Related papers: Flexible framework of computing binding free energ…
Binding energies calculated from using the Bethe-Salpeter equation in the simplest ladder approximation significantly differ from those obtained in the non-relativistic standard instantaneous approximation. While they should a priori be…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
We present a simple yet accurate numerical approach to compute the free energy of binding of multivalent objects on a receptor-coated surface. The method correctly accounts for the fact that one ligand can bind to at most one receptor. The…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
A method is presented for calculating binding energies and other properties of extended interacting systems using the projected density of transitions (PDoT) which is the probability distribution for transitions of different energies…
Solvation free energies are efficiently predicted by molecular density functionnal theory (MDFT) if one corrects the overpressure introduced by the usual homogeneous reference fluid approximation. Sergiievskyi et al. [Sergiievskyi et al.,…
Based on the reduced density matrix method, we compare two different approaches to calculate the dynamics of the electron transfer in systems with donor, bridge, and acceptor. In the first approach a vibrational substructure is taken into…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
The static-exchange model (SEM) and the modified static-exchange model (MSEM) recently introduced by Ray [1] is applied to study the elastic collision between two hydrogen-like atoms when both are in ground states considering the system as…
We consider the interacting Bose gas in the thermodynamic limit in a large box in $\R^d$ at positive temperature $1/\beta\in(0,\infty)$ with particle density $\sim\rho\in(0,\infty)$. We follow a path-integral approach and adopt from \cite…
The interacting quantum Bose gas is a random ensemble of many Brownian bridges (cycles) of various lengths with interactions between any pair of legs of the cycles. It is one of the standard mathematical models in which a proof for the…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
A recently developed statistical mechanical Quasi-Chemical Theory (QCT) has led to significant insights into solvation phenomena for both hydrophilic and hydrophobic solutes. The QCT exactly partitions solvation free energies into three…
Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…
Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such as thermodynamic integration (TI), free-energy perturbation, or Bennett's…
Flexible loads are a resource for the Balancing Authority (BA) of the future to aid in the balance of power supply and demand. In order to be used as a resource, the BA must know the capacity of the flexible loads to vary their power demand…
In this paper we present a numerical method for hydrodynamic models that arise from time dependent density functional theories of freezing. The models take the form of compressible Navier-Stokes equations whose pressure is determined by the…
We revisit the differential energy distribution of steady-state dynamical models. It has been shown that the differential energy distribution of steady-state spherical models does not vary strongly with the anisotropy profile, and that it…
The binding-energy differences for $^{163}\mathrm{Ho}^{q+}$ and $^{163}\mathrm{Dy}^{q+}$ ions with ionization degrees $q = 38$, $39$, and $40$ are calculated. The calculations are performed using the large-scale relativistic…