Chris Sweet

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111C Information Technology Center

Accelerating Biomolecular Simulations

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).

Protomol and Visarray

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 Notre Dame University. This OpenGL/Java project has now been extended to such diverse applications as viewing Fibrin Networks and Social Network analysis and examples can be seen at

Positions held

I am the the Associate Director of Cyberinfrastructure at the Center for Research Computing (CRC) at the University of Notre Dame. I have a concurrent faculty position as Research Assistant Professor in the Department of Computer Science and Engineering.

Visit my research webpage for more information.