相关论文: Finding Multiple Reaction Pathways of Ligand Unbin…

Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current structure-based generative models are limited in generating…

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) which converges back to a Brownian motion with reduced diffusion coefficient at long times, after the anomalous…

We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and…

We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final…

Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select'…

We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…

The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…

We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…

Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…

In this paper, we propose an optimization-based sparse learning approach to identify the set of most influential reactions in a chemical reaction network. This reduced set of reactions is then employed to construct a reduced chemical…

Transport of molecular motors, stimulated by interactions with specific links between consecutive binding sites (called ``bridges''), is investigated theoretically by analyzing discrete-state stochastic ``burnt-bridge'' models. When an…

Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional…

To ensure faithful information transmission, cells utilize nonequilibrium drives to reduce errors. Kinetic proofreading is a classic mechanism known to sharpen ligand discrimination by T lymphocytes. It remains an open question whether the…

This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and…

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…

In the study of grain-surface chemistry in the interstellar medium, there exists much uncertainty regarding the reaction mechanisms with few constraints on the abundances of grain-surface molecules. Bayesian inference can be performed to…

Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational…

The accuracy of rate constants calculated using transition state theory depends crucially on the correct identification of a recrossing--free dividing surface. We show here that it is possible to define such optimal dividing surface in…