Department of Computer Science | Institute of Theoretical Computer Science | CADMO

Theory of Combinatorial Algorithms

Prof. Emo Welzl and Prof. Bernd Gärtner

Mittagsseminar (in cooperation with A. Steger, D. Steurer and B. Sudakov)

Mittagsseminar Talk Information

Date and Time: Tuesday, July 19, 2011, 12:15 pm

Duration: 30 minutes

Location: OAT S15/S16/S17

Speaker: Chandrajit Bajaj (Univ. of Texas at Austin)

Octrees Revisited: Efficient Energetic Calculations and Neighborhood Maintenance for Molecular Simulations

The rate limiting step of molecular simulations for disease therapeutics, is the evaluation of the molecular configurational potential energy E, and the atomic derivatives of E.
I shall first present linear time (1+epsilon) approximation geometry algorithms based on octrees for computation of all the most compute intensive terms of E for a static molecule. Next I shall present a dynamic octree data structure that can be used for implicit maintenance of nblists using space linear in n but independent of d, and can be updated very efficiently as the configuration of the molecule changes. The truncation of nonbonded interactions based on distance cutoffs is traditionally handled through the use of a precalculated and periodically updated explicit list of interacting atom pairs, known as the "nonbonded list" or nblist. The size of an nblist grows linearly with the number of atoms in the system (say, n), and cubically with the distance cutoff (say, d). Dynamic octrees are more space-efficient, update-efficient and cache-efficient compared to traditional explicit nblists.

This is joint work with Rezaul Chowdhury.

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