Related papers: Experimental Free Energy Surface Reconstruction Fr…
The Jarzynski equality, which relates equilibrium free-energy difference to an average of non-equilibrium work, plays a central role in modern non-equilibrium statistical thermodynamics. In this paper, we study a weaker consequence of this…
We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…
Jarzynski Equality (JE) and the thermodynamic integration method are conventional methods to calculate free energy difference (FED) between two equilibrium states with constant temperature of a system. However, a number of ensemble samples…
Using a recently developed technique to estimate the equilibrium free energy of glassy materials, we explore if equilibrium simulation methods can be used to estimate the solubility of amorphous solids. As an illustration, we compute the…
One particle in a classical perfect gas is driven out of equilibrium by changing its mass over a short time interval. The work done on the driven particle depends on its collisions with the other particles in the gas. This model thus…
A general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the…
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem…
We investigate the kinetics and the free energy landscape of the crystallization of hard spheres from a supersaturated metastable liquid though direct simulations and forward flux sampling. In this first paper, we describe and test two…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecular behavior. These free energy surfaces are most commonly…
Classically, surface tension is seen as a force per unit length or as energy per unit area. The surface energy is calculated thermodynamically on the surface of a mathematical layer with no thickness. The surface energy concept is certainly…
We report extensive self-consistent calculations of jellium surface energies, by going beyond the local-density approximation. The density-response function of a bounded free-electron gas is evaluated within the random-phase approximation,…
The excess free energy of a molecular cluster is a key quantity in models of the nucleation of droplets from a metastable vapour phase; it is often viewed as the free energy arising from the presence of an interface between the two phases.…
The free-energy difference $\Delta F$ between two high-dimensional systems is notoriously difficult to compute, but very important for many applications, such as drug discovery. We demonstrate that an unconventional definition of work…
We extract values for the free symmetry energy as a function of the fragment size (the proton number Z) from antisymmetrized molecular dynamics (AMD) calculations of calcium collisions. Simple statistical physics describe well the…
The numerous combinations of cations and anions turn out possible to produce ionic liquids with fine-tuned properties once the correlation with the molecular structure is known. In this sense, computer simulations are useful tools to…
We discuss and qualify a previously unnoticed connection between two different phenomena in the physics of nanoscale friction, general in nature and also met in experiments including sliding emu- lations in optical lattices, and protein…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
The construction of accurate interatomic potentials, and related fields of forces, from equilibrium conformational distributions of molecules is a crucial step in coarse-grained modeling. In this work we show that in order to develop…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…