scholarly journals Thermodynamics of strongly‐coupled Yukawa systems near the one‐component‐plasma limit. II. Molecular dynamics simulations

1994 ◽  
Vol 101 (11) ◽  
pp. 9885-9893 ◽  
Author(s):  
R. T. Farouki ◽  
S. Hamaguchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Strongly Coupled ◽  
Component Plasma ◽  
The One ◽  
Dynamics Simulations

Substrate induced freezing, melting and depinning transitions in two-dimensional liquid crystalline systems

2022 ◽  
Author(s):  
Bharti bharti ◽  
Debabrata Deb
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystals ◽  
Molecular Dynamics Simulations ◽  
Liquid Crystalline ◽  
Two Dimensional ◽  
One Dimensional ◽  
The One ◽  
Dynamics Simulations

We use molecular dynamics simulations to investigate the ordering phenomena in two-dimensional (2D) liquid crystals over the one-dimensional periodic substrate (1DPS). We have used Gay-Berne (GB) potential to model the...

X-ray Scattering Measurements of the Ag(111) Surface Thermal Expansion

2001 ◽  
Vol 678 ◽  
Author(s):  
Cristian E. Botez ◽  
William C. Elliott ◽  
Paul F. Miceli ◽  
Peter W. Stephens
Keyword(s):  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Molecular Dynamics Simulations ◽  
Temperature Interval ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Scattering ◽  
Scattering Measurements ◽  
The One ◽  
Dynamics Simulations

AbstractWe have used synchrotron X-ray diffraction to study the thermal expansion of the Ag(111) surface. Throughout the temperature interval between 300 and 1100K, we observed that the separation between the first and the second atomic layers at the surface, 12 d, differs from its bulk counterpart, d, by less than 1%, indicating that the thermal expansion at the surface is similar to the one in the bulk. This result represents the first experimental confirmation of the predictions from molecular dynamics simulations, which indicate a small enhancement of the anharmonic effects at this surface.

scholarly journals Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

2019 ◽  
Author(s):  
Bradley W. Treece ◽  
Frank Heinrich ◽  
Arvind Ramanathan ◽  
Mathias Lösche
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Real Space ◽  
Time Averaging ◽  
One Dimensional ◽  
Neutron Reflection ◽  
Interfacial Structures ◽  
Associated Proteins ◽  
The One ◽  
Dynamics Simulations

AbstractWe present a method to incorporate structural results from neutron reflectometry, a technique that determines interfacial structures such as protein-membrane complexes at a solid surface, into molecular dynamics simulations. By analyzing component volume occupancy profiles, which describe the one-dimensional distribution of a particular molecular component within an interfacial architecture, we construct a real-space constraint in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown for an earlier investigation where an NR-derived structure was well captured by an independent MD simulation, and may lead to faster equilibration of ensemble structures. We further show that time averaging of the observable when biasing with this approach permits fluctuations about the average, which are necessary for conformational exploration of the protein. The method described here also provides insights into systems that are characterized by NR and MD when the two show slight differences in their profiles. This is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and take prohibitively long to equilibrate in simulations.

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