Related papers: A multiple replica approach to simulate reactive t…
The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
Free energy landscapes encode the kinetics, intermediates, and transition states that govern molecular processes and are thus a key target of single biomolecule research. Typical approaches to deriving optimal, error-minimizing,…
We derive a simple expression for the probability of trajectories of a master equation. The expression is particularly useful when the number of states is small and permits the calculation of observables that can be defined as functionals…
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many non-equilibrium processes can be described by suitable subsets of the equilibrium…
The multi-level method for discrete state systems, first introduced by Anderson and Higham [Multiscale Model. Simul. 10:146--179, 2012], is a highly efficient simulation technique that can be used to elucidate statistical characteristics of…
Model-based reinforcement learning (RL) is more sample efficient than model-free RL by using imaginary trajectories generated by the learned dynamics model. When the model is inaccurate or biased, imaginary trajectories may be deleterious…
The quantitative convergence to equilibrium for reaction-diffusion systems arising from complex balanced chemical reaction networks with mass action kinetics is studied by using the so-called entropy method. In the first part of the paper,…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
We propose a numerical methodology for the numerical simulation of distinct, interacting physical processes described by a combination of compressible, inert and reactive forms of the Euler equations, multiphase equations and elastoplastic…
Deducing an underlying multi-substate on-off kinetic scheme (KS) from the statistical properties of a two-state trajectory is the aim from many experiments in biophysics and chemistry, such as, ion channel recordings, enzymatic activity and…
We present a one-way shooting algorithm for transition path sampling that accepts every proposed trajectory, yet samples the correct transition path ensemble for systems with overdamped stochastic dynamics. The method is based on two key…
Transient stability assessment of power systems needs to account for increased risk from uncertainties due to the integration of renewables and distributed generators. The uncertain operating condition of the power grid hinders reliable…
To enhance the interpretability of Reinforcement Learning (RL), we propose Revealing Evolutionary Action Consequence Trajectories (REACT). In contrast to the prevalent practice of validating RL models based on their optimal behavior learned…
A procedure is developed and tested to recover the distribution of connectivity of an a priori unknown network, by sampling the dynamics of an ensemble made of reactive walkers. The relative weight between reaction and relocation is gauged…
We describe a new computational method for the numerically stable particle-based simulation of open-boundary flows, including volume conserving chemical reactions. The novel method is validated for the case of heterogeneous catalysis…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…
Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in…
In binary cascade dynamics, the nodes of a graph are in one of two possible states (inactive, active), and nodes in the inactive state make an irreversible transition to the active state, as soon as their precursors satisfy a predetermined…