Daniel Russel Email: drussel at salilab.org Mailing address: Mission Bay, Byers Hall 1700 4th Street, Suite 503B University of California, San Francisco San Francisco, CA 94158-2330

General Research Interests

• constraint based modeling of large protein complexes
• Practical behavior of geometric structures under motion
• High level combinatorial descriptions of protein structure and protein folding
• Good software design and implementation for geometry and motion

Current Research Projects

• Building a computational model of the nuclear pore complex for trying to understand protein transport into and out of the nucleus.
• Using spanners to describe linear structures such as protein.
• Understanding the space of protein conformations explored by folding/unfolding simulations.

Papers

• My thesis which includes work on handling degeneracies and filtering with kinetic data structures that has not been published elsewhere.
• Automated Crystallographic Building Using the Medial Axis Transform of an Electron Density Isosurface, with Jun Aishima, Leo Guibas, Axel Brunger and Paul Adams. Acta Crystallographica D, 2005
• Exploring Protein Folding Trajectories Using Spanners, with Leonidas Guibas, Pacific Symposium on Biocomputing, 2005
• An Empirical Comparison of Techniques for Updating Delaunay Triangulations, with Leonidas Guibas, SoCG, 2004
• A Computational Framework for Handling Motion, with Leonidas Guibas and Menelaos Karavelas, ALENEX, 2004
• Collision Dection for Deforming Necklaces, with Pankaj Agarwal, Leonidas Guibas, An Nguyen and Li Zhang, Computational Geometry: Theory and Applications, 2004. An earlier version appeared in SoCG in 2002

Software

• Kinetic data structures framework. It handles exact computation of certificate failure times, among other goodies. It is integrated into CGAL.
• Polynomial package for exact manipulation of polynomial roots. It too is part of CGAL.
• A C++ PDB reader. It is designed to be easily used and easily modified. It includes utilities for performing rigid alignment of proteins, computing distance matrices, cRMS and dRMS and splitting and merging pdb files among other operations. Documentation Code (1.0.4) Note that this reader has been subsumed into CGAL and is no longer developed as an independent package.
• A simple C++ argument parser utility. It allows you to easily implement various types of arguments without having to worry about any of the bookkeeping. Documentation Code. I recommend you look at Boost.Program_options instead.
• Autoconf script to check for CGAL and CGALQt

Other

• My CV
• The unstructured part of my web site can be found here
• My smugmug site
• My brother's smugmug site
• TND
• Natasha’s web page
• Afra’s web page
• My father’s web page
• My patent for how to cut up teeth (more or less).