Dynamical Systems & Modeling

Research

During my graduate research with Dr John Tyson, I built mathematical models to understand dynamical aspects:

• Modeling the START transition in the budding yeast cell cycle:

  • Built a detailed mathematical model (~100 ODEs, ~150 parameters) for the START transition in yeast and integrated it with our published model of the whole cell cycle.
  • Model addresses outstanding issues related to the precise mechanism and timing of transcriptional, post-translational and localization events, as well as size control under varying growth conditions.
  • Model consistent with ~200 experimental mutant phenotypes pertaining to the START transition and rest of the cell cycle.
  • Built a basic model for the nutritional effect of size control in budding yeast cells.
  • This mechanism has been incorporated into the existing model of the yeast cell cycle to explain an initial set of START mutants.

• Modeling bistability in the canonical Wnt pathway:

  • Built a simplified model based upon the core module of the Wnt canonical pathway, and incorporated additional key regulatory interactions.
  • Model shows that the Wnt signaling pathway can display bistability, in agreement with preliminary experimental results.

Related publications

• Ravi J^#, Samart K, Zwolak JW, Tyson JJ^#. Modeling the START transition in the budding yeast cell cycle. Model Submitted. ^#Co-corresponding authors.
• Cantoria MJ^*, Alizadeh E^*, Ravi J, Bunnag N, Kettenbach N, Ahmed Y, Paek AL, Tyson JJ, Doubrovinski K^#, Lee E^#, Thorne CA^#. Feedback in the β-catenin destruction complex imparts bistability and cellular memory. 2022 bioRxiv

Students

• Kewalin Samart

Collaborators

Virginia Tech

• John Tyson

Vanderbilt University

• Ethan Lee
• Curtis Thorne (now at University of Arizona)