相关论文: Interface of the polarizable continuum model of so…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in simulations of electronic structure is…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
This paper presents the Parallel Coupler for Multimodel Simulations (PCMS), a new GPU accelerated generalized coupling framework for coupling simulation codes on leadership class supercomputers. PCMS includes distributed control and field…
We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations…
Force-based atomistic-continuum hybrid methods are the only known pointwise consistent methods for coupling a general atomistic model to a finite element continuum model. For this reason, and due to their algorithmic simplicity, force-based…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Mathematical models of protein-protein dynamics, such as the heterodimer model, play a crucial role in understanding many physical phenomena. This model is a system of two semilinear parabolic partial differential equations describing the…
A high-performance gas kinetic solver using multi-level parallelization is developed to enable pore-scale simulations of rarefied flows in porous media. The Boltzmann model equation is solved by the discrete velocity method with an…
Phase-field models are widely employed to simulate microstructure evolution during processes such as solidification or heat treatment. The resulting partial differential equations, often strongly coupled together, may be solved by a broad…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
In our recent work [H. Zhang, F.X. Trias, A. Oliva, D. Yang, Y. Tan, Y. Sheng. PIBM: Particulate immersed boundary method for fluid-particle interaction problems. Powder Technology. 272(2015), 1-13.], a particulate immersed boundary method…
We trace with unprecedented numerical accuracy the phase diagram of the Gaussian-core model, a classical system of point particles interacting via a Gaussian-shaped, purely repulsive potential. This model, which provides a reliable…
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…
The intrusive (sample-free) spectral stochastic finite element method (SSFEM) is a powerful numerical tool for solving stochastic partial differential equations (PDEs). However, it is not widely adopted in academic and industrial…
This work constructs an advanced force field, the Completely Multipolar Model (CMM), to quantitatively reproduce each term of an energy decomposition analysis (EDA) for aqueous solvated alkali metal cations and halide anions and their ion…
As the need for computational power and efficiency rises, parallel systems become increasingly popular among various scientific fields. While multiple core-based architectures have been the center of attention for many years, the rapid…