Related papers: Velocity Jumps for Molecular Dynamics
We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the…
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary…
We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics…
Stochastic kinetic models (SKMs) are increasingly used to account for the inherent stochasticity exhibited by interacting populations of species in areas such as epidemiology, population ecology and systems biology. Species numbers are…
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP,…
Parallel replica dynamics is a method for accelerating the computation of processes characterized by a sequence of infrequent events. In this work, the processes are governed by the overdamped Langevin equation. Such processes spend much of…
This work introduces CLIP, a CUDA-accelerated phase-field lattice Boltzmann framework for simulating immiscible two-phase flows with high density and viscosity ratios in both two- and three-dimensional domains. By leveraging GPU…
This paper introduces a framework for simulating finite dimensional representations of (jump) diffusion sample paths over finite intervals, without discretisation error (exactly), in such a way that the sample path can be restored at any…
The generalized Langevin equation is used as a model for various coarse-grained physical processes, e.g., the time evolution of the velocity of a given larger particle in an implicitly represented solvent, when the relevant time scales of…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The Monte Carlo wave function method or the quantum trajectory/jump approach is a powerful tool to study dissipative dynamics governed by the Markovian master equation, in particular for high-dimensional systems and when it is difficult to…
We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients…
Markov jump processes (or continuous-time Markov chains) are a simple and important class of continuous-time dynamical systems. In this paper, we tackle the problem of simulating from the posterior distribution over paths in these models,…
We expand on the previously published Gr{\o}nbech-Jensen Farago (GJF) thermostat, which is a thermodynamically sound variation on the St{\o}rmer-Verlet algorithm for simulating discrete-time Langevin equations. The GJF method has been…
Dynamic jumps in the price and volatility of an asset are modelled using a joint Hawkes process in conjunction with a bivariate jump diffusion. A state space representation is used to link observed returns, plus nonparametric measures of…
This work introduces and studies a new family of velocity jump Markov processes directly amenable to exact simulation with the following two properties: i) trajectories converge in law when a time-step parameter vanishes towards a given…
For distributions over discrete product spaces $\prod_{i=1}^n \Omega_i'$, Glauber dynamics is a Markov chain that at each step, resamples a random coordinate conditioned on the other coordinates. We show that $k$-Glauber dynamics, which…
A hybrid computational method coupling the lattice-Boltzmann (LB) method and a Langevin-dynamics (LD) method is developed to simulate nanoscale particle and polymer (NPP) suspensions in the presence of both thermal fluctuation and…
Path reweighting is a principally exact method to estimate dynamic properties from biased simulations - provided that the path probability ratio matches the stochastic integrator used in the simulation. Previously reported path probability…
Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be…