Related papers: Rate calculation with correlated noise
Reaction-Diffusion (RD) systems provide a computational framework that governs many pattern formation processes in nature. Current RD system design practices boil down to trial-and-error parameter search. We propose a differentiable…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
We present a numerical method for calculation of Ruelle-Pollicott resonances of dynamical systems. It constructs an effective coarse-grained propagator by considering the correlations of multiple observables over multiple timesteps. The…
Many biological systems can be modeled as a chemical reaction network with unknown parameters. Data available to identify these parameters are often in the form of a stationary distribution, such as that obtained from measurements of a cell…
Resonant activation is one of classical effects demonstrating constructive role of noise. In resonant activation cooperative action of barrier modulation process and noise lead to the optimal escape kinetics as measured by the mean first…
Biological and artificial neural systems form high-dimensional neural representations that underpin their computational capabilities. Methods for quantifying geometric similarity in neural representations have become a popular tool for…
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…
Learning to forecast trajectories of intelligent agents has caught much more attention recently. However, it remains a challenge to accurately account for agents' intentions and social behaviors when forecasting, and in particular, to…
This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Exact inference in complex probabilistic models often incurs prohibitive computational costs. This challenge is particularly acute for autonomous agents in dynamic environments that require frequent, real-time belief updates. Existing…
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…
In this paper a stochastic reaction diffusion system is considered, which models the spread of a finite population reacting with a non-renewable resource in the presence of individual based noise. A two-parameter phase diagram is…
Classical transition state theory (TST) is the cornerstone of reaction rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross.…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
A multiscale analysis of 1D stochastic bistable reaction-diffusion equations with additive noise is carried out w.r.t. travelling waves within the variational approach to stochastic partial differential equations. It is shown with explicit…
Reactive motion generation in dynamic and unstructured scenarios is typically subject to essentially static perception and system dynamics. Reliably modeling dynamic obstacles and optimizing collision-free trajectories under perceptive and…
We consider a reaction-diffusion system where some components react and diffuse on the boundary of a region, while other components diffuse in the interior and react with those on the boundary through mass transport. We establish local…
Stochastic point processes with refractoriness appear frequently in the quantitative analysis of physical and biological systems, such as the generation of action potentials by nerve cells, the release and reuptake of vesicles at a synapse,…