Improvements to the APBS biomolecular solvation software suite

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 biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

Local Simulation Algorithms for Coulombic Interactions

We consider dynamically constrained Monte-Carlo dynamics and show that this leads to the generation of long ranged effective interactions. This allows us to construct a local algorithm for the simulation of charged systems without ever having to evaluate pair potentials or solve the Poisson equation. We discuss a simple implementation of a charged lattice gas as well as more elaborate off-lattice versions of the algorithm. There are analogies between our formulation of electrostatics and the bosonic Hubbard model in the phase approximation. Cluster methods developed for this model further improve the efficiency of the electrostatics algorithm.Comment: Proceedings Statphys22 10 page

Atomistic quantum transport modeling of metal-graphene nanoribbon heterojunctions

We calculate quantum transport for metal-graphene nanoribbon heterojunctions within the atomistic self-consistent Schr\"odinger/Poisson scheme. Attention is paid on both the chemical aspects of the interface bonding as well the one-dimensional electrostatics along the ribbon length. Band-bending and doping effects strongly influence the transport properties, giving rise to conductance asymmetries and a selective suppression of the subband formation. Junction electrostatics and p-type characteristics drive the conduction mechanism in the case of high work function Au, Pd and Pt electrodes, while contact resistance becomes dominant in the case of Al.Comment: 4 pages, 5 figure

Lorentz-Violating Electrostatics and Magnetostatics

The static limit of Lorentz-violating electrodynamics in vacuum and in media is investigated. Features of the general solutions include the need for unconventional boundary conditions and the mixing of electrostatic and magnetostatic effects. Explicit solutions are provided for some simple cases. Electromagnetostatics experiments show promise for improving existing sensitivities to parity-odd coefficients for Lorentz violation in the photon sector.Comment: 9 page