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In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…

In this paper, a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) model is presented as a nonlinear system of an electrostatic potential and multiple ionic concentrations. It mixes nonlinear algebraic equations with a…

In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…

exa-AMD is a Python-based application designed to accelerate the discovery and design of functional materials by integrating AI/ML tools, materials databases, and quantum mechanical calculations into scalable, high-performance workflows.…

Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be…

We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that…

Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked experimentally. These calculations typically employ…

Ab initio wavefunction methods provide accurate molecular simulations but their computational scaling restricts applications to small systems. We develop a workflow combining quantum embedding to decompose a molecule into fragments with a…

We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…

We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…

The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast…

Low-temperature plasmas are essential to both fundamental scientific research and critical industrial applications. As in many areas of science, numerical simulations have become a vital tool for uncovering new physical phenomena and…

In this paper, we develop and implement an efficient asymptotic-preserving (AP) scheme to solve the gas mixture of Boltzmann equations under the disparate mass scaling relevant to the so-called "epochal relaxation" phenomenon. The disparity…

We compare different Poisson solvers within the context of an electrostatic Vlasov-Poisson system. These schemes are implemented as part of the IPPL (Independent Parallel Particle Layer) library (Frey et al., 2024), which provides…

The Poisson-Boltzmann equation is a nonlinear elliptic equation with Dirac distribution sources, which has been widely applied to the prediction of electrostatics potential of biological biomolecular systems in solution. In this paper, we…

The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…

The US Department of Energy launched the Exascale Computing Project (ECP) in 2016 as part of a coordinated effort to achieve the next generation of high-performance computing (HPC) and to accelerate scientific discovery. The Exascale Proxy…

The Poisson-Nernst-Planck (PNP) equations are one of the most effective model for describing electrostatic interactions and diffusion processes in ion solution systems, and have been widely used in the numerical simulations of biological…

The accurate modeling of non-covalent interactions between helium and graphitic materials is important for understanding quantum phenomena in reduced dimensions, with the helium-benzene complex serving as the fundamental prototype. However,…

Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…