Related papers: A Simple and Effective Solution to the Constrained…
A general and local reactive boundary condition (RBC) for studying first-order equilibrium reactions using the lattice Boltzmann method (LBM) is presented. Its main characteristics are accurate reproduction of wall diffusion, invariance to…
Consistency Models (CM) (Song et al., 2023) accelerate score-based diffusion model sampling at the cost of sample quality but lack a natural way to trade-off quality for speed. To address this limitation, we propose Consistency Trajectory…
We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the…
Molecular docking (MD) is a crucial task in drug design, which predicts the position, orientation, and conformation of the ligand when bound to a target protein. It can be interpreted as a combinatorial optimization problem, where quantum…
MFC is an open-source tool for solving multi-component, multi-phase, and bubbly compressible flows. It is capable of efficiently solving a wide range of flows, including droplet atomization, shock-bubble interaction, and gas bubble…
Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [Ref: J. Comput. Chem. 2023, 44, 1174], we further propose 1)…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
We introduce a method for effectively identifying bound states in the continuum (BICs) - notably without computing the imaginary part of the eigenvalues - thereby simplifying the modeling and potentially reducing computation time. In real,…
This work aims to address the bottleneck issues of hardware resource limitation and decoherence error in the Hamiltonian simulation of quantum fluids, which are caused by the standard quantum Fourier transform and the evolution of momentum…
In molecular simulation and fluid mechanics, the coupling of a particle domain with a continuum representation of its embedding environment is an ongoing challenge. In this work, we show a novel approach where the latest version of the…
Several methods are available to compute the anharmonicity in semi-rigid molecules. However, such methods are not routinely employed yet because of their large computational cost, especially for large molecules. The potential energy surface…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
In this paper a numerical procedure to simulate low diffusivity scalar turbulence is presented. The method consists of using a grid for the advected scalar with a higher spatial resolutions than that of the momentum. The latter usually…
An algorithm is proposed to implement unsteady jump boundary conditions, presenting discontinuity in physical quantities, within the lattice Boltzmann method (LBM). This is useful to tackle problems involving mass or heat transfer through…
The boundary element method (BEM) provides an efficient numerical framework for solving multiple scattering problems in unbounded homogeneous domains, since it reduces the discretization to the domain boundaries, thereby condensing the…
We propose a modified suspension balance model (SBM) for the flow of red blood cells (RBCs) and other deformable particle suspensions in confined geometries. Specifically, the method includes the hydrodynamic lift force generated by…
Quantum corrections can be important for diffusion and the melting temperature of dense plasmas in compact astrophysical objects, particulary white dwarfs and neutron stars. Typically ions in these systems are modeled classically, but…
Statistical downscaling is a crucial component of the weather modeling field, where high-resolution outputs must be reconstructed from coarse-resolution inputs with the full cost of dynamical refinement. In this work, we investigate a…
Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple…
In the study of micro-swimmers, both artificial and biological ones, many-query problems arise naturally. Even with the use of advanced high performance computing (HPC), it is not possible to solve this kind of problems in an acceptable…