Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and trustworthiness of the method

In this paper, mesoscopic lattice–Boltzmann method (LBM) and microscopic molecular dynamics simulation method were used to simulate droplet dynamic wetting under microgravity. In terms of LBM, the wetting process of a droplet on a solid wall surface was simulated by introducing the fluid–fluid and solid–fluid interactions. In terms of molecular dynamics simulation, the spreading process of water on gold surface was simulated. Calculation results showed that two kinds of calculation methods were based on the microscopic molecular theory or mesoscopic kinetics theory, and such models could effectively overcome the contact line paradox issue, which results from the macro-continuum assumption and non-slip boundary condition assumption. The spreading exhibits two-stage behavior: fast spreading and slow spreading stages. For the two simulation methods, the ratio of fast spreading stage duration to slow spreading duration, spreading capacity (equilibrium contact radius/initial radius), and the spreading exponent of the rapid stage were very close. However, the predictive spreading index of the slow spreading stage was different, owing to the different spreading mechanisms between meso- and nanoscales.

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A HYBRID MOLECULAR DYNAMICS SIMULATION METHOD FOR SOLIDS

Computational Methods in Sciences and Engineering 2003 ◽

10.1142/9789812704658_0055 ◽

2003 ◽

Author(s):

S. ITOH ◽

M. IGAMI

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Method ◽

Dynamics Simulation

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Computer simulation of complex of lysine dendrigraft with molecules of therapeutic KED peptide

ITM Web of Conferences ◽

10.1051/itmconf/20192402008 ◽

2019 ◽

Vol 24 ◽

pp. 02008

Author(s):

Igor Neelov ◽

Valerii Bezrodnyi ◽

Anna Marchenko ◽

Emil Fatullaev ◽

Sofia Miktaniuk

Keyword(s):

Molecular Dynamics ◽

Computer Simulation ◽

Molecular Dynamics Simulation ◽

Complex Formation ◽

Simulation Method ◽

Dynamics Simulation ◽

Stable Complex ◽

Target Organs ◽

Therapeutic Peptides ◽

Drug And Gene Delivery

Lysine dendrimers and dendrigrafts are often used in biomedicine for drug and gene delivery to different target organs or cells. In present paper the possibility of complex formation by lysine dendrigraft and 16 molecules of therapeutic KED peptide was investigated using molecular dynamics simulation method. A system containing of one dendrigraftt and 16 KED peptides in water were studied. It was shown that stable complex consisting of the dendrigraft and the peptide molecules formed and structure of this complex was studied. Similar complexes could be used in future for delivery of other therapeutic peptides to target organs.

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Molecular Dynamics Simulation Method

Encyclopedia of Microfluidics and Nanofluidics ◽

10.1007/978-0-387-48998-8_1052 ◽

2008 ◽

pp. 1391-1398

Author(s):

Dongyan Xu ◽

Deyu Li

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Method ◽

Dynamics Simulation

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Molecular Dynamics Simulation of Nanoindentation on Diamond Crystal [100] Surface

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.399-401.751 ◽

2011 ◽

Vol 399-401 ◽

pp. 751-759

Author(s):

Jian Liu ◽

Jin Xing Kong ◽

Da Jiang Lei ◽

Ya Lin Zhang ◽

Hai Feng Li ◽

...

Keyword(s):

Crystal Structure ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lattice Distortion ◽

Diamond Crystal ◽

Simulation Method ◽

Dynamics Simulation ◽

Bond Breaking ◽

Light Load ◽

Structure Changes

The nanoindentation of diamond crystal [100] surface is studied in this paper, by using molecular dynamics simulation method and Tersoff potential. The total number of atoms in the model is exceed to 2,000,000. The crystal structure changes and the bond formations of C atoms under pressure load are analyzed. A light load causes lattice distortion but cannot cause bond breaking or hybridization transition from sp3 to sp2. When the load is enough heavy, the energy be imposed on the workpiece will beyond the range of lattice distortion, which can cause bond break and hybridization transition from sp3 to sp2.

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Molecular Dynamics Simulations of Hot Electrons and Lattice Relaxation in Realistic Cascade Volumes

MRS Proceedings ◽

10.1557/proc-278-383 ◽

1992 ◽

Vol 278 ◽

Author(s):

A.M. Mazzone

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Molecular Dynamics Simulations ◽

Classical Mechanics ◽

Lattice Relaxation ◽

Simulation Method ◽

High Energy ◽

Hot Electrons ◽

Dynamics Simulation ◽

Dynamics Simulations

AbstractThis work presents a molecular dynamics simulation method designed to describe the processes of electron and lattice relaxation taking place in typical cascade volumes formed by high-energy implants. The simulation method is based on classical mechanics and includes the motions of electrons and nuclei. The results are in agreement with experiments.

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Molecular Dynamics Simulation of Rarefied Gaseous Flows in Nano-Channels

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.446-447.12 ◽

2013 ◽

Vol 446-447 ◽

pp. 12-17

Author(s):

Zhi Hong Mao ◽

Fu Bing Bao ◽

Yuan Lin Huang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Slip Velocity ◽

Average Velocity ◽

Single Layer ◽

Simulation Method ◽

Dynamics Simulation ◽

Channel Height ◽

Gaseous Flows ◽

Pressure Driven

Molecular dynamics simulation method was used to study the rarefied gaseous flows in nanochannels. A pressure-driven force was introduced to drive the gas to flow between two parallel walls. The effects of driven force magnitude and channel height were investigated. The results show that a single layer of gaseous molecules is adsorbed on the wall surface. The density of adsorption layer decreases with the increase of channel height, but doesnt vary with driven force. The velocity profile across the channel has the traditional parabolic shape. The average velocity and gas slip velocity on the wall increase linearly with the increase of pressure-driven force. The gas slip velocity decreases linearly with the increase of channel height. The ratio of slip to average velocity decreases linearly with the increase of channel height.

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