Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

Dynamics of a Delayed Epidemic Model with Beddington-DeAngelis ‎Incidence Rate and a Constant Infectious Period

In this paper, an SIR epidemic model with an infectious period and a non-linear Beddington-DeAngelis type incidence rate function is considered. The dynamics of this model depend on the reproduction number R0. Accurately, if R0 < 1, we show the global asymptotic stability of the disease-free equilibrium by analyzing the corresponding characteristic equation and using compa...

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework.

In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non-covalent bonding in drug-receptor systems. I show that most of the pitfalls and entanglements for the binding free energy evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues ...

Statistical Physics ( PHY 831 ) : Part 1 - The foundations Phillip

Part 1: (LL, PB) Foundations: (11 lectures) History of thermodynamics, kinetic theory and equilibrium statistical mechanics. Axioms of equilibrium statistical physics, Master equation, Liouville equation. Equilibrium conditions, Boltzmann weights and partition functions. Free energies and relation to partition functions. Survey of many particle, spin and field systems: the case of classical par...

Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations

Bayesian inference is used to obtain self-consistent estimates of free energies and position-dependent diffusion coefficients along complex reaction coordinates from molecular dynamics simulation trajectories. Effectively, exact solutions for the dynamics of a diffusive model are matched globally to the observed molecular dynamics data. The approach is first tested for a simple onedimensional d...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations