Related papers: Generating High-Precision Force Fields for Molecul…
Simulating electrified metal/water interfaces with explicit solvent under constant potential is essential for understanding electrochemical processes, yet remains prohibitively expensive with ab initio methods. We present TRECI, a…
The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility,…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
Coarse-grained modeling in molecular simulations serves not only to extend accessible time and length scales beyond atomistic limits, but also to reduce high-dimensional chemical data to low-dimensional representations that expose the…
Reaction-diffusion processes play an important role in a variety of physical, chemical, and biological systems. Conventionally, the kinetics of these processes are described by the law of mass action. However, there are various cases where…
We propose a reinforcement learning based method to identify important configurations that connect reactant and product states along chemical reaction paths. By shooting multiple trajectories from these configurations, we can generate an…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps…
Accurate knowledge of the atomistic transition pathways in materials and material surfaces is crucial for many material science problems. However, conventional simulation techniques used to find these transitions are extremely…
Quantum mechanical methods have been devised for the elucidation and clarification of reaction paths of chemical processes over decades. While they are typically deployed in routine calculations on systems for which some insights have…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new…
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…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
We examine the problem of causal response estimation for complex objects (e.g., text, images, genomics). In this setting, classical \emph{atomic} interventions are often not available (e.g., changes to characters, pixels, DNA base-pairs).…
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamental tool to characterize biomolecular dynamics and their…
To accurately study chemical reactions in the condensed phase or within enzymes, both a quantum-mechanical description and sufficient configurational sampling is required to reach converged estimates. Here, quantum mechanics/molecular…
Observing non-classical nucleation pathways remains challenging in simulations of complex materials with technological interests. This is because it requires very accurate force fields that can capture the whole complexity of their…