Related papers: Improved random batch Ewald method in molecular dy…
In recent years, reduced basis methods (RBMs) have been adapted to the many-body eigenvalue problem and they have been used, largely in nuclear physics, as fast emulators able to bypass expensive direct computations while still providing…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
In this paper, we develop a new accelerated stochastic gradient method for efficiently solving the convex regularized empirical risk minimization problem in mini-batch settings. The use of mini-batches is becoming a golden standard in the…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
Simulating the static and dynamic properties of semidilute polymer solutions with Brownian dynamics (BD) requires the computation of a large system of polymer chains coupled to one another through excluded-volume and hydrodynamic…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
Often, machine learning applications have to cope with dynamic environments where data are collected in the form of continuous data streams with potentially infinite length and transient behavior. Compared to traditional (batch) data…
The random batch method provides an efficient algorithm for computing statistical properties of a canonical ensemble of interacting particles. In this work, we study the error estimates of the fully discrete random batch method, especially…
The many-body expansion (MBE) of energies of molecular clusters or solids offers a way to detect and analyze errors of theoretical methods that could go unnoticed if only the total energy of the system was considered. In this regard, the…
Robust Markov Decision Processes (RMDPs) intend to ensure robustness with respect to changing or adversarial system behavior. In this framework, transitions are modeled as arbitrary elements of a known and properly structured uncertainty…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
Estimation of Distribution Algorithms (EDAs) require flexible probability models that can be efficiently learned and sampled. Restricted Boltzmann Machines (RBMs) are generative neural networks with these desired properties. We integrate an…
We propose in this work RBM-SVGD, a stochastic version of Stein Variational Gradient Descent (SVGD) method for efficiently sampling from a given probability measure and thus useful for Bayesian inference. The method is to apply the Random…
Recommender systems inherently exhibit a low-rank structure in latent space. A key challenge is to define meaningful and measurable distances in the latent space to capture user-user, item-item, user-item relationships effectively. In this…
We present a technique to efficiently compute long-range interactions in systems with periodic boundary conditions. We extend the well-known Ewald method by using a linear combination of screening Gaussian charge distributions instead of…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…