Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2017 at "Chemical Physics Letters"
DOI: 10.1016/j.cplett.2017.03.034
Abstract: Abstract The absolute binding free energy of an inhibitor to HIV-1 Protease (PR) was determined throughout evaluation of the non-bonded interaction energy difference between the two bound and unbound states of the inhibitor and surrounding… read more here.
Keywords: using non; absolute binding; binding free; equilibrium molecular ... See more keywords
Reverse non-equilibrium molecular dynamics simulations on the thermal conductivity of three-dimensional graphene nano-ribbon foams
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Physics and Chemistry of Solids"
DOI: 10.1016/j.jpcs.2019.109130
Abstract: Abstract In this study, thermal conducting characteristics of a novel hybrid nanostructure consisting of covalently bonded graphene nanoribbon units with/without fullerenes are investigated by performing reverse non-equilibrium molecular dynamics simulations. Simulation results imply that the… read more here.
Keywords: non equilibrium; dynamics simulations; molecular dynamics; reverse non ... See more keywords
Non equilibrium molecular dynamics simulation study of thermal conductivity in doped graphene nanoribbons
Sign Up to like & getrecommendations! Published in 2019 at "Physica B: Condensed Matter"
DOI: 10.1016/j.physb.2018.12.026
Abstract: Abstract Thermal conductivity of graphene nanoribbons modified by atomic substitution is studied by molecular dynamics simulations. The substitutional doping by nitrogen, boron or silicon results in a non-linear decrease of thermal conductivity (κ) as the… read more here.
Keywords: non equilibrium; graphene nanoribbons; molecular dynamics; thermal conductivity ... See more keywords
Controlling hydrogen release from remaining-intact Clathrate hydrates by electromagnetic fields: molecular engineering via microsecond non-equilibrium molecular dynamics
Sign Up to like & getrecommendations! Published in 2022 at "RSC Advances"
DOI: 10.1039/d1ra07471g
Abstract: In view of the recently-predicted hydrogen release from type-II (sII) clathrate hydrates in the general 140–180 K temperature range [J. Phys. Chem. C, 125, 8430–8439 (2021)], we have investigated in the present study, by means… read more here.
Keywords: hydrogen; clathrate hydrates; non equilibrium; hydrogen release ... See more keywords
Semiexperimental equilibrium molecular structures of the maleimide and phthalimide
Sign Up to like & getrecommendations! Published in 2019 at "Molecular Physics"
DOI: 10.1080/00268976.2018.1510139
Abstract: ABSTRACT Semiexperimental (SE) equilibrium molecular structures of the title compounds are determined using rotational and ab initio data. Cubic force constants for the parent molecules and a number of isotopologues are calculated at the B2PLYP… read more here.
Keywords: semiexperimental equilibrium; equilibrium molecular; basis; correlation consistent ... See more keywords
Interfacial thermal resistance calculations for weak solid–liquid atom interactions using equilibrium molecular dynamics
Sign Up to like & getrecommendations! Published in 2023 at "Molecular Simulation"
DOI: 10.1080/08927022.2023.2202763
Abstract: ABSTRACT This study investigates the use of equilibrium molecular dynamics (EMD) simulations for determining interfacial thermal resistance (ITR) at solid-liquid interfaces. The Green-Kubo theorem is typically used for this purpose, but it may not be… read more here.
Keywords: using instantaneous; interfacial thermal; solid liquid; molecular dynamics ... See more keywords
Interpretation of apparent thermal conductivity in finite systems from equilibrium molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2021 at "Physical Review B"
DOI: 10.1103/physrevb.103.035417
Abstract: We propose a way to properly interpret the apparent thermal conductivity obtained for finite systems using equilibrium molecular dynamics simulations (EMD) with fixed or open boundary conditions in the transport direction. In such systems the… read more here.
Keywords: apparent thermal; finite systems; molecular dynamics; thermal conductivity ... See more keywords