Chandrajit Bajaj

Bajaj, Chandrajit
Computational Applied Mathematics Chair in Visualization
Director of Center for Computational Visualization

E-mail: bajaj@cs.utexas.edu

Website: http://www.cs.utexas.edu/~bajaj

Main Office: ACE 2.324A
Phone: 512-471-8870

Alternate Office: ACE 2.404
Phone: 512-232-7405

Mailing Address:
201 East 24th Street, ACES 2.324A
1 University Station, C0200
Austin, TX 78712-0027

Graduate Students:

  • Bettadapura Raghu, Prasad
  • Chen, Albert SC
  • Gillette, Andrew
  • Gopinath, Ajay
  • Kwon, Bong-June
  • Mollere, Alex
  • Moussalem, Maysam
  • Rahseed, Muhibur
  • Subramanian, Bharadwaj
  • Zhao, Wenqi

    • Post Doc Students:

  • Chowdhury, Rezaul
  • Goswami, Samrat
  • Rumsey, Clifton
  • Zhang, Qin
  • Zhang, Jessica

    • Research Summary:
       My research interests span the algorithmic and computational mathematics underpinnings of Structural Biology and Biophysics, Image Processing, Geometric Modeling, Computer Graphics, and Visualization. I am applying these algorithms and mathematics to: (a) structure elucidation and reconstruction of spatially realistic models of molecules, organelles, cells, tissues, and organs, from electron microscopy, and bio-imaging, (b) fast high-dimensional search and scoring procedures for identifying energetically favorable molecular binding conformations (e.g virtual screening for anti-viral drugs), (c) integrated approaches to computational modeling, analysis and interrogative visualization, especially for dynamic bio-medical phenomena My research is currently funded by grants from the National Science Foundation (NSF) and the National Institutes of Health (NIH). One of my NIH grants is R01-GM074258 on Hierarchical Methods for Large Biomolecular Complexes. The principal aims are to develop and implement efficient algorithms for determining structural features of macromolecules from 3D-EM (Electron Microscopy) maps at multiple resolutions, and for generating hierarchical, volumetric spline approximations of the determined structural features to facilitate fast Fourier based matching of geometry and imaging. Another NIH grant with a subcontract to Drs Art Olson and Michel Sanner of The Scripps Research Institute, is R01-GM073087 entitled A New Approach to Rapid Protein-Protein Docking. The principal aims are to develop, implement and test novel mathematical algorithms that speed up computational protein-protein docking especially for larger problems, as well as to significantly improve the prediction of protein-protein binding. A collaborative research grant from NSF-ITR-EIA-0325550: Subnanometer Structure Based Fold Determination of Biological Complexes is an interdisciplinary collaboration with Prof. Wah Chiu of Baylor College of Medicine, and Prof. Andrej Sali of University of California, San Francisco, to develop computational and visualization tools for feature extraction and structure modeling of large macromolecular complexes based on sequence data and in conjunction with sub-nanometer resolution cryo-Electron Microscopy (cryo-EM). See also http://ccvweb.csres.utexas.edu/ccv/projects/ for more details
     
    Research Images:

    Multiresolution Visualization of the Haloarcula Marismortui Large Ribosomal 50S subunit (1JJ2) - Visualization of the Haloarcula Marismortui Large Ribosomal 50S subunit (1JJ2) crystal structure(cf. Klein, Schmeing, Moore, Steitz) and based on protein and RNA classification. Light Yellow and Pale Pink are the 5S and 23S Rrna at coarse resolution while the remaining colors are proteins at near atomic resolution

    Visualization of the immunoglobulin complexed with Intact Human Rhinovirus

    Segmentation of a reconstructed 3D cryo-EM Map of the Herpes simplex virus into capsomeres

    Segmentation of a reconstructed 3D cryo-EM Map of the P22 Bacteriophage into capsomeres

    Visualization of a Mictorubule at Atomic Resolution

    Electrostatics Potential on the Solvent Accessible Surface of 50S Ribosomal Unit (1PNY)

     
    Publications:
    Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: Bridging the gap between microscopic imaging and mathematical simulation. (2008) J Struct Biol.
    Three-dimensional architecture of hair-bundle linkages revealed by electron-microscopic tomography. (2008) J Assoc Res Otolaryngol.
    PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems. (2008) Philos Transact A Math Phys Eng Sci. 366, 3045-65.
    Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow (2007) Computer Methods in Applied Mechanics and Engineering 196, 2943-2959.
    Computational Approaches for Automatic Structural Analysis of Large Bio-molecular Complexes (2007) IEEE Computer Society Digital Library. IEEE Computer Society, 22 Jun 07.
    Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Structural Similarity (2006) Multiscale Modeling and Simulation 5(4), 1196-1213.
    Quality Meshing of Implicit Solvation Models of Biomolecular (2006) Computer Aided Geometric Design 23, 510-530.
    Automatic Ultra-structure Segmentation of Reconstructed Cryo-EM Maps (2005) IEEE Transactions on Image Processing 14, 1324- 1337.

     
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