High-Density Hydration Layer of Lysozymes:  Molecular Dynamics Decomposition of Solution Scattering Data

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

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Emulsification of Surfactant on Oil Droplets by Molecular Dynamics Simulation

Molecules ◽

10.3390/molecules25133008 ◽

2020 ◽

Vol 25 (13) ◽

pp. 3008

Author(s):

Yaoshuang Cheng ◽

Shiling Yuan

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Heavy Oil ◽

Molecular Level ◽

Sodium Dodecyl ◽

Mean Square Displacement ◽

Dynamics Simulation ◽

Oil Droplets ◽

Hydration Layer ◽

Oil Droplet

Heavy oil in crude oil flooding is extremely difficult to extract due to its high viscosity and poor fluidity. In this paper, molecular dynamics simulation was used to study the emulsification behavior of sodium dodecyl sulfonate (SDSn) micelles on heavy oil droplets composed of asphaltenes (ASP) at the molecular level. Some analyzed techniques were used including root mean square displacement, hydrophile-hydrophobic area of an oil droplet, potential of mean force, and the number of hydrogen bonds between oil droplet and water phase. The simulated results showed that the asphaltene with carboxylate groups significantly enhances the hydration layer on the surface of oil droplets, and SDSn molecules can change the strength of the hydration layer around the surface of the oil droplets. The water bridge structure between both polar heads of the surfactant was commonly formed around the hydration layer of the emulsified oil droplet. During the emulsification of heavy oil, the ratio of hydrophilic hydrophobic surface area around an oil droplet is essential. Molecular dynamics method can be considered as a helpful tool for experimental techniques at the molecular level.

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MD Analysis of Effect of Relative Humidity on Molecular Chain’s Network Structure of PEM

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.725.238 ◽

2016 ◽

Vol 725 ◽

pp. 238-242

Author(s):

Isamu Riku ◽

Keisuke Kawanishi ◽

Koji Mimura

Keyword(s):

Molecular Dynamics ◽

Relative Humidity ◽

Computational Model ◽

Network Structure ◽

Water Channel ◽

High Density ◽

Nafion Membrane ◽

Water Molecules ◽

Low Density ◽

Density Of Water

To clarify the effect of relative humidity on molecular chain’s network structure, we at first employ Molecular Dynamics (MD) method to constitute the computational model for Nafion membrane, in which the water channel is artificially reproduced with an aggregation of water molecules. And then, relaxation calculation is performed and a relatively stable microstructure of Nafion membrane is derived. It is found that the regions of relatively low density of molecular chain’s network appear interchangeably together with those of relatively high density of water molecules.

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Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

PLoS Computational Biology ◽

10.1371/journal.pcbi.1007870 ◽

2020 ◽

Vol 16 (4) ◽

pp. e1007870 ◽

Cited By ~ 7

Author(s):

Andreas Haahr Larsen ◽

Yong Wang ◽

Sandro Bottaro ◽

Sergei Grudinin ◽

Lise Arleth ◽

...

Keyword(s):

Molecular Dynamics ◽

Neutron Scattering ◽

Molecular Dynamics Simulations ◽

Small Angle ◽

Scattering Data ◽

X Ray ◽

Dynamics Simulations

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Conformational states of Zika virus non-structural protein 3 determined by molecular dynamics simulations with small-angle X-Ray scattering data

Progress in Biophysics and Molecular Biology ◽

10.1016/j.pbiomolbio.2018.09.005 ◽

2019 ◽

Vol 143 ◽

pp. 13-19

Author(s):

Guanhua Zhu ◽

Ankita Pan ◽

Gerhard Grüber ◽

Lanyuan Lu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Small Angle ◽

Zika Virus ◽

Scattering Data ◽

Structural Protein ◽

Conformational States ◽

X Ray ◽

X Ray Scattering ◽

Dynamics Simulations

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Solution structure of macromolecules using small angle neutron scattering and molecular simulations

EPJ Web of Conferences ◽

10.1051/epjconf/202023603003 ◽

2020 ◽

Vol 236 ◽

pp. 03003

Author(s):

Jayesh S. Bhatt

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Neutron Scattering ◽

Small Angle ◽

Small Angle Neutron Scattering ◽

Solution Structure ◽

Molecular Simulations ◽

Liquid Solution ◽

Scattering Data ◽

Monte Carlo Techniques

An introductory account of using molecular simulations to deduce solution structure of macromolecules using small angle neutron scattering data is presented for biologists. The presence of a liquid solution provides mobility to the molecules, making it difficult to pin down their structure. Here a simple introduction to molecular dynamics and Monte Carlo techniques is followed by a recipe to use the output of the simulations along with the scattering data in order to infer the structure of macromolecules when they are placed in a liquid solution. Some practical issues to be watched for are also highlighted.

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