Bala Krishnamoorthy

Research Interests

I am interested in both the thory and applications of integer optimization (or integer programming, or IP).
I have been studying Pre-conditioning Integer Programs using Column Basis Reduction, on which I
started working with my advisor Gabor Pataki. Here are some pre-prints on this topic.

Integer programming reformulation and decomposable knapsack problems (Accepted in Discrete Optimization).

Bounds on the size of branch-and-bound proofs for integer knapsacks (OR Letters, 2008, Vol 36, No. 1, p19-25; DOI: 10.1016/j.orl.2007.04.011).

Is Thinner Better? - Cascade Knapsack Problems (abstract and instances).
Cascade Knapsack Problems: Talk given at MIP 2008

I am working with Bill Webb and Nathan Moyer (PhD student) on basis reduction and its applications to
cryptography, especially public-key knapsack-like cryptosystems. Here is a talk (now OLD!) on this topic
that I gave at ISMP 2006 in Rio.

Another application of basis reduction I've been working on is to the number partitioning problems.

Basis Reduction-based Heuristics for Number Partitioning (abstract )
Fair Division (mostly NPP): Talk given at IBM Watson (May 2008)

I am interested in computational biology and bioinformatics, especially protein structure, and the
applications of computational geometry and topology to study proteins. I've been working on the
development of A Topological Characterization of Protein Structure , (started this work under
the guidance of Scott Provan and Alex Tropsha). Here are a couple of pre-prints:

A topological characterization of protein structure (book chapter in Biocomputing ,
proceedings of the Conference on Data Mining in Biomedicine held at the University of Florida).
Another abstract: Characaterization of protein structure using geometry and topology.

I have developed (not from scratch) a four-Body statistical scoring function for discriminating
non-native conformations of proteins from the native structure.

Development of a four-body statistical pseudo-potential to discriminate native from non-native
protein conformations (Bioinformatics, 19, 2003; p1540-1548).

Additional results, and program executables are available here. Working with Chris Deutsch, I recently developed
the four-body scoring function for predicting the effects of mutations on the stability/reactivity of proteins. Details
are here.

Four-Body Scoring Function for Mutagenesis (Bioinformatics 23, 2007; p3009-3015).

I also work on applications of optimization (mainly IP) to problems from (computational) biology. Here is a
sample talk on an IP model for protein sequencing.

I am a co-PI in the NSF program UBM - Training of Undergraduates in Biological and Mathematical Sciences .

Recent Conferences and Deadlines

INFORMS 07 Talk on Habitat management using IP.
AMS-MAA 08