Molecular dynamics simulations of n-butane and n-hexane diffusion in silicalite

1995 ◽  
Vol 448 (1932) ◽  
pp. 143-160 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Guest Molecule ◽  
Measured Data ◽  
Zeolite Framework ◽  
Adsorbed Molecules ◽  
Molecule Interactions ◽  
Dynamics Simulations ◽  
And Diffusion ◽  
Good Agreement

We report molecular dynamics simulations of n-butane and n-hexane adsorbed in the zeolite silicalite. These systems have been modelled within a rigid framework approximation and a Ryckaert-Bellemans model was adopted to describe the adsorbed molecules. The parametrization due to June, Bell and Theodorou has been used to describe the host-guest molecule interactions. Long simulations (1000 ps) have been performed, modelling these systems at a variety of sorbate loadings and temperatures. These have allowed us to investigate how the presence of the zeolite framework affects the thermodynamic properties, confomational distributions and diffusion related properties of the adsorbed molecules, and their response to changes in the loading and temperature. We have obtained estimates of the diffusion coefficients and activation energies which are in good agreement with experimentally measured data.

Size-Dependent Elasticity of Silicon Nanowires

2009 ◽  
Vol 60-61 ◽  
pp. 315-319 ◽  
Author(s):  
W.W. Zhang ◽  
Qing An Huang ◽  
H. Yu ◽  
L.B. Lu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Silicon Nanowires ◽  
First Principles ◽  
Si Nanowires ◽  
Size Dependent ◽  
Reconstructed Surfaces ◽  
Strain Relationship ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular dynamics simulations are carried out to characterize the mechanical properties of [001] and [110] oriented silicon nanowires, with the thickness ranging from 1.05nm to 3.24 nm. The nanowires are taken to have ideal surfaces and (2×1) reconstructed surfaces, respectively. A series of simulations for square cross-section Si nanowires have been performed and Young’s modulus is calculated from energy–strain relationship. The results show that the elasticity of Si nanowires is strongly depended on size and surface reconstruction. Furthermore, the physical origin of above results is analyzed, consistent with the bond loss and saturation concept. The results obtained from the molecular dynamics simulations are in good agreement with the values of first-principles. The molecular dynamics simulations combine the accuracy and efficiency.

Molecular simulations of analyte partitioning and diffusion in liquid crystal sensors

2020 ◽  
Vol 5 (1) ◽  
pp. 304-316 ◽  
Author(s):  
Jonathan K. Sheavly ◽  
Jake I. Gold ◽  
Manos Mavrikakis ◽  
Reid C. Van Lehn
Keyword(s):  
Molecular Dynamics ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Molecular Simulations ◽  
Activation Time ◽  
Dynamics Simulations ◽  
And Diffusion ◽  
Analyte Transport

Molecular dynamics simulations predict the effect of analyte transport on the activation time of chemoresponsive liquid crystal sensors to improve sensor selectivity.

Thermal Conductivity of Amorphous and Crystalline SiO2 Nano-Films from Molecular Dynamics Simulations

2012 ◽  
Vol 501 ◽  
pp. 64-69 ◽  
Author(s):  
Yan He ◽  
Yuan Zheng Tang ◽  
Man Ding ◽  
Lian Xiang Ma
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Film Thickness ◽  
Molecular Dynamics Simulations ◽  
Grain Morphology ◽  
Nonequilibrium Molecular Dynamics ◽  
Calculated Temperature ◽  
Dynamics Simulations ◽  
Different Thickness ◽  
Good Agreement

Normal thermal conductivity of amorphous and crystalline SiO2nano-films is calculated by nonequilibrium molecular dynamics (NEMD) simulations in the temperature range from 100 to 700K and thicknesses from 2 to 6nm. The calculated temperature and thickness dependences of thermal conductivity are in good agreement with previous literatures. In the same thickness, higher thermal conductivity is obtained for crystalline SiO2nano-films. And more importantly, for amorphous SiO2nano-films, thickness can be any direction of x, y, z-axis without effect on the normal thermal conductivity, for crystalline SiO2nano-films, the different thickness directions obtain different thermal conductivity results. The different results of amorphous and crystalline SiO2nano-films simply show that film thickness and grain morphology will cause different effects on thermal conductivity.

