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The immersed boundary method is a mathematical formulation and numerical method for solving fluid-structure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a…
In this work we show the advantages of using the Coulomb-hole plus screened-exchange (COHSEX) approach in the calculation of potential energy surfaces. In particular, we demonstrate that, unlike perturbative $GW$ and partial self-consistent…
Local electronic-structure methods in quantum chemistry operate on the ability to compress electron correlations more efficiently in a basis of spatially localized molecular orbitals than in a parent set of canonical orbitals. However, many…
Accurate calculation of electrostatic potential and gradient on the molecular surface is highly desirable for the continuum and hybrid modeling of large scale deformation of biomolecules in solvent. In this article a new numerical method is…
Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
We present high-quality reference data for two fundamentally important groups of molecular properties related to a compound's utility as a lithium battery electrolyte. The first property is energy changes associated with charge excitations…
In order to realize the significant potential of optical materials such as metal halides, computational techniques which give accurate optical properties are needed, which can work hand-in-hand with experiments to generate high efficiency…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…
Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional…
Inspired by Grimme's simplified Tamm-Dancoff density functional theory approach [S. Grimme, J. Chem. Phys. \textbf{138}, 244104 (2013)], we describe a simplified approach to excited state calculations within the GW approximation to the…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Fewest-switches surface hopping (FSSH) is the most popular method for simulating photochemical processes of molecular systems. Recently, we have constructed long short-term memory (LSTM) networks as a propagator for electronic subsystems in…
Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum…
We present a highly efficient method for the extraction of optical properties of very large molecules via the Bethe-Salpeter equation. The crutch of this approach is the calculation of the action of the effective Coulombic interaction, $W$,…
We study the behaviour of total-energy supercell calculations for dipolar molecules and charged clusters. Using a cutoff Coulomb interaction within the framework of a plane-wave basis set formalism, with all other aspects of the method…
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…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…