 (31) ◽  
pp. 6541-6547 ◽  
Author(s):  
I. R. Sasselli ◽  
I. P. Moreira ◽  
R. V. Ulijn ◽  
T. Tuttle
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Self Assembly ◽  
Peptide Libraries ◽  
Coarse Grained ◽  
Molecular Dynamic Simulations ◽  
New Materials ◽  
Dynamic Simulations ◽  
Dynamics Simulations

Coarse grained molecular dynamic simulations demonstrate that interactions between species in dynamic peptide libraries can cause a disrupting self-assembly effect that affects the possible discovery of new materials.

scholarly journals Molecular Dynamics Simulations and Empirical Observations on Soy Lecithin Liposome Preparation

2018 ◽  
Vol 16 (2) ◽  
pp. 222 ◽  
Author(s):  
Rini Dwiastuti ◽  
Muhammad Radifar ◽  
Marchaban Marchaban ◽  
Sri Noegrohati ◽  
Enade Perdana Istyastono
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Molecular Dynamic Simulations ◽  
Soy Lecithin ◽  
Dynamic Simulations ◽  
Liposome Size ◽  
Dynamics Simulations

Soy lecithin is a phospholipid often used in liposome formulations. Determination of water and phospholipid composition is one of the problems in the liposome formulation. This study is using molecular dynamics simulation and empirical observation in producing liposome preparations. Phospholipids 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) were objected in molecular dynamics simulations using Coarse Grained Molecular Dynamics (CGMD) approaches. The result showed that the molecular dynamic simulations could be employed to predict the liposome size. The molecular dynamic simulations resulted in liposome size of 71.22 ± 2.54 nm, which was located within the range of the liposome size resulted from the empirical observations (95.99 ± 43.02 nm). Moreover, similar liposome forms were observed on both results of molecular dynamics simulations and empirical approaches.

Water structures on a Pt(111) electrode from ab initio molecular dynamic simulations for a variety of electrochemical conditions

2020 ◽  
Vol 22 (19) ◽  
pp. 10431-10437 ◽  
Author(s):  
Sung Sakong ◽  
Axel Groß
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Metal Electrode ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Dynamics Simulations

Water structures on a Pt(111) metal electrode critically depend on the electrochemical conditions, as shown by ab initio molecular dynamics simulations.

scholarly journals Molecular dynamic simulations on TKX-50/HMX cocrystal

RSC Advances ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 6795-6799 ◽  
Author(s):  
Shuling Xiong ◽  
Shusen Chen ◽  
Shaohua Jin ◽  
Zhe Zhang ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Dynamics Simulations

TKX-50/HMX cocrystal model was established and calculated using PCFF force field by molecular dynamics simulations.

scholarly journals Conformational Preferences of Triantennary and Tetraantennary Hybrid N-Glycans in Solution: Insights from 20 μS Long Atomistic Molecular Dynamic Simulations

2020 ◽  
Author(s):  
Rajarshi Roy ◽  
Sayan Poddar ◽  
Parimal Kar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Conformational Dynamics ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Conformational Preferences ◽  
Dynamics Simulations

In the current study, we have investigated the conformational dynamics of a triantennary and a tetraantennary hybrid N-glycan associated with HIV glycoprotein using 20 micro-second long all-atom molecular dynamics simulations. <br>

scholarly journals Conformational Preferences of Triantennary and Tetraantennary Hybrid N-Glycans in Solution: Insights from 20 μS Long Atomistic Molecular Dynamic Simulations

2020 ◽  
Author(s):  
Rajarshi Roy ◽  
Sayan Poddar ◽  
Parimal Kar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Conformational Dynamics ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Conformational Preferences ◽  
Dynamics Simulations

In the current study, we have investigated the conformational dynamics of a triantennary and a tetraantennary hybrid N-glycan associated with HIV glycoprotein using 20 micro-second long all-atom molecular dynamics simulations. <br>

Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations

2016 ◽  
Vol 12 (1) ◽  
pp. 76-84 ◽  
Author(s):  
Wei-Kang Li ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Free Energy Calculations ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Energy Calculations ◽  
Dynamics Simulations

Molecular dynamic simulations and MMPBSA calculations of tvMyb2-ap65-1 complex and its mutants, our work give important information to understand the interactions between tvMyb2-ap65-1.

scholarly journals Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 589 ◽  
Author(s):  
Andrew R. Dalby ◽  
Mohd Shahir Shamsir
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Arrhenius Equation ◽  
Limited Range ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Dynamics Simulations ◽  
High Degree ◽  
Very High

Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

Molecular dynamic simulations of pressure-driven water transport through polyamide nanofiltration membranes at different membrane densities

RSC Advances ◽  
2016 ◽  
Vol 6 (68) ◽  
pp. 63586-63596 ◽  
Author(s):  
Luying Wang ◽  
Randall S. Dumont ◽  
James M. Dickson
Keyword(s):  
Molecular Dynamics ◽  
Porous Structure ◽  
Molecular Dynamic ◽  
Water Transport ◽  
Aromatic Polyamide ◽  
Molecular Dynamic Simulations ◽  
Nanofiltration Membranes ◽  
Dynamic Simulations ◽  
Dynamics Simulations ◽  
Pressure Driven

The amorphous aromatic polyamide membranes with different membrane densities were modeled to study the porous structure of free-volume pores and the pressure-driven water transport by using molecular dynamics simulations.

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