相关论文: Bounding Transient Moments of Stochastic Chemical …
In the stochastic formulation of chemical kinetics, the stationary moments of the population count of species can be described via a set of linear equations. However, except for some specific cases such as systems with linear reaction…
Moment dynamics in stochastic chemical kinetics often involve an infinite chain of coupled equations, where lower-order moments depend on higher-order ones, making them analytically intractable. Moment bounding via semidefinite programming…
The use of approximate solution techniques for the Chemical Master Equation is common practice for the analysis of stochastic chemical systems. Despite their widespread use, however, many such techniques rely on unverifiable assumptions and…
Model-based prediction of stochastic noise in biomolecular reactions often resorts to approximation with unknown precision. As a result, unexpected stochastic fluctuation causes a headache for the designers of biomolecular circuits. This…
Applying the method of moments to the chemical master equation (CME) appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
A highly efficient formulation of moment equations for stochastic reaction networks is introduced. It is based on a set of binomial moments that capture the combinatorics of the reaction processes. The resulting set of equations can be…
Stochastic chemical reaction networks (SRNs) in cellular systems are commonly modeled as continuous-time Markov chains (CTMCs) describing the dynamics of molecular copy numbers. The exact evaluation of transient copy number statistics is,…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
This paper develops a unified methodology for probabilistic analysis and optimal control design for jump diffusion processes defined by polynomials. For such systems, the evolution of the moments of the state can be described via a system…
This paper proposes a semidefinite programming based method for estimating moments of a stochastic hybrid system (SHS). For polynomial SHSs -- which consist of polynomial continuous vector fields, reset maps, and transition intensities --…
Identifying transition states (TSs), the high-energy configurations that molecules pass through during chemical reactions, is essential for understanding and designing chemical processes. However, accurately and efficiently identifying…
Inferring parameters of models of biochemical kinetics from single-cell data remains challenging because of the uncertainty arising from the intractability of the likelihood function of stochastic reaction networks. Such uncertainty falls…
Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally…
The dynamics of cellular chemical reactions are variable due to stochastic noise from intrinsic and extrinsic sources. The intrinsic noise is the intracellular fluctuations of molecular copy numbers caused by the probabilistic encounter of…
Transition states (TSs) govern the rates and outcomes of chemical reactions, making their accurate prediction a central challenge in computational chemistry. Although recent machine-learning models achieve near chemical accuracy in the…
This paper studies a novel approach for approximating the behavior of compartmental spreading processes. In contrast to prior work, the methods developed describe a dynamics which bound the exact moment dynamics, without explicitly…
The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…
The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At non-dilute conditions, interactions among the components can give rise to coexisting…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…