Comparison of the Hydration and Diffusion of Protons in Perfluorosulfonic Acid Membranes with Molecular Dynamics Simulations

2008 ◽  
Vol 112 (42) ◽  
pp. 13273-13284 ◽  
Author(s):  
Shengting Cui ◽  
Junwu Liu ◽  
Myvizhi Esai Selvan ◽  
Stephen J. Paddison ◽  
David J. Keffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Perfluorosulfonic Acid ◽  
Perfluorosulfonic Acid Membranes ◽  
Dynamics Simulations ◽  
And Diffusion

Rheological Properties of Water Films Nanoconfined in Parallel Au Plates by Molecular Dynamics Simulations

2007 ◽  
Vol 121-123 ◽  
pp. 1109-1114
Author(s):  
M.L. Liao ◽  
Shin Pon Ju ◽  
Jenn Sen Lin ◽  
Y.S. Lin
Keyword(s):  
Molecular Dynamics ◽  
Shear Rate ◽  
Molecular Dynamics Simulations ◽  
Rheological Properties ◽  
Shear Viscosity ◽  
Water Film ◽  
Water Molecules ◽  
Water Films ◽  
Dynamics Simulations ◽  
And Diffusion

Rheological properties of water films nanoconfined in two parallel Au plates are investigated with the aid of molecular dynamics simulations. The density distribution, velocity profile, and diffusion coefficients of the water film in a Couette flow are studied. Shear viscosity and its dependence on the shear rate of the water film are also examined in the present research. It is found that the density of the water molecules near the plates is much higher than that in the other regions. This indicates that many water molecules are adsorbed by the plates and adsorbed layers are formed in the vicinity of the plates. The diffusion of the whole film increases dramatically as the shear rate becomes greater than 1010 s-1. The shear viscosity decreases as the shear rate increases, especially for the water film with a small thickness, which indicates the shear-thinning behavior for viscosity of the nanoconfined film. Moreover, an increase in shear viscosity with a decrease in the film thickness can also be found in the present study.

scholarly journals Interrogating RNA-small molecule interactions with structure probing and AI augmented-molecular simulations

2021 ◽  
Author(s):  
Yihang Wang ◽  
Shaifaly Parmar ◽  
John S. Schneekloth ◽  
Pratyush Tiwary
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ligand Recognition ◽  
Binding Affinities ◽  
Structure Probing ◽  
Mutational Profiling ◽  
In Vitro Measurements ◽  
Molecule Interactions ◽  
Dynamics Simulations

While there is increasing interest in the study of RNA as a therapeutic target, efforts to understand RNA-ligand recognition at the molecular level lag far behind our understanding of protein-ligand recognition. This problem is complicated due to the more than ten orders of magnitude in timescales involved in RNA dynamics and ligand binding events, making it not straightforward to design experiments or simulations. Here we make use of artificial intelligence (AI)-augmented molecular dynamics simulations to directly observe ligand dissociation for cognate and synthetic ligands from a riboswitch system. The site-specific flexibility profiles from our simulations are in excellent agreement with in vitro measurements of flexibility using Selective 2' Hydroxyl Acylation analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP). Our simulations reproduce known binding affinity profiles for the cognate and synthetic ligands, and pinpoint how both ligands make use of different aspects of riboswitch flexibility. On the basis of our dissociation trajectories, we also make and validate predictions of pairs of mutations for both the ligand systems that would show differing binding affinities. These mutations are distal to the binding site and could not have been predicted solely on the basis of structure. The methodology demonstrated here shows how molecular dynamics simulations with all-atom force-fields have now come of age in making predictions that complement existing experimental techniques and illuminate aspects of systems otherwise not trivial to understand.

Sign in / Sign up

Export Citation Format

Share Document