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The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet it only achieves first-order spatial accuracy near embedded boundaries. In this paper, we introduce a new high-order…
This paper presents a steady-state and transient heat conduction analysis framework using the polygonal scaled boundary finite element method (PSBFEM) with polygon/quadtree meshes. The PSBFEM is implemented with commercial finite element…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
The kernel-free boundary integral (KFBI) method has successfully solved partial differential equations (PDEs) on irregular domains. Diverging from traditional boundary integral methods, the computation of boundary integrals in KFBI is…
The paper is concerned with the development of efficient and accurate solution procedures for the isogeometric boundary element method (BEM) when applied to problems that contain inclusions that have elastic properties different to the…
Meshfree particle methods, such as Smoothed Particle Hydrodynamics (SPH) and the Moving Particle Semi-Implicit (MPS) method, are widely used to simulate complex free-surface and multiphase flows. A key challenge in these methods is the…
Multigrid solvers are among the most efficient methods for solving the Poisson equation, which is ubiquitous in computational physics. For example, in the context of incompressible flows, it is typically the costliest operation. The present…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
Implicit solvers present strong limitations when used on supercomputing facilities and in particular for adaptive mesh-refinement codes. We present a new method for implicit adaptive time-stepping on adaptive mesh refinement-grids. We…
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 Intrinsic Surface Finite Element Method (ISFEM) was recently proposed to solve Partial Differential Equations (PDEs) on surfaces. ISFEM proceeds by writing the PDE with respect to a local coordinate system anchored to the surface and…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
Heterogeneous computing environments combining CPU and GPU resources provide a great boost to large-scale scientific computing applications. Code generation utilities that partition the work into CPU and GPU tasks while considering data…
Ferroelectric materials can be used for the development of multiple device concepts combining non-volatility, small dimensions, low-power actuation, and electrical tunability. Such development demands efficient and precise design of…
Boundary element methods (BEM) are used for forward computation of bioelectromagnetic fields in multi-compartment volume conductor models. Most BEM approaches assume that each compartment is in contact with at most one external compartment.…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
Multiscale optimization is an attractive research field recently. For the most of optimization tools, design parameters should be updated during a close loop. Therefore, a simple Python code is programmed to obtain effective properties of…
Typical areas of application of explicit dynamics are impact, crash test, and most importantly, wave propagation simulations. Due to the numerically highly demanding nature of these problems, efficient automatic mesh generators and…
We develop an open-source python workflow package, $py$GWBSE to perform automated first-principles calculations within the GW-BSE (Bethe-Salpeter) framework. GW-BSE is a many body perturbation theory based approach to explore the…
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is…