Related papers: Flexible framework of computing binding free energ…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
We use molecular simulation to compute the thermodynamic properties of 7 rigid models for water (SPC/E, TIP3P, TIP4P, TIP4P/2005, TIP4P/Ew, TIP5P, OPC) over a wide range of temperature and pressure. Carrying out Expanded Wang-Landau…
We prove an upper bound for the free energy (per unit volume) of the dilute Bose gas in the thermodynamic limit, showing that the free energy at density $\rho$ and inverse temperature $\beta$ differs from that of the non-interacting system…
In the Nelson model particles interact through a scalar massless field. For hydrogen-like atoms there is a nucleus of infinite mass and charge $Ze$, $Z > 0$, fixed at the origin and an electron of mass $m$ and charge $e$. This system forms…
The aim of this work is to investigate how energy depends on the two-body interaction potential in Bose-Einstein condensation (BEC) phenomena. An equation of state is obtained which is valid both for low and high energy BEC, through the…
We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which…
Methods for estimating the correlation energy of molecules and other electronic systems are discussed based on the assumption that the correlation energy can be partitioned between atomic regions. In one method, the electron density is…
Using a calix[4]arene-benzene complex as a test system we compare the potential of mean force for when the calix[4]arene is tethered versus free. When the complex is in vacuum our results show that the difference between tethered and free…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
The soft wall AdS/QCD holographic model provides simple estimates for the spectra of light mesons and glueballs satisfying linear Regge trajectories. It is also an interesting tool to represent the confinement/deconfinement transition of a…
The exchange contribution to the energy of the hydrogen atom interacting with a proton is calculated from the polarization expansion of the wave function using the conventional surface-integral formula and two formulas involving volume…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
We investigate the coarse-graining of host-guest systems under the perspective of the local distribution of pore occupancies, along with the physical meaning and actual computability of the coarse-interaction terms. We show that the widely…
A new reference state for density functional theory, termed the independent atom ansatz, is introduced in this work. This ansatz allows for the exact representation of electron density in terms of non-interacting, atom-localized orbitals.…
Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory but replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity.…
We present results of theoretical study and numerical calculation of the dynamics of molecular liquids based on combination of the memory equation formalism and the reference interaction site model - RISM. Memory equations for the site-site…