Theoretical studies of transition states by the multioverlap molecular dynamics methods

2006 ◽  
Vol 124 (10) ◽  
pp. 104103 ◽  
Author(s):  
Satoru G. Itoh ◽  
Yuko Okamoto
Keyword(s):  
Molecular Dynamics ◽  
Transition States ◽  
Theoretical Studies ◽  
Molecular Dynamics Methods

scholarly journals Proton Transport Mechanism and Pathways in the Superprotonic Phase of M3H(AO4)2 Solid Acids from Ab Initio Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Boris Merinov ◽  
Sergey Morozov
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Dynamics Simulations ◽  
Experimental And Theoretical Studies ◽  
Superprotonic Phase

The proton transport mechanism in superprotonic phases of solid acids is a subject of experimental and theoretical studies for a number of years. Despite this, details of the mechanism still...

Microstructure evolution and plastic deformation of Ni47Co53 alloy under tension

CrystEngComm ◽  
2022 ◽  
Author(s):  
ruibo ma ◽  
Lili Zhou ◽  
Yong-Chao Liang ◽  
Ze-an Tian ◽  
Yun-Fei Mo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Rapid Solidification ◽  
Microstructural Evolution ◽  
Microstructure Evolution ◽  
Cooling Rates ◽  
Solidification Processes ◽  
Molecular Dynamics Methods

To investigate microstructural evolution and plastic deformation under tension conditions, the rapid solidification processes of Ni47Co53 alloy are first simulated by molecular dynamics methods at cooling rates of 1011, 1012...

scholarly journals Structural Properties of G,T-Parallel Duplexes

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Anna Aviñó ◽  
Elena Cubero ◽  
Raimundo Gargallo ◽  
Carlos González ◽  
Modesto Orozco ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Theoretical Studies ◽  
Duplex Structure ◽  
Strong Stabilization ◽  
The Stability ◽  
The Impact

The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

scholarly journals Molecular Dynamics Simulation of Zener Pinning by Differently Shaped and Oriented Particles

2021 ◽  
Vol 8 ◽  
Author(s):  
Yi Li ◽  
Jian Zhou ◽  
Runjie Li ◽  
Qingyu Zhang
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Pinning Force ◽  
Theoretical Studies ◽  
Constant Energy ◽  
Zener Pinning ◽  
Interaction Processes ◽  
Interface Characteristics ◽  
Theoretical Predictions ◽  
Ag Particle

Zener pinning between a curved Cu grain boundary (GB) and a differently shaped and oriented Ag particle has been simulated via molecular dynamics. The computed magnitudes of the maximum pinning force agreed with theoretical predictions only when the force was small. As the force increased, discrepancy became obvious. Through careful inspection of the structures of the Cu–Ag interfaces, detailed interaction processes, and variation of the Cu GB during the interaction, the discrepancy is found to correlate with GB faceting, which very likely reduces the maximum pinning force and facilitates boundary passage. GB anisotropy and/or interface characteristics are also found to slightly contribute to the discrepancy. These findings suggest that the assumption of an isotropic GB with constant energy utilized in previous theoretical studies for deriving the maximum pinning force might be inappropriate and that an accurate maximum pinning force could not be predicted without knowing the effects of GB evolution together with detailed properties of both GBs and interfaces.

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