Noise in biomolecular systems: Modeling, analysis, and control implications

C Briat, M Khammash - Annual Review of Control, Robotics, and …, 2023 - annualreviews.org
While noise is generally associated with uncertainties and often has a negative connotation
in engineering, living organisms have evolved to adapt to (and even exploit) such …

Bounds on stochastic chemical kinetic systems at steady state

GR Dowdy, PI Barton - The Journal of chemical physics, 2018 - pubs.aip.org
The method of moments has been proposed as a potential means to reduce the
dimensionality of the chemical master equation (CME) appearing in stochastic chemical …

General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks

M Reis, JA Kromer, E Klipp - Journal of mathematical biology, 2018 - Springer
Multimodality is a phenomenon which complicates the analysis of statistical data based
exclusively on mean and variance. Here, we present criteria for multimodality in hierarchic …

Dynamic bounds on stochastic chemical kinetic systems using semidefinite programming

GR Dowdy, PI Barton - The Journal of chemical physics, 2018 - pubs.aip.org
Applying the method of moments to the chemical master equation appearing in stochastic
chemical kinetics often leads to the so-called closure problem. Recently, several authors …

The Arsenal of Perturbation Bounds for Finite Continuous-Time Markov Chains: A Perspective

AY Mitrophanov - Mathematics, 2024 - mdpi.com
Perturbation bounds are powerful tools for investigating the phenomenon of insensitivity to
perturbations, also referred to as stability, for stochastic and deterministic systems. This …

On differences between deterministic and stochastic models of chemical reactions: Schlögl solved with ZI-closure

M Vlysidis, YN Kaznessis - Entropy, 2018 - mdpi.com
Deterministic and stochastic models of chemical reaction kinetics can give starkly different
results when the deterministic model exhibits more than one stable solution. For example, in …

Maximum entropy prediction of non-equilibrium stationary distributions for stochastic reaction networks with oscillatory dynamics

PH Constantino, YN Kaznessis - Chemical engineering science, 2017 - Elsevier
Many chemical reaction networks in biological systems present complex oscillatory
dynamics. In systems such as regulatory gene networks, cell cycle, and enzymatic …

A linearization method for probability moment equations

M Vlysidis, YN Kaznessis - Computers & Chemical Engineering, 2018 - Elsevier
We present a new method for calculating the time-transient behavior of stochastic reaction
networks. We first derive the set of equations for the moments of the master probability …

ZI-Closure Scheme: A Method to Solve and Study Stochastic Reaction Networks

M Vlysidis, PH Constantino, YN Kaznessis - … , Multiscale Modeling, and …, 2017 - Springer
We use an example to present in exhaustive detail the algorithmic steps of the zero-
information (ZI) closure scheme (Smadbeck and Kaznessis, Proc Natl Acad Sci USA 110 …

Using semidefinite programming to bound distributions in chemical engineering systems

GR Dowdy - 2019 - dspace.mit.edu
Distributions appear in many forms in models of chemical engineering systems. Such
distributions account for microscopic variability in the system while simultaneously …