BME Seminar Series

Event Date: April 10, 2013
Time: 9:30 a.m.
Location: MJIS 1001, WL Campus
"Computational modeling of spatial and dynamic properties of biological systems at multiscale: Protein functions, bionanopores, stochastic networks, and tissue patterning" presented by Jie Liang, Ph.D., Molecular and Systems Computational Bioengineering Lab (MoSCoBL), Department of Bioengineering, University of Illinois at Chicago.

Although the genetic blueprint of many species are known, understanding how living organisms work require a multi-scale approach combining studies of individual gene/protein, interactions of multiple proteins, molecular network, and cellular/tissue pattern formation.  At the molecular level, we discuss how new insights can be gained by computation of protein geometric structures, including the characterization of voids and pockets, and the origin of their existence.  We further illustrate how to predict protein functions from structures at large scale through reconstruction of the evolutionary history of binding surfaces using a Bayesian Monte Carlo method.  We also describe a new method for studying assembly of beta barrel membrane proteins, including prediction of oligomerization state, protein-protein interaction interface, relative melting temperature, as well as general stabilization strategy that is applicable for design of stable bionanopore.  At the network level, we describe the discrete chemical master equation (dCME) approach to account for the full stochasticity of rare and small copy number events important for cell fate by solving the chemical master equation exactly without Gillespie simulation or Fokker-Planck/Langevin approximation.  We show how to relate the computed landscape probability to phenomenological characterization of networks such as bi-stability, and the robustness of wild type versus mutant lambda phages.  At the cellular level, we describe a geometric model and an algorithm for simulating dynamic pattern formation of cell populations, where cells can grow, divide, differentiate, die, according to changes in mechanical or environment properties.  We showed how topological distribution of cells ranging from cucumber, drosophila, and animal can all be recovered from our model, as well as insight gained on the importance of cell proliferation in elongated tissue shape formation.  Preliminary results on tissue size control and would healing based on simulation of stem cells will also be presented.  It is our belief that this multi-scale approach will be useful for future engineering of biological systems.  (Please visit for further information).

The seminar will be teleconferenced to SL-220 at IUPUI.

~BME Faculty Host: Dr. Ann Rundell~

***Coffee and juice will be provided at West Lafayette***