Related papers: Constant pH Simulation with FMM Electrostatics in …
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
A new numerical method is presented to efficiently simulate the inelastic hard sphere (IHS) model for granular media, when fluid and frozen regions coexist in the presence of gravity. The IHS model is extended by allowing particles to…
A numerical method for simulation of bubble dynamics in three-dimensional potential flows is presented. The approach is based on the boundary element method for the Laplace equation accelerated via the fast multipole method implemented on a…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show…
We present HTMPC, a Heavily Templated C++ library for large-scale simulations implementing multi-particle collision dynamics (MPC), a particle-based mesoscale hydrodynamic simulation method. The implementation is plugin-based, and designed…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
An ultracold gas of heteronuclear alkali dimer molecules with hyperfine structure loaded into a one-dimensional optical lattice is investigated. The \emph{Hyperfine Molecular Hubbard Hamiltonian} (HMHH), an effective low-energy lattice…
GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…
In order to resolve the pressure checkerboard field problem with collocated grid, it is essential to employ the momentum interpolation method when formulating the pressure equation, and the flux reconstruction method when updating the…
Traditional dynamic security assessment faces challenges as power systems are experiencing a transformation to inverter-based-resource (IBR) dominated systems, for which electromagnetic transient (EMT) dynamics have to be considered.…
Preparing the thermal density matrix $\rho_{\beta} \propto e^{-\beta H}$ corresponding to a given Hamiltonian $H$ is a task of central interest across quantum many-body physics, and is particularly salient when attempting to study it with…
We discuss an implementation of adaptive fast multipole methods targeting hybrid multicore CPU- and GPU-systems. From previous experiences with the computational profile of our version of the fast multipole algorithm, suitable parts are…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
Implementing electrophysiological recordings within an MRI environment is challenging due to complex interactions between recording probes and MRI-generated fields, which can affect both safety and data quality. This study aims to develop…
Static disorder plays a crucial role in the electronic dynamics and spectroscopy of complex molecular systems. Traditionally, obtaining observables averaged over static disorder requires thousands of realizations via direct sampling of the…
This paper studies the nonlinear evolution of magnetic field turbulence in proximity of steady ideal MHD configurations characterized by a small electric current, a small plasma flow, and approximate flux surfaces, a physical setting that…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
A novel smooth immersed boundary method (IBM) based on a direct-forcing formulation is proposed to simulate incompressible dense particle-laden flows. This IBM relies on a regularization of the transfer function between the Eulerian grid…
Quantum dynamics simulation via Hamilton simulation algorithms is one of the most crucial applications in the quantum computing field. While this task has been relatively considered the target in the fault-tolerance era, the experiment for…