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Quantum computing has the potential to reduce the computational cost required for quantum dynamics simulations. However, existing quantum algorithms for coupled electron-nuclear dynamics simulation either require fault-tolerant devices, or…
Coupled cluster theory is a vital cornerstone of electronic structure theory and is being applied to ever-larger systems. Stochastic approaches to quantum chemistry have grown in importance and offer compelling advantages over traditional…
Many Material Point Method implementations favor explicit time integration. However large time steps are often desirable for special reasons - for example, for partitioned coupling with another large-step solver, or for imposing…
An efficient algorithm for time propagation of the time-dependent Kohn-Sham equations is presented. The algorithm is based on dividing the Hamiltonian into small time steps and assuming that it is constant over these steps. This allows for…
We investigate how dynamical decoupling methods may be used to manipulate the time evolution of quantum many-body systems. These methods consist of sequences of external control operations designed to induce a desired dynamics. The systems…
This work introduces novel unconditionally stable operator splitting methods for solving the time dependent nonlinear Poisson-Boltzmann (NPB) equation for the electrostatic analysis of solvated biomolecules. In a pseudo-transient…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
Couplings of a system to other degrees of freedom (that is, environmental degrees of freedom) lead to energy dissipation when the number of environmental degrees of freedom is large enough. Here we discuss quantal treatments for such energy…
Micro- and nano-scale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Quantum dynamics can be simulated on a quantum computer by exponentiating elementary terms from the Hamiltonian in a sequential manner. However, such an implementation of Trotter steps has gate complexity depending on the total Hamiltonian…
We describe a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods provide effective convergence acceleration and preconditioning on all…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
A scheme for separating the high- and low-frequency molecular dynamics modes in Hybrid Monte Carlo (HMC) simulations of gauge theories with dynamical fermions is presented. The algorithm is tested in the Schwinger model with Wilson…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…