Related papers: Fast Surface Based Electrostatics for biomolecules…
We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed…
Core-electron x-ray photoelectron spectroscopy is a powerful technique for studying the electronic structure and chemical composition of molecules, solids and surfaces. However, the interpretation of measured spectra and the assignment of…
The electromagnetic behavior of plasmonic structures can be predicted after discretizing and solving a linear system of equations, derived from a continuous surface integral equation (SIE) and the appropriate boundary conditions, using a…
In order to rigorously evaluate the energy and dipole moment of a certain configuration of molecules one needs to solve the Schr\"odinger equation. Repeating this for many different configurations allows one to determine the potential…
The diffraction of fast atoms at grazing incidence on crystal surfaces (GIFAD) was first interpreted only in terms of elastic diffraction from a perfectly periodic rigid surface with atoms fixed at equilibrium position. Recently, a new…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
We develop a new numerical scheme for solving the radiative transfer equation in a spherically symmetric system. This scheme does not rely on any kind of diffusion approximation and it is accurate for optically thin, thick, and intermediate…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
The local approach to computing electrostatic interactions proposed by Maggs and adapted by Pasichnyk for molecular dynamics simulations is extended to situations where the dielectric background medium is inhomogeneous. We furthermore…
The smooth particle mesh Ewald (SPME) method is an FFT based method for the fast evaluation of electrostatic interactions under periodic boundary conditions. A highly optimized implementation of this method is available in GROMACS, a widely…
The full-wave simulation of complex electromagnetic surfaces such as reflectarrays and metasurfaces is a challenging problem. In this paper, we present a macromodeling approach to efficiently simulate complex electromagnetic surfaces…
Variational quantum eigensolver (VQE) is demonstrated to be the promising methodology for quantum chemistry based on near-term quantum devices. However, many problems are yet to be investigated for this methodology, such as the influences…
We present a method aimed at sampling charge density fluctuations in Coulomb systems. The derivation follows from a functional integral representation of the partition function in terms of charge density fluctuations. Starting from the…
A combination of molecular quantum electrodynamics, perturbation theory, and ab initio calculations was used to create a computational methodology capable of estimating the rate of 3-body singlet upconversion in organic molecular…
We present a modification of the $\Delta$SCF method of calculating energies of excited states, in order to make it applicable to resonance calculations of molecules adsorbed on metal surfaces, where the molecular orbitals are highly…
We present a robust scheme for solving the electrokinetic equations. This goal is achieved by combining the lattice-Boltzmann method (LB) with a discrete solution of the convection-diffusion equation for the different charged and neutral…
The Poisson-Boltzmann equation (PBE) is an implicit solvent continuum model for calculating the electrostatic potential and energies of ionic solvated biomolecules. However, its numerical solution remains a significant challenge due strong…
Energy-based fragmentation methods approximate the potential energy of a molecular system as a sum of contribution terms built from the energies of particular subsystems. Some such methods reduce to truncations of the many-body expansion…
We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the \textit{morphometric} calculation of $n$-body correlations. We calculate absolute free energies of local geometric…
Microstructure characterisation has been greatly enhanced through the use of electron backscatter diffraction (EBSD), where rich maps are generated through analysis of the crystal phase and orientation in the scanning electron microscope…