Chandrajit Bajaj
Biography Research Publications Teaching Group Projects Software Sponsors Collaborators
Left image shows AchR's placement parameters (intra-extra cellular extents in the cell membrane) and one example embedding. Once the placement of one molecule is achieved, the process can be repeated to place the whole set where the density is guided by another parameter. The paremeters required to place the molecules (AchR, AchE). These parameters are crucial to obtain a spatially realistic model of the whole system.

Additional images for NMJ project
Link to Movie: NMJ LOD


Publications

Image Interpretation

  • C. Bajaj, S. Goswami
    Modeling Cardiovascular Anatomy from Patient-Specific Imaging Data
    Advances in Computational Vision and Medical Image Processing: Methods and Applications, ed. Joao Manuel R.S.Tavares and R.M. Natal Jorge, Chapter 1, pg 1 - 28, Springer, 2008

  • S. Park, C. Bajaj
    Feature Selection of 3D Volume Data through Multi-Dimensional Transfer Functions
    Pattern Recognition Letters, 28, 3, pp. 367-374, 2007. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Computational Approaches for Automatic Structural Analysis of Large Bio-molecular Complexes
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, (digital library) 22 June 2007 (pdf) (abstract)

  • Y. Zhang, Y. Bazilives, S. Goswami, T. Hughes, C. Bajaj
    Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
    Computer Methods in Applied Mechanics and Engineering (CMAME), 196 (29-30) 2943-2959. 2007

  • J. Oden, K. Diller, J. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Prudhomme, M. Rylander, R. Stafford, Y. Zhang
    Dynamic Data-Driven Finite Element Models for Laser Treatment of Cancer
    Journal of Numerical Methods for Partial Differential Equations, 23 (4) 901-922, 2007

  • Y. Zhang, Y. Bazilevs, S. Goswami, C. Bajaj, T. Hughes
    Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
    Proceedings of 15th International Meshing Roundtable, pp. 73-92. Birmingham, AL. September 17-20, 2006.

  • M. Baker, Z. Yu, W. Chiu, C. Bajaj
    Automated Segmentation of Molecular Subunits in Electron Cryomicroscopy Density Maps
    Journal of Structural Biology, 2006. Accepted. (pdf)

  • S. Park, C. Bajaj, G. Gladish
    Artery-Vein Separation of Human Vasculature from 3D Thoracic CT Angio Scans
    CompIMAGE. Coimbra, Portugal. October 20-21, 2006.

  • C. Bajaj, S. Goswami
    Secondary and Tertiary Structural Fold Elucidation from 3D EM Maps of Macromolecules
    Proceedings of the Fifth Indian Conference on Computer Vision, Graphics & Image Processing, ICVGIP 2006, LNCS 4338, Springer Verlag, 2006, 264 - 275. (abstract)

  • R. Araiza, M. Averill, G. Keller, S. Starks, C. Bajaj
    3-D Image Registration Using Fast Fourier Transform, With Potential Applications To Geoinformatics and Bioinformatics
    Proceedings of the International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems IPMU06, Paris, France, July 2-7, 2006, pp. 817-824. (pdf) (ps) (abstract)

  • Y. Zhang, C. Bajaj, B. Sohn
    3D Finite Element Meshing from Imaging Data
    Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194, 48-49, 5083-5106, 2005. (pdf) (abstract)

  • C. Bajaj, J. Castrillon-Candas, V. Siddavanahalli, Z. Xu
    Compressed Representations of Macromolecular Structures and Properties
    Structure, Volume 13, Issue 3, March 2005, Pages 463-471. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Automatic Ultrastructure Segmentation of Reconstructed CryoEM Maps of Icosahedral Viruses
    IEEE Transactions on Image Processing: Special Issue on Molecular and Cellular Bioimaging, 2005 Sep;14(9):1324-37. (pdf) (abstract)

  • B. Sohn, C. Bajaj, V. Siddavanahalli
    Volumetric Video Compression and Interactive Playback
    Computer Vision and Image Understanding, special issue on "Model-based and Image-based 3D Scene Representation for Interactive Visualization", 96(3), Pages 435-452, 2004. (pdf) (abstract)

