Computational biology: Where computer science meets math, physics, chemistry, and biology

Speaker: Dr Ramamoorthy Anandakrishnan, IITK Alumnus.
Date:      Thursday, February  02, 2012
Time:      05:30 P.M.
Venue:    L-11.

Tea to be served at 5:15 p.m.

Abstract:

Many revolutionary innovations result from inter-disciplinary research and development. An MIT white paper calls the convergence of life sciences, physical sciences and engineering the “third revolution” in biological  sciences. This work demonstrates the importance of inter-disciplinary  education, research and development. It is focused on developing practical  computer models of bio-molecular systems with the ultimate objective being  “rational drug design”. More specifically, a novel method is developed for approximating the protonation probability (pK) of ionizable sites in bio-molecules, which is critical for accurately modeling biological systems. Determining pK involves calculating the partition function Z from statistical mechanics, which is in general computationally intractable (NP complete). My method – the Direct Interaction Algorithm (DIA)–approximates Z as a combinatorial sum of products known as elementary symmetric functions (ESFs). A binary split-merge algorithm was developed to compute the ESFs in N2 operations, where N is the number of ionizable sites. The DIA was used to calculate equilibrium thermodynamic properties of the classic 2D Ising model for ferromagnetism. Test results show that the DIA can be a practical alternative for some problems where the commonly used Monte Carlo method converges slowly. This work indicates a successful voyage from computer science (modeling), to biology (drug design), to chemistry (pK), to physics (Z), to math (ESF), and back to computer science (algorithms).