Growth Properties of the Si(100) Steps: A Molecular Dynamics Study

1991 ◽  
Vol 237 ◽  
Author(s):  
Christopher Roland ◽  
George H. Gilmer
Keyword(s):  
Molecular Dynamics ◽  
Surface Diffusion ◽  
Binding Sites ◽  
Activation Energies ◽  
Step Edge ◽  
Lower Activation ◽  
Growth Properties ◽  
Molecular Dynamics Methods ◽  
Energy Surfaces

ABSTRACTWe have mapped out the energy surfaces seen by a single silicon adatom over the Si(100) surface and Si(100) steps, using Molecular Dynamics methods. This identifies the most likely binding sites as well as the activation energies for diffusion over the terraces and steps. We find that only the 5e step with no rebonded atoms is a good sink for adatoms - the SA, rebonded Sb and Db steps are weak sinks. Because of a higher density of binding sites and lower activation energies for surface diffusion along die step edge, we expect mat growth at the Sb and Db steps take place much more readily man at the SA step.

Molecular Dynamics Studies of Defect Motion in a-Si:H

1994 ◽  
Vol 336 ◽  
Author(s):  
P. A. Fedders
Keyword(s):  
Molecular Dynamics ◽  
Time Evolution ◽  
First Principles ◽  
Activation Energies ◽  
Dangling Bond ◽  
Dangling Bonds ◽  
Relaxation Effects ◽  
Molecular Dynamics Methods ◽  
First Principles Molecular Dynamics

ABSTRACTFirst principles molecular dynamics methods are used to study the motion of defects including dangling bonds and H. We study motion among H passivating dangling bonds, bond centered H, and tetrahedral H. We find that relaxation effects can reduce activation energies by up to one eV. Our studies also include the actual simulation of the time evolution of an a-Si:H system for several picosec. Here we observe the motion of a dangling bond over several hops and the motion of an H atom by means dangling bond exchange.

Computer Simulation of Surface Diffusion of Silver

1993 ◽  
Vol 317 ◽  
Author(s):  
A. Kumagai ◽  
K. Ogawa ◽  
Masao Doyama
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Surface Diffusion ◽  
Activation Energies ◽  
Binding Energies ◽  
Embedded Atom ◽  
Atom Clusters

ABSTRACTThe binding energies to silver (111) surface of a silver ad-atom and its cluster have been calculated. The activation energies of motion of these ad-atom clusters, vacancies and divacancies on silver (111) surface have been calculated by use of n-body embedded atom potentials and molecular dynamics.

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

scholarly journals Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1051
Author(s):  
Edgardo Becerra ◽  
Giovanny Aguilera-Durán ◽  
Laura Berumen ◽  
Antonio Romo-Mancillas ◽  
Guadalupe García-Alcocer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Binding Energy ◽  
Binding Site ◽  
Binding Sites ◽  
Adenosine Monophosphate ◽  
Competitive Inhibitor ◽  
Umbrella Sampling ◽  
Coarse Grained ◽  
Nucleotide Polymorphisms

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

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