Welcome to Chris Sweet's home page.
The simulation of proteins to obtain statistically and dynamically relevant data is a rapidly evolving field. To model systems of reasonable complexity with this dynamic range requires an integrated approach to modeling and numerics, incorporating, for example, dynamical perturbations and boundary conditions that allow for computation of stochastic averages, and adaptive decomposition of dynamics into fast and slow components. I am collaborating in this area with Jesús Izaguirre at the Laboratory for Computational Life Sciences at the University of Notre Dame, and Vijay Pande at Stanford University. My work there is aimed at developing powerful, practical schemes to accelerate the simulation of complex biomolecular models using various paradigms for high performance computing (including GPGPU).
I am also actively involved in the development of multiscale models for venous thrombosis simulation. This is a collaboration with the group of Mark Alber in the Mathematics department at the University of Notre Dame. Current new developments are the introduction of sub-cellular elements (SCE), for accurate cellular representation, and Langevin flow coupling, to couple the continuum model to the SCE.
I am one of the developers of Protomol, the open source C++ prototyping code where most of my ideas are implemented.
I am also interested in visualization software and have developed 3D Java Molecular Viewer code in a collaboration with James Sweet of Stafford University, UK. This OpenGL/Java project has now been extended to such diverse applications as viewing Fibrin Networks and Social Network analysis.
I am the Associate Director for Cyberinfrastructure at the Center for Research Computing (CRC) at the University of Notre Dame.
My contact information is:
Center for Research Computing,
University of Notre Dame,
111c OIT building,
Previously taught courses at Notre Dame: Math 20210 - Computer Programming and Problem Solving.