Prof. Chandrajit Bajaj will be delivering the first lecture in the Barr Systems distinguished lecture series for 2013-14. The seminar will be held on Tuesday, October 15th from 4-5PM in CSE E121.
Automated Prediction of Molecular Assemblies
Prof. Chandrajit Bajaj, University of Texas, Austin
Most bio-molecular complexes involve three or more molecules. We consider the automated prediction of bimolecular structure assemblies formulating it as the solution of a non-convex geometric optimization problem. The conformation of the molecules with respect to each other are optimized with respect to a hierarchical interface matching score. The assembly prediction decision procedure involves both search and scoring over very high dimensional spaces, [O(6n) for n rigid molecules], and moreover is provably NP-hard. To make things even more complicated, predicting bio-molecular complexes requires search optimization to include molecular flexibility and induced conformational changes as the assembly interfaces complementarily align. In this talk I shall first present a general approximation algorithm to predict multi-piece 3D assemblies, and then describe a provably polynomial time approximation scheme (PTAS) for the special case of predicting symmetric 3D spherical shell assemblies, given a constant number of primitive component molecules that make up the asymmetric unit. This spherical shell assembly solution utilizes a novel 6D parameterization (independent of the total number of individual molecules) of the search space and includes symmetric decorations of periodic and aperiodic spherical tilings.
Bio (adapted from Wikipedia):
Chandrajit Bajaj is a Professor of Computer Science at the University of Texas at Austin holding the Computational Applied Mathematics Chair in Visualization and is the director of the Computational Visualization Center, in the Institute for Computational Engineering and Sciences (ICES).
Bajaj's research has been in the fields of computational biology, geometric modeling, image processing, computational geometry, computer graphics, compression, mesh generation, scientific computation, and visualization.
Bajaj has been selected as a fellow of the Association for Computing Machinery (2009) and the American Association of the Advancement of Sciences (2008). His research has been awarded the Moncrief Grand Challenge Faculty Award in 2011. Several of his publications have been selected for best paper awards including Computer Aided Design and the 2010 Symposium on Solid and Physical Modeling.