  • Y. Zhu, B. Carragher, R. Glaeser, D. Fellmann, C. Bajaj, M. Bern, F. Mouche, F. Haas, R. Hall, D. Kriegman, S. Ludtke, S. Mallick, P. Penczek, A. Roseman, F. Sigworth, N. Volkmann, C. Potter
    Automatic Particle Selection: Results of a comparative study
    Journal of Structural Biology, Volume 145, 2004, Pages 3-14. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Detecting Circular and Rectangular Particles Based on Geometric Feature Detection in Electron Micrographs
    Journal of Structural Biology, Volume 145, 2004, Pages 168-180. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    A Fast and Adaptive Algorithm for Image Contrast Enhancement
    Proceedings of 2004 IEEE International Conference on Image Processing (ICIP'04), Volume 2, Oct. 24-27 2004, Pages 1001-1004, Singapore. (pdf) (ps) (abstract)

  • Z. Yu, C. Bajaj
    A Segmentation-Free Approach for Skeletonization of Gray-Scale Images via Anisotropic Vector Diffusion
    Proceedings of 2004 IEEE International Conference on Computer Vision and Pattern Recognition (CVPR'04), Volume 1, Pages 415-420, Washington, DC. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Visualization of Icosahedral Virus Structures from Reconstructed Volumetric Maps
    Technical Report TR-04-10, Department of Computer Sciences, The University of Texas at Austin, April 9, 2004. (pdf) (abstract)

  • C. Bajaj, Z. Yu, M. Auer
    Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143. (pdf)

  • W. Jiang, M. Baker, Q. Wu, C. Bajaj, W. Chiu
    Applications of Bilateral Denoising Filter in Biological Electron Microscopy
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 114-122. (pdf)

  • Z. Yu, C. Bajaj
    A clustering-based method for particle detection in electron micrographs
    Proceedings of the 5th International Conference on Advances in Pattern Recognition(ICAPR'03), pp. 137-140, Calcutta, India, December 2003. (pdf) (abstract)

  • B. Sohn, C. Bajaj
    Time-Varying Contour Topology
    Technical Report TR-03-61, Department of Computer Sciences, The University of Texas at Austin, December 12, 2003. (pdf)

  • C. Bajaj, Q. Wu, G. Xu
    Level-set Based Volumetric Anisotropic Diffusion for 3D Image Denoising
    ICES Technical Report 03-10, The University of Texas at Austin, 2003. (pdf)

  • Z. Yu, C. Bajaj
    A Geometric Feature Detection Approach to Particle Picking in Electron Micrographs
    Technical Report TR-03-30, Department of Computer Sciences, The University of Texas at Austin, July 28, 2003. (pdf)

  • C. Bajaj, Z. Yu, M. Auer
    Volumetric Filtering, Feature Extraction, and Visualization of Volumetric Tomographic Molecular Imaging
    Technical Report TR-03-31, Department of Computer Sciences, The University of Texas at Austin, July 28, 2003. (pdf) (abstract)

  • B. Duerstock, C. Bajaj, R. Borgens
    A Comparative Study of the Quantitative Accuracy of Three-Dimensional Reconstructions of Spinal Cord from Serial Histological Sections
    Journal of Microscopy, 210:2, (2003), 138-148. (pdf)

  • Z. Yu, C. Bajaj
    Normalized Gradient Vector Diffusion and Image Segmentation
    Proceedings of the 7th European Conference on Computer Vision (LNCS 2352), vol. 3, pp. 517-530, (Published by Springer Press), Copenhagen, Denmark, May 28-31, 2002. (pdf)

  • Z. Yu, C. Bajaj
    Image Segmentation Using Gradient Vector Diffusion and Region Merging
    Proceedings of the 16th International Conference on Pattern Recognition, vol. 2, pp. 941-944, (Published by IEEE CS-Press), Quebec, Canada, August 11-15, 2002. (pdf)

  • Z. Yu, C. Bajaj
    Anisotropic Vector Diffusion in Image Smoothing
    Proceeding of the 9th IEEE International Conference on Image Processing, vol. 1, pp. 828-831, (Published by IEEE CS Press), Rochester, New York, September 22-25, 2002. (pdf)

  • S. Park, C. Bajaj, V. Siddavanahalli
    Case Study: Interactive Rendering of Adaptive Mesh Refinement Data
    Proceedings of IEEE Visualization, Pages 521-524, 2002, Boston, MA. (pdf)

  • B. Sohn, C. Bajaj, V. Siddavanahalli
    Feature Based Volumetric Video Compression for Interactive Playback
    Proceedings of IEEE/SIGGRAPH Symposium on Volume Visualization and Graphics, Pages 89-96, 2002, Boston, MA. (pdf)

  • C. Bajaj, A. Shamir, B. Sohn
    Progressive Tracking of Isosurfaces in Time-Varying Scalar Fields
    CS & ICES Technical Report, University of Texas at Austin, 2002. (pdf)

