Related papers: O(N) continuous electrostatics solvation energies …
The formation energy of a solid surface can be extracted from slab calculations if the bulk energy per atom is known. It has been pointed out previously that the resulting surface energy will diverge with slab thickness if the bulk energy…
An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with…
Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These…
Accurate predictions of charge excitation energies of molecules in the disordered condensed phase are central to the chemical reactivity, stability, and optoelectronic properties of molecules and critically depend on the specific…
We propose a systematic, {\em a priori} approach to the problem of the calculation of solvation energies using continuum dielectric models coupled to quantum mechanical description of reacting molecules. Our method does not rely on…
Self-consistent multi-particle simulation plays an important role in studying beam-beam effects and space charge effects in high-intensity beams. The Poisson equation has to be solved at each time-step based on the particle density…
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent…
We propose a new method for calculating total energies of systems of interacting electrons, which requires little more computational resources than standard density-functional theories. The total energy is calculated within the framework of…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
Within the framework of Gaussian equivalent representation method a new procedure of obtaining equations of state for simple liquids is discussed in some technical details. The developed approach permits one to compute partition and…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is…
In the given paper we describe methods finding analytical gradients (derivatives) of solvation energy over atomic coordinates. It is made both for not polar energy and for the polar energy found by methods PCM, COSMO and SGB. These…
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…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…
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…
The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful…
We present a new numerical algorithm based on a relative energy scaling for collisional kinetic equations allowing to study numerically their long time behavior, without the usual problems related to the change of scales in velocity…
A novel energy minimization formulation of electrostatics that allows computation of the electrostatic energy and forces to any desired accuracy in a system with arbitrary dielectric properties is presented. An integral equation for the…