Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems
A dynamical approach to nonequilibrium molecular dynamics (D-NEMD), proposed in the
1970s by Ciccotti et al., is undergoing a renaissance and is having increasing impact in the …
1970s by Ciccotti et al., is undergoing a renaissance and is having increasing impact in the …
Molecular Dynamics Method for Supercritical CO2 Heat Transfer: A Review
This paper reviews molecular dynamics (MD) concepts on heat transfer analysis of
supercritical CO2, and highlights the major parameters that can affect the accuracy of …
supercritical CO2, and highlights the major parameters that can affect the accuracy of …
Particle-shape-, temperature-, and concentration-dependent thermal conductivity and viscosity of nanofluids
In this study, using the Green-Kubo-method-based molecular dynamics simulations,
correlations for predicting the thermophysical properties of nanofluids are developed based …
correlations for predicting the thermophysical properties of nanofluids are developed based …
Transport coefficients of the Lennard-Jones fluid close to the freezing line
Molecular dynamics simulations have been carried out along four Lennard-Jones (LJ) fluid
isomorphs close to the freezing line, covering a temperature, T, in the range of 0.8–350 and …
isomorphs close to the freezing line, covering a temperature, T, in the range of 0.8–350 and …
Dynamical nonequilibrium molecular dynamics simulations reveal allosteric networks, signal transduction mechanisms, and sites associated with drug resistance in …
B Balega, M Beer, J Spencer, G Colombo… - Molecular …, 2024 - Taylor & Francis
The dynamical approach to nonequilibrium molecular dynamics (D-NEMD), conceptualised
by Ciccotti et al. in the 1970s, has seen resurgence in recent years. In the biomolecular …
by Ciccotti et al. in the 1970s, has seen resurgence in recent years. In the biomolecular …
Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions
Exact values for bulk and shear viscosity are important to characterize a fluid, and they are a
necessary input for a continuum description. Here we present two novel methods to compute …
necessary input for a continuum description. Here we present two novel methods to compute …
Non-equilibrium by molecular dynamics: a dynamical approach
Some time ago, Ciccotti and Jacucci [Phys. Rev. Lett. 1975; 35: 789-792]–on the basis of
Onsager regression hypothesis as explained by Kubo–suggested and implemented an …
Onsager regression hypothesis as explained by Kubo–suggested and implemented an …
Longitudinal viscosity of two-dimensional Yukawa liquids
The longitudinal viscosity η l is obtained for a two-dimensional (2D) liquid using a Green-
Kubo method with a molecular dynamics simulation. The interparticle potential used has the …
Kubo method with a molecular dynamics simulation. The interparticle potential used has the …
Single trajectory transport coefficients and the energy landscape by molecular dynamics simulations
The Green–Kubo (GK) method is widely used to calculate the transport coefficients of model
liquids by Molecular Dynamics (MD) simulation. A reformulation of GK was proposed by …
liquids by Molecular Dynamics (MD) simulation. A reformulation of GK was proposed by …
Volume viscosity and ultrasonic relaxation of ethanol–water mixtures studied by molecular dynamics simulations
T Yamaguchi - Physical Chemistry Chemical Physics, 2022 - pubs.rsc.org
The volume viscosity of ethanol–water mixtures at various compositions was calculated by
means of equilibrium molecular dynamics simulations, and the results were compared with …
means of equilibrium molecular dynamics simulations, and the results were compared with …