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We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn-Sham Density Functional Theory functionals on simulation of small to medium-size proteins…
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104},…
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain structural information on biomolecules or soft-matter complexes in solution. Deriving a molecular interpretation of the scattering signals requires methods for…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
A key part of planning CO2 storage sites is to devise a monitoring strategy. The aim of this strategy is to fulfill the requirements of legislations and lower cost of the operation by avoiding operational problems. If CCS is going to be a…
In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (SASA) analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to…
First-principles methods have recently established themselves in the field of photocathode research to provide microscopic, quantum-mechanical characterization of relevant materials for electron sources. While most of the existing studies…
Describing analytically the transport properties of electrolytes, such as their conductivity or the self-diffusion of the ions, has been a central challenge of chemical physics for almost a century. In recent years, this question has…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Self-consistent-field (SCF) approximations formulated using Hartree-Fock (HF) or Kohn-Sham Density Functional Theory (KS-DFT) both have the potential to yield multiple solutions. However, the formal relationship between multiple solutions…
In this work, we implement a new London equation module for superconductivity in the GPU-enabled ARTEMIS framework, and couple it to a finite-difference time-domain solver for Maxwell's equations. We apply this two-fluid approach to model a…
In this article we develop an algorithm for the efficient simulation of electrolytes in the presence of physical boundaries. In previous work the Discrete Ion Stochastic Continuum Overdamped Solvent (DISCOS) algorithm was derived for triply…
Density gradient theory (DGT) allows fast and accurate determination of surface tension and density profile through a phase interface. Several algorithms have been developed to apply this theory in practical calculations. While the…
In this work we study and contrast implicit solvation models against explicit atomistic, quantum mechanical models in the description of the band alignment of semiconductors in aqueous environment, using simulations based on density…
In this work, we propose a novel transport model for soluble surfactants in two-phase flows. In a two-phase flow, the soluble surfactants can adsorb/desorb from/into the bulk of any of the phases to the interface and can modify the…
Spectrum Sensing (SS) constitutes the most critical task i n Cognitive Radio (CR) systems for Primary User (PU) detection. Cooperative Spectrum Sensing (CSS) is introduced to enhance the detection reliability of the PU in fading…
The implementation of an efficient self-consistent field (SCF) method including both scalar relativistic effects and spin-orbit interaction in density functional theory (DFT) is presented. We make use of Gaussian-type orbitals (GTOs) and…
This paper characterizes sharp solute-solvent interfaces in hydrophobic environments, and there are three major ingredients. The first is the variational implicit solvent model (VISM) which establishes the free energy functional of…
We propose a novel adaptive damping algorithm for the self-consistent field (SCF) iterations of Kohn-Sham density-functional theory, using a backtracking line search to automatically adjust the damping in each SCF step. This line search is…
The Polarizable Continuum Model (PCM) can be used in conjunction with Density Functional Theory (DFT) and its time-dependent extension (TDDFT) to simulate the electronic and optical properties of molecules and nanoparticles immersed in a…