Patrice Koehl
Department of Computer Science
Genome Center
Room 4319, Genome Center, GBSF
451 East Health Sciences Drive
University of California
Davis, CA 95616
Phone: (530) 754 5121
koehl@cs.ucdavis.edu




Research Overview

Biological systems have shapes that control their functions; these shapes are defined by a complex network of physical interactions, both internal to the systems and external through interactions with their environment. My research addresses this connection between physics, geometry and biology. I am interested in how the morphology of a biological system is specified and how it changes over time. I focus on molecular systems; some of my projects however extend to other fields, such as neurobiology and evolutionary biology. Although seemingly disparate, these areas share common methods and advances in one area produce knowledge that is often transformative in another.

The main scientific questions I ask can be categorized as:

  • Computational algorithmic developments. How do we handle the "Big Data" inherent to biological experiments, where "Big" refers to size, velocity, and complexity?
  • Morphometry. How is the morphology of biological systems specified and quantified? This concerns for example the measurements of brain structures and changes thereof during development, aging, learning, disease and evolution.
  • Morphogenesis. Can we predict how molecular shapes form from fundamental principles? I am particularly interested in predicting and manipulating bio-molecular structures such as proteins and RNA.
  • Morphodynamics. How do shapes evolve with time? How do we simulate for example the structural transition between two known forms of a macromolecule?
I do this by developing new mathematical and physical models, as well as new methods in computational geometry and scientific computing, and by employing large-scale high performance computing simulations for the analysis of biological systems.






  Page last modified 13 August 2013 http://www.cs.ucdavis.edu/~koehl/