相关论文: Finding Multiple Reaction Pathways of Ligand Unbin…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Since Kramers' pioneering work in 1940, significant efforts have been devoted to studying Langevin equations applied to physical and chemical reactions projected onto few collective variables, with particular focus on the inference of their…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
We study numerically the energetics and atomic mechanisms of misfit dislocation nucleation and stress relaxation in a two-dimensional atomistic model of strained epitaxial layers on a substrate with lattice misfit. Relaxation processes from…
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…
Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity…
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
Reaction rates of chemical reactions under nonequilibrium conditions can be determined through the construction of the normally hyperbolic invariant manifold (NHIM) [and moving dividing surface (DS)] associated with the transition state…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…
Mass-action kinetics is frequently used in systems biology to model the behaviour of interacting chemical species. Many important dynamical properties are known to hold for such systems if they are weakly reversible and have a low…
The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
We propose an efficient method to compute reaction rate constants of thermally activated processes occurring in many-body systems at finite temperature. The method consists in two steps: first, paths are sampled using a transition path…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical…
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…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
A central challenge in materials science is characterizing chemical processes that are elusive to direct measurement, particularly in functional materials operating under realistic conditions. Here, we demonstrate that mechanical strain…