Related papers: Electrostatic interactions in concentrated protein…
In this work, we elucidate the mathematical structure of the integral that arises when computing the electron-ion temperature equilibration time for a homogeneous weakly-coupled plasma from the Lenard-Balescu equation. With some minor…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
We present a theory which allows us to calculate the interaction potential between charge-regulated metal nanoparticles inside an acid-electrolyte solution. The approach is based on the recently introduced model of charge regulation which…
In this paper we study the electrostatic properties of `Janus' spheres with unequal charge densities on both hemispheres. We introduce a method to compare primitive-model Monte Carlo simulations of the ionic double layer with predictions of…
We propose an experimental approach for determining thermodynamic properties of ultracold atomic gases with short-range interactions. As a test case, we focus on the one-dimensional (1D) Bose gas described by the integrable Lieb-Liniger…
The Debye-H\" uckel formula for ionic activity coefficients is extended for concentrated solutions by solving a simple model of many-body Coulomb correlations and adding the Born solvation energy. Given the bulk permittivity, our formula is…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…
Intermolecular interactions in protein solutions in general contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid-liquid phase separation (LLPS) that is metastable with respect to…
The lattice fluid model of the system with short range and long range Coulomb interactions is suggested. In the framework of the collective variables method, the screening of the Coulomb interactions in the bulk is considered. It is shown…
We present a nonlocal statistical field theory of a dilute electrolyte solution with small additive of dipolar particles. We postulate that every dipolar particle is associated with an arbitrary probability distribution function (PDF) of…
The energy functional, the governing partial differential equation(s) (PDE), and the boundary conditions need to be consistent with each other in a modeling system. In electrolyte solution study, people usually use a free energy form of an…
Using a new semi empirical method for calculating molecular polarizabilities and the Clausius Mossotti relation, we calculated the static dielectric constants of dry proteins for all structures in the protein data bank (PDB). The mean…
Understanding the response of the surface of metallic solids to external electric field sources is crucial to characterize electrode-electrolyte interfaces. Continuum electrostatics offer a simple description of the induced charge density…
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the…
The Helmholtz free-energy W is calculated as a function of separation distance for two molecules in a fluid, A and B, whose mutual interaction is described by a spherically symmetric potential. For the equilibrium A + B = AB occurring in a…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
We propose a semi-empirical formula for the cross section of ionization by electron impact. The formula involves adjustable parameters which are determined by comparison with measured or numerically calculated cross sections. In the latter…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…