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University of California, San Diego


UC San Diego is dedicated to the advancement of knowledge through excellence in education and research at the undergraduate, graduate, professional school and postdoctoral levels. The campus is committed to community engagement, public service and industry partnerships in order to advance the health and well-being of our region, state, nation and the world. Our academic community of world-renowned faculty, bright students and dedicated staff is characterized by a culture of interdisciplinary collaboration and innovation which spans the globe.




  • MutInf & K-L Div/J-S Div: information theory analysis of molecular dynamics sims ( Software )

    MutInf is an analysis package written in Python. inline C, and R that analyses data from Molecular Dynamics Simulations to identify statistically significant correlated motions and calculate residue-by-residue conformational entropies. Our work has shown that the pattern of mutual information between residues can be used to predict potential allosteric sites, identify couplings between allosteric sites, and identify residues that might be important in mediating these couplings. Recently, we've also included a module to compare conformational ensembles from MD sims or sets of MD sims using the Kullback-Leibler Divergence / Jensen-Shannon Divergence expansion. This is useful for comparing simulations of wildtype/mutant proteins, apo/holo, simulations started from different conformations, etc. Please see McClendon et. al., JCTC, 2012. for more information.

    Keywords: allosteric communication, allosteric communication paths, allostery, correlated motions, entropy, Jensen-Shannon Divergence, Kullback-Leibler Divergence, mutual information

  • SimVascular: Cardiovascular Modeling and Simulation Application ( Software )

    This project is an open source release of tools for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. Commercial components have been used in the model construction, mesh generation and flow solver components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC. Discussion forums for the project can be accessed at https://simtk.org/forum/?group_id=188 (or click Advanced -> Public Forums from the links on the left).

    Keywords: 1D boundary conditions, blood flow, cardiovascular, finite element, fluid dynamics, image-based geometric modeling, Image segmentation, Mesh generation, vascular

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Last updated: 2013-10-01T11:04:45.783-05:00

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