1. Presentation-SC2001 Interactive Molecular Dynamics (IMD) IMD allows the user to guide and receive feedback from a running simulation Our demo illustrates IMD using the following components –Visualization program (VMD, UIUC) –Simulation program (ProtoMol, Notre Dame) –IMD API (UIUC/Notre Dame) –Haptic Device (Phantom, Sensable Technologies) –Web based collaboratory for sharing applications and data (BioCoRE, UIUC, www.ks.uiuc.edu/Research/biocore/) www.ks.uiuc.edu/Research/biocore/

2. Presentation-SC2001 Interactive Simulation Interfaces OBJECTIVE: Interactive interfaces for ProtoMol User friendly interface to setup, monitor, and steer simulations Ability to quickly experiment with molecules and cells APPROACH: 3-D Visualization using OpenGL Sockets interface between ProtoMol and visualization component Haptic Device interface Availability over the web through a generic GUI (BioCoRE, http://www.ks.uiuc.edu/Research/bioco re/) http://www.ks.uiuc.edu/Research/bioco re/

3. Presentation-SC2001 ProtoMol OBJECTIVE: Make ProtoMol a more scalable parallel program Hundreds of nodes Heterogeneous platforms APPROACH: Abstract parallel layer Dynamic load balancing Multithreading More scalable algorithms Future availability of ProtoMol simulations over web (thru’ BioCoRE) ProtoMol--parallel software framework for the simulation of bio-molecules ProtoMol is open source and available at http://www.cse.nd.edu/~lcls/Protomol.html

4. Presentation-SC2001 VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. VMD is available at: http://www.ks.uiuc.edu/Research/v md http://www.ks.uiuc.edu/Research/v md VMD is already available as an application and data sharing model for web based collaboratory research at BioCoRE (http://www.ks.uiuc.edu/Research/ biocore/)http://www.ks.uiuc.edu/Research/ biocore/ VMD