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Projects - Graduate Student Collaboration

Cluster Simulation Automation

Collaborating with David Stockton on a simulation automation framework for HPC environments.

PI: Dr. Fidel Santamaria


Diffusion Simulation on HPC Cluster Using MCell

Collaborating with Namrata Mohapatra to enable MCell based simulations in an HPC cluster environment.

PI: Dr. Fidel Santamaria


Molecular Dynamics with NAMD on GPU Support

Collaborating with Jeremiah J. Babcock, Ph.D. Candidate (UTSA Department of Physics & Astronomy) to provide support for utilization of Cheetah Cluster GPU nodes towards running GPU enabled Molecular Dynamics simulations with the NAMD software package.

Website: Molecular Biophysics Laboratory
Contact: cbiadmin@utsa.edu


Signal-CTF: Prediction of Signal Peptide Cleavage Sites

Collaborating with Dr. Yufei Huang (UTSA Department of Electrical Engineering) to provide programming support services to compile MATLAB codes and externalize them on the web. This project allows users/paper reviewers to try the algorithm from a website hosted by the CBI. In addition, this approach allows the externalization of algorithms implemented in the robust MATLAB programming environment to multiple users without the need for multiple MATLAB licenses and the overhead of requiring users to install MATLAB or the MATLAB Compiler Runtime on their systems.

Website: Signal-CTF
Contact: yufei.huang@utsa.edu