Related papers: High-productivity, high-performance workflow for v…
High-intensity focused ultrasound (HIFU) is a promising treatment modality for the non-invasive ablation of pathogenic tissue in many organs. Optimal treatment planning strategies based on high-performance computing methods are expected to…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
The fundamental properties of molecules bridge experiment and theory. Transport properties (diffusion, thermal diffusion, thermal conductivity and viscosity) of binary mixtures are measurable in experiments, and well-defined in theory, but…
In this study, we introduce a method based on Separable Physics-Informed Neural Networks (SPINNs) for effectively solving the BGK model of the Boltzmann equation. While the mesh-free nature of PINNs offers significant advantages in handling…
A multi-relaxation-time discrete Boltzmann model (DBM) with split collision is proposed for both subsonic and supersonic compressible reacting flows, where chemical reactions take place among various components. The physical model is based…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…
The peridynamic theory brings advantages in dealing with discontinuities, dynamic loading, and non-locality. The integro-differential formulation of peridynamics poses challenges to numerical solutions of complicated and practical problems.…
This work proposes a fast iterative method for local steric Poisson--Boltzmann (PB) theories, in which the electrostatic potential is governed by the Poisson's equation and ionic concentrations satisfy equilibrium conditions. To present the…
Realistic simulations in engineering or in the materials sciences can consume enormous computing resources and thus require the use of massively parallel supercomputers. The probability of a failure increases both with the runtime and with…
A systematic study is carried out on a fully resolved fluid-particle model which couples the Lattice Boltzmann Method (LBM) and the Discrete Element Method (DEM) using an immersed moving boundary technique. Similar algorithms have been…
The Exascale Computing Project (ECP) is invested in co-design to assure that key applications are ready for exascale computing. Within ECP, the Co-design Center for Particle Applications (CoPA) is addressing challenges faced by…
The linear matter power spectrum is an essential ingredient in all theoretical models for interpreting large-scale-structure observables. Although Boltzmann codes such as CLASS or CAMB are very efficient at computing the linear spectrum,…
Metal additive manufacturing via laser-based powder bed fusion (PBF-LB/M) faces performance-critical challenges due to complex melt pool and vapor dynamics, often oversimplified by computational models that neglect crucial aspects, such as…
This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
This work further improves the pseudo-transient approach for the Poisson Boltzmann equation (PBE) in the electrostatic analysis of solvated biomolecules. The numerical solution of the nonlinear PBE is known to involve many difficulties,…
We consider the Poisson-Boltzmann equation in a periodic cell, representative of a porous medium. It is a model for the electrostatic distribution of $N$ chemical species diluted in a liquid at rest, occupying the pore space with charged…
Although many programs have been published for fully numerical Hartree--Fock (HF) or density functional (DF) calculations on atoms, we are not aware of any that support hybrid DFs, which are popular within the quantum chemistry community…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…