Related papers: Exact rate calculations by trajectory parallelizat…
For a transition between two stable states, the committor is the probability that the dynamics leads to one stable state before the other. It can be estimated from trajectory data by minimizing an expression for the transition rate that…
Nuclear reaction rates determine the abundances of isotopes in stellar burning processes. A multitude of reactions determine the reaction flow pattern which is described in terms of reaction network simulations. The reaction rates are…
In this paper, we address the modeling issues of cell movement and division with a special focus on the phenomenon of volume exclusion in a lattice-based, exact stochastic simulation framework. We propose a new exact method, called Reduced…
We study the problem of a run and tumble particle in a harmonic trap, with a finite run and tumble time, by a direct integration of the equation of motion. An exact 1D steady state distribution, diagram laws and a programmable Volterra…
We introduce expandable partial propensity direct method (EPDM) - a new exact stochastic simulation algorithm suitable for systems involving many interacting molecular species. The algorithm is especially efficient for sparsely populated…
Temporal point processes are powerful generative models for event sequences that capture complex dependencies in time-series data. They are commonly specified using autoregressive models that learn the distribution of the next event from…
Path thermodynamic formulation of non-equilibrium reactive systems is considered. It is shown through simple practical examples that this approach can lead to results that contradict well established thermodynamic properties of such…
Estimating density ratios between pairs of intractable data distributions is a core problem in probabilistic modeling, enabling principled comparisons of sample likelihoods under different data-generating processes across conditions and…
We describe a simple method to compute the Cramer-Rao limit of a high energy experiment, i.e., the smallest error with which a parameter can in principle be determined in a reaction. This precision remains a theoretical paradigm since it…
A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a…
Considering the paradigmatic driven Brownian motion, we perform extensive numerical analysis on the performance of optimal linear-response processes far from equilibrium. We focus on the overdamped regime where exact optimal processes are…
We propose an algorithm to actively estimate the parameters of a linear dynamical system. Given complete control over the system's input, our algorithm adaptively chooses the inputs to accelerate estimation. We show a finite time bound…
Chemotactic active particles, such as bacteria and cells, exhibit an adaptive run-and-tumble motion, giving rise to complex emergent behaviors in response to external chemical fields. This motion is generated by the conversion of internal…
Recent advances in steady-state analysis of power systems have introduced the equivalent split-circuit approach and corresponding continuation methods that can reliably find the correct physical solution of large-scale power system…
The ability to estimate the rate of convergence for the distributions of regenerative processes is in great demand. These processes are often encountered in queuing theory and in related problems. In some papers on regenerative processes,…
For a prepared state exact expressions for the time dependent mean fidelity as well as for the mean inverse paricipation ratio are obtained analytically. The distribution function of fidelity in the long time limit and of inverse…
The entropy production rate of nonequilibrium systems is studied via the Fokker-Planck equation. This approach, based on the entropy production rate equation given by Schnakenberg from a master equation, requires information of the…
A quantum version of a recent formulation of transition state theory in {\em phase space} is presented. The theory developed provides an algorithm to compute quantum reaction rates and the associated Gamov-Siegert resonances with very high…
Random-matrix theory is applied to transition-rate matrices in the Pauli master equation. We study the distribution and correlations of eigenvalues, which govern the dynamics of complex stochastic systems. Both the cases of identical and of…
We address in this paper a model for the simulation of turbulent deflagrations in industrial applications. The flow is governed by the Euler equations for a variable composition mixture and the combustion modelling is based on a…