The engineering biology team at NIST is working to enable predictive engineering in synthetic biology. I am contributing in this direction by developing computational tools for: (a) simulating the interaction between genetic sensors and cells to study the efficiency of signal transduction, and (b) determining mutual information and other information theoretic quantities from widely-used experimental measurements (e.g. flow cytometry).
The 2nd and 3rd projects are part of NIST’s mission to accelerate materials innovation for the objectives of the Materials Genome Initiative. Specifically, I am developing methods to simulate polymer network growth as a stochastic process governed by the reaction-diffusion master nist-equation. Using this method, we can determine the effect of polymerization rate (or curing protocols) on the topological disorder in the network. We further compute the material properties of the disordered network. Thereby, computationally mapping polymerization protocols to transient and end-of-cure polymer properties. More details available on our MGI project site.
Sarkar, S., & Lin‐Gibson, S. (2018). Computational Design of Photocured Polymers Using Stochastic Reaction–Diffusion Simulation (Adv. Theory Simul. 7/2018). Advanced Theory and Simulations, 1(7), 1870016. (Cover article)
Sarkar, S., Baker, P. J., Chan, E. P., Lin-Gibson, S., & Chiang, M. Y. (2017). Quantifying the sensitivity of the network structure and properties from simultaneous measurements during photopolymerization. Soft matter, 13(21), 3975-3983.
Sarkar, S., Warner, J. E., Aquino, W., & Grigoriu, M. D. (2014). Stochastic reduced order models for uncertainty quantification of intergranular corrosion rates. Corrosion Science, 80, 257-268.
Sarkar, S., & Aquino, W. (2013). Changes in electrodic reaction rates due to elastic stress and stress-induced surface patterns. Electrochimica Acta, 111, 814-822.
Sarkar, S., Warner, J. E., & Aquino, W. (2012). A numerical framework for the modeling of corrosive dissolution. Corrosion Science, 65, 502-511.
Sarkar, S., & Aquino, W. (2011). Electroneutrality and ionic interactions in the modeling of mass transport in dilute electrochemical systems. Electrochimica Acta, 56(24), 8969-8978.