scholarly journals Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

2012 ◽  
Vol 116 (29) ◽  
pp. 8375-8382 ◽  
Author(s):  
David Shirvanyants ◽  
Feng Ding ◽  
Douglas Tsao ◽  
Srinivas Ramachandran ◽  
Nikolay V. Dokholyan
Keyword(s):  
Molecular Dynamics ◽  
Simulation Method ◽  
Protein Characterization ◽  
Discrete Molecular Dynamics

scholarly journals Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

2009 ◽  
Vol 131 (7) ◽  
pp. 2541-2546 ◽  
Author(s):  
Costin M. Gherghe ◽  
Christopher W. Leonard ◽  
Feng Ding ◽  
Nikolay V. Dokholyan ◽  
Kevin M. Weeks
Keyword(s):  
Molecular Dynamics ◽  
Tertiary Structures ◽  
Discrete Molecular Dynamics

Femtosecond photoelectron spectroscopy of the I2− anion: A semiclassical molecular dynamics simulation method

1999 ◽  
Vol 110 (8) ◽  
pp. 3736-3747 ◽  
Author(s):  
Victor S. Batista ◽  
Martin T. Zanni ◽  
B. Jefferys Greenblatt ◽  
Daniel M. Neumark ◽  
William H. Miller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Photoelectron Spectroscopy ◽  
Simulation Method ◽  
Dynamics Simulation

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

scholarly journals Molecular Dynamics Study on the Mechanism of Nanoscale Jet Instability Reaching Supercritical Conditions

2018 ◽  
Vol 8 (10) ◽  
pp. 1714 ◽  
Author(s):  
Qingfei Fu ◽  
Yunxiao Zhang ◽  
Chaojie Mo ◽  
Lijun Yang
Keyword(s):  
Molecular Dynamics ◽  
Growth Rate ◽  
Theoretical Result ◽  
Molecular Model ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Jet Instability ◽  
Subcritical Region ◽  
Thermodynamic Conditions ◽  
Spatio Temporal

This paper investigates the characteristics of a nitrogen jet (the thermodynamic conditions ranging from subcritical to supercritical) ejected into a supercritical nitrogen environment using the molecular dynamics (MD) simulation method. The thermodynamic properties of nitrogen obtained by molecular dynamics show good agreement with the Soave-Redlich-Kwong (SRK) equation of state (EOS). The agreement provides validation for this nitrogen molecular model. The molecular dynamics simulation of homogeneous nitrogen spray is carried out in different thermodynamic conditions from subcritical to supercritical, and a spatio-temporal evolution of the nitrogen spray is obtained. The interface of the nitrogen spray is determined at the point where the concentration of ejected fluid component reaches 50%, since the supercritical jet has no obvious vapor-liquid interface. A stability analysis of the transcritical jets shows that the disturbance growth rate of the shear layer coincides very well with the classical theoretical result at subcritical region. In the supercritical region, however, the growth rate obtained by molecular dynamics deviates from the theoretical result.

Gradient-Driven Diffusion Using Dual Control Volume Grand Canonical Molecular Dynamics (DCV-GCMD)

1995 ◽  
Vol 408 ◽  
Author(s):  
Frank Van Swol ◽  
Grant S. Heffelfinger
Keyword(s):  
Molecular Dynamics ◽  
Chemical Potential ◽  
Control Volume ◽  
Simulation Method ◽  
Steady State Mode ◽  
Transient Phenomena ◽  
Insertion And Deletion ◽  
Separate Control ◽  
Control Volumes ◽  
Grand Canonical

AbstractRecently we developed a new nonequilibrium molecular simulation method [1] that allows the direct study of interdiffusion in multicomponent mixtures. The method combines stochastic insertion and deletion moves characteristic of grand canonical (GC) simulations with molecular dynamics (MD) to control the chemical potential μi of a species i. Restricting the insertions and deletions to two separate control volumes (CV's) one can apply different μ's in distinct locations, and thus create chemical potential gradients. DCV-GCMD can be used to study transient phenomena such as the filling of micropores or used in steady-state mode to determine the diffusion coefficients in multicomponent fluid mixtures. We report on the effects of molecular interactions and demonstrate how in a sufficiently nonideal ternary mixture this can lead to up-hill or reverse diffusion. In addition we introduce a novel extension of DCV-GCMD that is specifically designed for the study of gradient-driven diffusion of molecules that are simply too large to be inserted and deleted.

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