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Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal…
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in…
Biochemical reaction systems may be viewed as discrete event processes characterized by a number of states and state transitions. These systems may be modeled as state transition systems with transitions representing individual reaction…
Acid-base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in many fields, from biochemistry to industrial catalysis. Unfortunately, experiments only give limited information without much insight into the…
The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path…
We present a method to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive…
Hydrogen is vital for sectors like chemicals and others, driven by the need to reduce carbon emissions. Proton Electrolyte Membrane Water Electrolysis (PEMWE) is a key technology for the production of green hydrogen under fluctuating…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Porous media processes involve various physical phenomena such as mechanical deformation, transport, and fluid flow. Accurate simulations must capture the strong couplings between these phenomena. Choosing an efficient solver for the…
This mini-review synthesizes our understanding of the equilibrium behavior of particle models with short-range attractive and long-range repulsive (SALR) interactions. These models, which can form stable periodic microphases, aim to…
We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub \textit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer…
Many additive manufacturing (AM) technologies rely on powder feedstock, which is fused to form the final part either by melting or by chemical binding with subsequent sintering. In both cases, process stability and resulting part quality…
Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…
Accurate low dimension chemical kinetic models for methane are an essential component in the design of efficient gas turbine combustors. Kinetic models coupled to computational fluid dynamics (CFD) provide quick and efficient ways to test…