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Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
Turbulent reacting flows occur in a variety of engineering applications such as chemical reactors and power generating equipment (gas turbines and internal combustion engines). Turbulent reacting flows are characterized by two main…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
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…
Molecular Dynamics simulations are essential tools for understanding the dynamic behavior of biomolecules, yet extracting meaningful molecular pathways from these simulations remains challenging due to the vast amount of generated data. In…
In this work, we introduce a flow based machine learning approach, called reaction coordinate (RC) flow, for discovery of low-dimensional kinetic models of molecular systems. The RC flow utilizes a normalizing flow to design the coordinate…
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability…
Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these…
We present an overview of the reaction coordinate approach to handling strong system-reservoir interactions in quantum thermodynamics. This technique is based on incorporating a collective degree of freedom of the reservoir (the reaction…
Identifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often based on heuristic knowledge. However,…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. They are critical for understanding protein function and…
The reaction-coordinate mapping is a useful technique to study complex quantum dissipative dynamics into structured environments. In essence, it aims to mimic the original problem by means of an 'augmented system', which includes a suitably…
Computing accurate rate constants for catalytic events occurring at the surface of a given material represents a challenging task with multiple potential applications in chemistry. To address this question, we propose an approach based on a…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
Many chemical reactions and molecular processes occur on timescales that are significantly longer than those accessible by direct simulation. One successful approach to estimating dynamical statistics for such processes is to use many short…