Related papers: Fast Surface Based Electrostatics for biomolecules…
We study the long time behavior of light particles, e.g. an electron swarm in which Coulomb interactions are unimportant, subjected to an external field and elastic collisions with an inert neutral gas. The time evolution of the velocity…
Using a reactive molecular beam with high kinetic energy ($E_{kin}$) it is possible to speed gas-surface reactions involving high activation barriers ($E_{act}$), which would require elevated pressures ($P_0$) if a random gas with a…
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…
Density functional theory (DFT) calculations of charged molecules and surfaces are critical to applications in electro-catalysis, energy materials and related fields of materials science. DFT implementations such as the Vienna ab-initio…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
The Poisson-Boltzmann equation (PBE) is a nonlinear elliptic PDE that arises in biomolecular modeling and is a fundamental tool for structural biology. It is used to calculate electrostatic potentials around an ensemble of fixed charges…
We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
We consider finite element methods of multiscale type to approximate solutions for two-dimensional symmetric elliptic partial differential equations with heterogeneous $L^\infty$ coefficients. The methods are of Galerkin type and follow the…
Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schr\"odinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise…
This paper presents an enhancement to the free surface lattice Boltzmann method (FSLBM) for the simulation of bubbly flows including rupture and breakup of bubbles. The FSLBM uses a volume of fluid approach to reduce the problem of a…
Rechargeable battery electrodes have highly complex microstructures, consisting of nonuniform electrode particles, tortuous electrolyte channels, and irregular particle-electrolyte interfaces. Moreover, the electrochemical processes involve…
The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical…
The traditional explicit electrostatic momentum-conserving Particle-in-cell algorithm requires strict resolution of the electron Debye length to deliver numerical accuracy. The explicit electrostatic energy-conserving Particle-in-Cell…
We present a computational approach for solving reaction-diffusion equations on evolving surfaces which have been obtained from cell image data. It is based on finite element spaces defined on surface triangulations extracted from time…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed…
An experimental and computational investigation of the space-charge effects occurring in ultrafast photoelectron spectroscopy from the gas phase is presented. The target sample CF$_3$I is excited by ultrashort (100 fs) far-ultraviolet…
We review two common numerical schemes for Coulomb potential evaluation that differ only in their radial part of the solutions in the spherical harmonic expansion (SHE). One is based on finite-difference method (FDM) while the other is…
Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical…