Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials

Using Molecular Dynamics Simulations to Understand Electron Beam Interactions with Macromolecules in Liquid-phase Transmission Electron Microscopy

Microscopy and Microanalysis ◽

10.1017/s1431927621010084 ◽

2021 ◽

Vol 27 (S1) ◽

pp. 2892-2893

Author(s):

John Smith ◽

Chang Liu ◽

Qian Chen

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Transmission Electron Microscopy ◽

Electron Beam ◽

Liquid Phase ◽

Transmission Electron ◽

Phase Transmission ◽

Neural Network Based Molecular Dynamics Simulations of Sputtering Processes

10.1109/escience51609.2021.00041 ◽

2021 ◽

Author(s):

Shokirbek Shermukhamedov ◽

Michael Probst ◽

Lei Chen

Keyword(s):

Neural Network ◽

Molecular Dynamics ◽

Artificial neural network correction for density-functional tight-binding molecular dynamics simulations

MRS Communications ◽

10.1557/mrc.2019.80 ◽

2019 ◽

Vol 9 (3) ◽

pp. 867-873 ◽

Cited By ~ 6

Author(s):

Junmian Zhu ◽

Van Quan Vuong ◽

Bobby G. Sumpter ◽

Stephan Irle

Keyword(s):

Neural Network ◽

Molecular Dynamics ◽

Artificial Neural Network ◽

Density Functional ◽

Tight Binding ◽

Artificial Neural ◽

Dynamics Simulations ◽

Image Position

Abstract

Characterizing interface structure between crystalline and ion bombarded silicon by transmission electron microscopy and molecular dynamics simulations

Applied Surface Science ◽

10.1016/j.apsusc.2020.148278 ◽

2021 ◽

Vol 540 ◽

pp. 148278

Author(s):

Alexander V. Rumyantsev ◽

Nikolay I. Borgardt ◽

Alexander S. Prikhodko ◽

Yuri A. Chaplygin

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Transmission Electron Microscopy ◽

Interface Structure ◽

Transmission Electron ◽

Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases

Journal of Molecular Modeling ◽

10.1007/s00894-019-3984-9 ◽

2019 ◽

Vol 25 (5) ◽

Cited By ~ 1

Author(s):

Karl M. García-Ruiz ◽

Andrés F. Marmolejo-Valencia ◽

Augusto González-Navejas ◽

Laura Dominguez ◽

Carlos Amador-Bedolla

Keyword(s):

Molecular Dynamics ◽

Small Molecules ◽

Using Molecular Dynamics Simulations to Compare the Stability of Lysenin Structures Obtained through X-ray Crystallography and Single-Particle Cryo-Electron Microscopy

Biophysical Journal ◽

10.1016/j.bpj.2017.11.1883 ◽

2018 ◽

Vol 114 (3) ◽

pp. 337a

Author(s):

Vivek Govind Kumar

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Single Particle ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

The Stability ◽

2P135 Analysis of translocation of tRNA molecules through ribosome using electron microscopy density map and molecular dynamics simulations(The 48th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.50.s106_1 ◽

2010 ◽

Vol 50 (supplement2) ◽

pp. S106

Author(s):

Hisashi Ishida

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

Annual Meeting ◽

Biophysical Society ◽

Density Map ◽

Membrane permeability of small molecules from unbiased molecular dynamics simulations

The Journal of Chemical Physics ◽

10.1063/5.0013429 ◽

2020 ◽

Vol 153 (12) ◽

pp. 124107 ◽

Cited By ~ 2

Author(s):

Andreas Krämer ◽

An Ghysels ◽

Eric Wang ◽

Richard M. Venable ◽

Jeffery B. Klauda ◽

...

Keyword(s):

Molecular Dynamics ◽

Small Molecules ◽

Membrane Permeability ◽

Low-energy-deposited Au clusters investigated by high-resolution electron microscopy and molecular dynamics simulations

Physical Review B ◽

10.1103/physrevb.62.10383 ◽

2000 ◽

Vol 62 (15) ◽

pp. 10383-10393 ◽

Cited By ~ 102

Author(s):

B. Pauwels ◽

G. Van Tendeloo ◽

W. Bouwen ◽

L. Theil Kuhn ◽

P. Lievens ◽

...

Keyword(s):

Electron Microscopy ◽

Molecular Dynamics ◽

High Resolution ◽

High Resolution Electron Microscopy ◽

Low Energy ◽

Au Clusters ◽

Resolution Electron ◽

Binding affinity between small molecules in solvent and polymer film using molecular dynamics simulations

Colloids and Surfaces A Physicochemical and Engineering Aspects ◽

10.1016/j.colsurfa.2017.02.075 ◽

2017 ◽

Vol 522 ◽

pp. 152-160 ◽

Cited By ~ 5

Author(s):

Enqiang Lin ◽

Xiaorong You ◽

Robert M. Kriegel ◽

Ronald D. Moffitt ◽

Romesh C. Batra

Keyword(s):

Molecular Dynamics ◽

Small Molecules ◽

Polymer Film ◽

Binding Affinity ◽