Related papers: Velocity jump processes : an alternative to multi-…
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of non-reactive force fields. However, most of the implemented functional forms for the coupling terms depend on complex…
Switching dynamical systems provide a powerful, interpretable modeling framework for inference in time-series data in, e.g., the natural sciences or engineering applications. Since many areas, such as biology or discrete-event systems, are…
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon…
Novel methods are presented in this initial study for the fusion of GPU kernels in the artificial compressibility method (ACM), using tensor product elements with constant Jacobians and flux reconstruction. This is made possible through the…
Relativistic molecular dynamics are described in ultra-high temperature and MeV energy behaviors. In strongly-coupled systems, the Coulomb electrostatic field is collected in the infinite space, and the electromagnetic fields are added in…
A self-interacting velocity jump process is introduced, which behaves in large time similarly to the corresponding self-interacting diffusion, namely the evolution of its normalized occupation measure approaches a deterministic flow.
Generative models have emerged as a powerful paradigm for solving physics systems and modeling complex spatiotemporal dynamics. However, achieving high physical accuracy without incurring high computational cost remains a fundamental…
Anderson Acceleration is a well-established method that allows to speed up or encourage convergence of fixed-point iterations. It has been successfully used in a variety of applications, in particular within the Self-Consistent Field (SCF)…
Based on the particle-in-cell (PIC) plasma simulation method, the speed-limited PIC (SLPIC) method delivers faster kinetic plasma simulation in cases where the particle distributions evolve slowly compared with the maximum stable PIC…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
By monitoring multiple molecular transitions, force-clamp and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or…
An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation,…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Based on a previously developed recursive approach for calculating the short-time expansion of the propagator for systems with time-independent potentials and its time-dependent generalization for simple single-particle systems, in this…
A first-principles based methodology for efficiently and accurately finding thermodynamically stable and metastable atomic structures is introduced and benchmarked. The approach is demonstrated for gas-phase metal-oxide clusters in…
We are launching FindBounce, a Mathematica package for the evaluation of the Euclidean bounce action that enters the decay rate of metastable states in quantum and thermal field theories. It is based on the idea of polygonal bounces, which…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…