We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable dynamical system. We then extend the class of non-...
We review a dynamical approach to non‐equilibrium MD (D‐NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non‐equilibrium state produced by a suitable dynamical system. We then extend the class of non...
The hexagonal string phase appears approximately at a value of half shear thinning for the MD system, whereas the BD liquid manifests the string phase only at much higher equivalent shear rates at the onset of the second Newtonian plateau. These differences are explained in terms of the more ...
The shear viscosity of n-butane has been computed by the method of molecular dynamics (MD), by both the Green-Kubo technique and a non-equilibrium method employing a weak fictitious external field inducing a symmetric velocity gradient (pure deformational flow). In this last case, non-...
Corrigendum to ‘Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations’ Journal of Molecular Graphics and Modelling, Volume 103, March 2021, Pages 107805 Nguyen Thi Mai, Ngo Thi Lan, Thien Y Vu, Phuong Thi Mai Duong, Nguyen Thanh Tung, Huong...
1011 K s−1,1012 K s−1,1013 K s−1, and instant quench (more MD data are shown inSupplementary Fig. 3). Yellow curve is the extracted equilibrium line from MD data. To reproduce the equilibrium line through equation (7), the expectedWandμshould have the forms of...
Present address: Dept. of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21218, USA Authors and Affiliations Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA Lisa M. Alexander, Daniel H. Goldman & Carlos Bustamante ...
DSMC (direct simulation Monte Carlo) simulations are employed with the dynamic molecular collision (DMC) model and the multi-stage (MS) model based on molecular dynamics (MD) simulation of nitrogen molecules. Those models do not need any empirical parameters such as inelastic collision parameter ...
We review our quantum chemical molecular dynamics (QM/MD)-based studies of carbon nanostructure formation under nonequilibrium conditions that were conducted over the past 10+ years. Fullerene, carbon nanotube, and graphene formation were simulated on th
-exponential kinetic behaviours. Although the interpretation can be assisted by density functional theory (DFT), time-dependent DFT and molecular dynamics (MD) simulations3, the current understanding of the process needs to be refined down to the molecular level before descriptive and predictive models...