q-bio Summer School and Conference, 2022

Dr. Zachary R. Fox

Dr. Zachary R. Fox

Center for NonLinear Studies

Los Alamos National Laboratory

Lecture: Chemical Master Equations

Date: Monday June 13 @ 09:00 – 10:00

Abstract: In this lecture, we will start with what we learned last week about stochastic simulations and move to describing chemical reaction networks in terms of the Chemical Master Equation (CME). We will derive a solution to the CME for a simple gene regulatory model and discuss how the CME can be treated computationally for more complex systems using the Finite State Projection algorithm. We will conclude with the current limitations of such approaches and discuss broadly state of the art approaches to solving the CME. 


  1. McQuarrie, 1967 (https://www.cambridge.org/core/journals/journal-of-applied-probability/article/abs/stochastic-approach-to-chemical-kinetics/12E51C722EC1B42B73B587FC79B14759)
  2. Munsky and Khammash, 2006https://aip.scitation.org/doi/full/10.1063/1.2145882
  3. Vo and Sidje, 2017https://aip.scitation.org/doi/full/10.1063/1.4994917
  4. Fox, Neuert, Munsky. JCP 2016 https://aip.scitation.org/doi/full/10.1063/1.4960505
  5. Fox and Munsky. PLoS Comp Bio 2019 https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006365
  6. Fox, Neuert, Munsky. Complexity 2020 https://www.hindawi.com/journals/complexity/2020/8536365/

Presenter Biosketch: Zachary Fox received his doctorate in Biomedical Engineering from Colorado State University in 2019 where he developed new methods to integrate single-cell microscopy data and stochastic models of gene expression. These tools include new approaches to infer model parameters from data and use stochastic models to design more informative experiments. Zach then attended the Institut Pasteur in Paris, France, where he did his postdoc in microscopy automation and optogenetic control of gene expression in synthetically engineered yeast using stochastic models. He worked with Gregory Batt and Jakob Ruess. He is now working on a secondary postdoc at the Center for Nonlinear Studies and Computer, Computational, and Statistical Science at Los Alamos National Lab, with Dr. Yen Ting Lin and Dr. Anatoly Zlotnik.

Presenter Website: Zach Fox

Presenter Email: zachrfox@gmail.com

Slides: Zachary Fox Slides