Role of donor–acceptor macrocycles in sequence specific peptide recognition and their optoelectronic properties: a detailed computational insight

2016 ◽  
Vol 18 (30) ◽  
pp. 20682-20690 ◽  
Author(s):  
Arkamita Bandyopadhyay ◽  
Swapan K Pati
Keyword(s):  
Molecular Dynamics ◽  
Optoelectronic Properties ◽  
Peptide Recognition ◽  
Classical Molecular Dynamics ◽  
Donor Acceptor ◽  
Specific Peptide

We have demonstrated sequence specific peptide recognition by donor–acceptor macrocycles by performing DFT and classical molecular dynamics studies.

scholarly journals Deformation twinning and the role of amino acids and magnesium in calcite hardness from molecular simulation

2015 ◽  
Vol 17 (31) ◽  
pp. 20178-20184 ◽  
Author(s):  
A. S. Côté ◽  
R. Darkins ◽  
D. M. Duffy
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Simulation ◽  
Elastic Properties ◽  
Deformation Twinning ◽  
Pure Crystal ◽  
Classical Molecular Dynamics ◽  
Deformation Twins

We employ classical molecular dynamics to calculate elastic properties and to model the nucleation and propagation of deformation twins in calcite, both as a pure crystal and with magnesium and aspartate inclusions.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal–organic frameworks

2021 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Zeyu Zhang ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Catalytic Activity ◽  
Metal Organic Frameworks ◽  
Structural Flexibility ◽  
Classical Molecular Dynamics ◽  
Structural Deformations ◽  
Metal Organic

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal–organic frameworks.

scholarly journals Energy dissipation to tungsten surfaces upon hot-atom and Eley–Rideal recombination of H2

2018 ◽  
Vol 20 (33) ◽  
pp. 21334-21344 ◽  
Author(s):  
Oihana Galparsoro ◽  
H. Fabio Busnengo ◽  
Alejandra E. Martinez ◽  
Joseba Iñaki Juaristi ◽  
Maite Alducin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Energy Dissipation ◽  
Molecular Dynamics Simulations ◽  
Surface Structure ◽  
Hole Pair ◽  
Electron Hole ◽  
Classical Molecular Dynamics ◽  
Electron Hole Pair ◽  
Dynamics Simulations

Adiabatic and nonadiabatic quasi-classical molecular dynamics simulations are performed to investigate the role of electron–hole pair excitations in hot-atom and Eley–Rideal H2 recombination mechanisms on H-covered W(100). The influence of the surface structure is analyzed by comparing with previous results for W(110).

scholarly journals Delineating the role of ripples on the thermal expansion of 2D honeycomb materials: graphene, 2D h-BN and monolayer (ML)-MoS2

2017 ◽  
Vol 19 (16) ◽  
pp. 10518-10526 ◽  
Author(s):  
P. Anees ◽  
M. C. Valsakumar ◽  
B. K. Panigrahi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
2D Crystals

Thermally excited ripples are inevitable in 2D crystals, and they can affect the thermophysical properties of these materials significantly. We delineated the role of ripples on the thermal expansion of 2D honeycomb materials using classical molecular dynamics simulations.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

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