Related papers: Flexible framework of computing binding free energ…
The free energy of barium titanate is computed around the Curie temperature as a function of polarization from the first-principles derived effective hamiltonian of Zhong, Vanderbilt and Rabe [Phys. Rev. Lett. 73, 1861 (1994)], through…
Simulating the irreversible quantum dynamics of exciton and electron transfer problems poses a nontrivial challenge. Because the irreversibility of the system dynamics is a result of quantum thermal activation and dissipation caused by the…
We used a thermodynamic integration scheme, which is specifically designed for disordered systems, to compute the interfacial free energy of the solid-liquid interface in the hard-sphere model. We separated the bulk contribution to the…
We propose a new method for the problems of computing free energy and surface pressure for various statistical mechanics models on a lattice $\Z^d$. Our method is based on representing the free energy and surface pressure in terms of…
The key problem of statistical physics standing over one hundred years is how to exactly calculate the partition function (or free energy) of many-body interaction systems, which severely hinders application of the theory for realistic…
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand between the receptor…
We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force field to the SAMPL9 bCD host-guest binding free energy prediction challenge that comprises a combination of complexes formed between five phenothiazine…
The van der Waals and Casimir-Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. This configuration models the…
Simulation of a system consisted of free particle bouncing on a vertically vibrated based is performed. Two different states, which are steady and unsteady energy transfer state are found. The vibrating based is hold at constant vibration…
The ground-state energy of a quantum impurity model can be calculated using the numerical renormalization group with a modified discretization scheme, with sufficient accuracy to reliably extract physical information about the system. The…
We present the concept, derivation, and implementation of dynamical configuration interaction, a quantum embedding theory that combines Green's function methodology with the many-body wave function. In a strongly-correlated active space, we…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
We show how thermodynamic properties of molecular models can be computed over a large, multidimensional parameter space by combining multistate reweighting analysis with a linear basis function approach. This approach reduces the…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
Different computational techniques in combination with molecular dynamics computer simulation are used to to determine the wall-liquid and the wall-crystal interfacial free energies of a modified Lennard-Jones (LJ) system in contact with a…
We use analytical calculations and event-driven molecular dynamics simulations to study a small number of hard sphere particles in a spherical cavity. The cavity is taken also as the thermal bath so that the system thermalizes by collisions…
We formulate a new theory for how caging constraints in glass-forming liquids at a surface or interface are modified and then spatially transferred, in a layer-by-layer bootstrapped manner, into the film interior in the context of the…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
We propose a data-driven method to describe consistent equations of state (EOS) for arbitrary systems. Complex EOS are traditionally obtained by fitting suitable analytical expressions to thermophysical data. A key aspect of EOS are that…
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…