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A novel extension of a rapid compression machine (RCM), namely a Rapid Compression Expansion Machine (RCEM), is described and its use for studying chemical kinetics is demonstrated. Like conventional RCMs, the RCEM quickly compresses a…
We present the explicit bonding Reaction ensemble Monte Carlo (eb-RxMC) method, designed to sample reversible bonding reactions in macromolecular systems in thermodynamic equilibrium. Our eb-RxMC method is based on the Reaction ensemble…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
Reinforcement learning (RL) is highly suitable for devising control strategies in the context of dynamical systems. A prominent instance of such a dynamical system is the system of equations governing fluid dynamics. Recent research results…
Optimizing Neural networks is a difficult task which is still not well understood. On the other hand, fixed representation methods such as kernels and random features have provable optimization guarantees but inferior performance due to…
Empirical Dynamic Modeling (EDM) is a state-of-the-art non-linear time-series analysis framework. Despite its wide applicability, EDM was not scalable to large datasets due to its expensive computational cost. To overcome this obstacle,…
Biochemical molecules interact through modification and binding reactions, giving raise to a combinatorial number of possible biochemical species. The time-dependent evolution of concentrations of the species is commonly described by a…
Electrochemically mediated selective adsorption is an emerging electrosorption technique that utilizes Faradaically enhanced redox active electrodes, which can adsorb ions not only electrostatically, but also electrochemically. The superb…
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or…
Obtainable computational efficiency is evaluated when using an Adaptive Mesh Refinement (AMR) strategy in time accurate simulations governed by sets of conservation laws. For a variety of 1D, 2D, and 3D hydro- and magnetohydrodynamic…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed…
We review recent results of molecular dynamics simulations of two models of liquid water, the extended simple point charge (SPC/E) and the Mahoney-Jorgensen transferable intermolecular potential with five points (TIP5P), which is closer to…
Forecasting atmospheric flows with traditional discretization methods, also called full order methods (e.g., finite element methods or finite volume methods), is computationally expensive. We propose to reduce the computational cost with a…
Machine learning potentials (MLPs) represent atomic interactions with quantum mechanical accuracy offering an efficient tool for atomistic simulations in many fields of science. However, most MLPs rely on local atomic energies without…
To further develop accurate and large-scale simulations of electrochemical interfaces, we propose a unified explicit electric potential framework to simultaneously predict atomic forces and electron density distributions. The framework…
The expectation-maximization (EM) algorithm is a well-known iterative method for computing maximum likelihood estimates from incomplete data. Despite its numerous advantages, a main drawback of the EM algorithm is its frequently observed…
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…
Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been…