Related papers: Flexible framework of computing binding free energ…
We propose a predictive Density Functional Theory (DFT) for the calculation of solvation free energies. Our approach is based on a Helmholtz free-energy functional that is consistent with the perturbed-chain SAFT (PC-SAFT) equation of…
The contribution to the binding energy of a two-body system due to the crossed two-boson exchange contribution is calculated, using the Bethe-Salpeter equation. This is done for distinguishable, scalar particles interacting via the exchange…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a rapid self-consistent approximation of the side chain free energy at every…
Based on simplifications of previous numerical calculations [Graf and L\"{o}wen, Phys. Rev. E \textbf{59}, 1932 (1999)], we propose algebraic free energy expressions for the smectic-A liquid crystal phase and the crystal phases of hard…
We reconsider the applicability of classical nucleation theory (CNT) to the calculation of the free energy of solid cluster formation in a liquid and its use to the evaluation of interface free energies from nucleation barriers. Using two…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
We perform deep variational free energy calculations to investigate the dense hydrogen system at 1200 K and high pressures. In this computational framework, neural networks are used to model the free energy through the proton Boltzmann…
The development and first applications of a new periodic energy decomposition analysis (pEDA) scheme for extended systems based on the Kohn-Sham approach to density functional theory are described. The pEDA decomposes the binding energy…
We investigate both free energy and complexity of the spherical bipartite spin glass model. We first prove a variational formula in high temperature for the limiting free energy based on the well-known Crisanti-Sommers representation of the…
In this paper, we propose a framework for coordinating distributed energy resources (DERs) connected to a power distribution system, the model of which is not completely known, so that they collectively provide a specified amount of active…
We studied acetylhistidine (AcH), bare or microsolvated with a zinc cation by simulations in isolation. First, a global search for minima of the potential energy surface combining both, empirical and first-principles methods, is performed…
The energy density is calculated in coordinate space for $^{12}$C, $^{40}$Ca, $^{48}$Ca, and $^{208}$Pb using a dispersive optical model constrained by all relevant data including the corresponding energy of the ground state. The energy…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
The independent atom ansatz of density functional theory yields an accurate analytical expression for dynamic correlation energy in the H$_{2}$ molecule: $E_{c} = 0.5(1 - \sqrt{2})(ab|ba)$ for the atom-additive self-consistent density $\rho…
We present relativistic many-body calculations of total electron binding energy of neutral atoms up to element $Z=120$. Binding energy for ions may be found by subtracting known ionization potentials. Accuracy of the results for $17<Z…
In this paper we provide a highly accurate value for the binding energy of benzene to proton-ordered crystalline water ice (XIh), as a model for interstellar ices. We compare our computed value to the latest experimental data available from…
Using molecular simulation, we analyze the capillary condensation and evaporation processes for Argon confined in a cylindrical nanopore. For this purpose, we define the entropy of the adsorbed fluid as a reaction coordinate and determine…