I just got my PhD in physics under William R. Holmes at Vanderbilt University.
In a few months, I’ll be studying theoretical neuroscience in Jan Drugowitsch’s lab.
I use tools from physics (like path integrals) to study intrinsic noise in gene regulatory networks, and am partial to analytic approaches. I am very interested in the different ways to model noise, and how noise qualitatively impacts landscapes and single cell trajectories. More broadly, I am fascinated by the relationship between models describing the same system at different scales; how should we understand these relationships, and how can the emergence of new features be ‘observed’ as we move between descriptions?
Published:
J.J. Vastola and W.R. Holmes, Chemical Langevin equation: a path-integral view of Gillespie’s derivation, Physical Review E (2020)
Submitted:
J.J. Vastola, Solving the chemical master equation for monomolecular reaction systems analytically: a Doi-Peliti path integral view
– J.J. Vastola, G. Gorin, L. Pachter, W.R. Holmes, Analytic solution of chemical master equations involving gene switching. I: Representation theory and diagrammatic approach to exact solution
Preprints:
– J.J. Vastola and W.R. Holmes, Stochastic path integrals can be derived like quantum mechanical path integrals
– J.J. Vastola, The chemical birth-death process with additive noise
– J.J. Vastola, The chemical birth-death process with Gillespie noise
In Preparation:
– J.J. Vastola, G. Gorin, L. Pachter, W.R. Holmes, Analytic solution of chemical master equations involving gene switching. II: Path integral approach to exact solution and applications to parameter inference
– J.J. Vastola and W.R. Holmes, Different noise assumptions yield qualitatively different landscapes and transition paths in gene regulation models
Essays:
– J.J. Vastola, Can Brazilian butterfly flaps destroy the universe? How fundamental limits on knowledge and computation force Laplace’s demon to become a scientist, Essay about variants of Laplace’s demon and what aspects of the world are ultimately accessible to scientific inquiry. Written for the Foundational Questions Institute’s 2020 Undecidability, Uncomputability, and Unpredictability Essay Contest.
– J.J. Vastola, Who’s Afraid of Max Delbrück?, Essay about labels on the interface of physics and biology. Won runner-up in 2020 History of Physics Essay Contest put on by the Forum on the History of Physics.
Email: John.J.Vastola AT Vanderbilt.edu