  • H. Pfister, B. Lorenson, C. Bajaj, G. Kindlmann, W. Schroeder, L. Avila, K. Raghu, R. Machiraju, J. Lee
    The Transfer Function Bake-off
    IEEE Computer Graphics and Applications, Volume 21: Issue 3. May/June 2001. Pages 16-22. (pdf)

  • C. Bajaj, I. Ihm, S. Park
    3D RGB Image Compression for Interactive Applications
    ACM Transactions on Graphics, 20, 1, (2001), 10-38. (pdf) (ps) (abstract)

  • X. Zhang, C. Bajaj, W. Blanke
    Scalable Isosurface Visualization of Massive Datasets on COTS-Cluster
    Proc. of IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, pp. 51-58, San Diego, CA, 2001. (pdf)

  • C. Bajaj, I. Ihm, S. Park
    Visualization-Specific Compression of Large Volume Data
    Proc. of Pacific Graphics, pp. 212-222, 2001, Tokyo, Japan, Oct 2001. (pdf) (ps)

  • B. Duerstock, C. Bajaj, V. Pascucci, D. Schikore. K. Lin, R. Borgens
    Advances in three-dimensional reconstruction of the experimental spinal cord injury
    Computerized Medical Imaging and Graphics, Volume 24, Issue 6, November 2000, Pages 389-406. (pdf)

  • C. Bajaj, I. Ihm, S. Park
    Compression-Based 3D Texture Mapping for Real-Time Rendering
    Graphical Models, 62:6, (2000), 391-410. (pdf) (abstract)

  • C. Bajaj, V. Pascucci
    Time Critical Isosurface Refinement and Smoothing
    Proceedings of the ACM/IEEE Volume Visualization and Graphics Symposium 2000, Salt lake City, Utah, pp. 33- 42. (pdf) (ps)

  • C. Bajaj, I. Ihm, S. Park, D. Song
    Compression-Based Ray Casting of Very Large Volume Data in Distributed Environments
    HPC-Asia 2000, Pages 720-725, Beijing, China, May 2000. (pdf) (ps)

  • C. Bajaj, I. Ihm, S. Park
    Visualization-Specific Compression of Large Volume Data
    TICAM Technical Report #00-17. (pdf) (ps)

  • C. Bajaj, V. Pascucci, G. Zhuang
    Single Resolution Compression of Arbitrary Triangular Meshes with Properties
    Computational Geometry: Theory and Applications, Volume 14, Issues 1-3, 30 November 1999, Pages 167-186. (pdf) (ps)

  • C. Bajaj, I. Ihm, G Koo, S. Park
    Parallel Ray Casting of Visible Human on Distributed Memory Architectures
    In Proceedings of Joint EUROGRAPHICS - IEEE TCVG Symposium on Visualization, May 26-28, 1999, Vienna, Austria. pp. 269-276. (pdf) (ps)

  • C. Bajaj, V. Pascucci, G. Zhuang
    Progressive Compression and Transmission of Arbitrary Triangular Meshes
    In Proceedings of the 10th IEEE Visualization 1999 Conference, October 24-29, 1999. San Francisco, CA, pp. 307 - 316. (pdf) (ps)

  • C. Bajaj, I. Ihm, S. Park
    Making 3D Textures Practical
    In Proceedings of Pacific Graphics, October 5-7, 1999, Seoul, Korea, Pages 259-268. (pdf) (ps)

  • C. Bajaj, V. Pascucci, G. Zhuang
    Single Resolution Compression of Arbitrary Triangular Meshes with Properties
    Data Compression Conference 1999. Snowbird, Utah. Pages 247-256. (pdf) (ps)

  • C. Bajaj, V. Pascucci, D. Schikore
    Seed Sets and Search Structures for Optimal Isocountour Extraction
    TICAM Technical Report #99-35. (pdf) (ps)

  • C. Bajaj, V. Pascucci
    Progressive IsoContouring
    TICAM Technical Report #99-36. (pdf) (ps)

  • B. Duerstock, C. Bajaj, V. Pascucci, D. Schikore. K. Lin, R. Borgens
    Three-Dimensional Imaging of the Experimental Spinal Cord Injury
    TICAM Technical Report #99-37. (pdf) (ps)

  • C. Bajaj, V. Pascucci, R. Holt, A. Netravali
    Active Contouring of Images with Physical A-Splines
    TICAM Technical Report #99-03. (pdf) (ps)

  • L. Moriarty, B. Duerstock, C. Bajaj, K. Lin, R. Borgens
    Two and Three Dimensional Computer Graphics Evaluation of the Subacute Spinal Cord Injury
    Journal of Neurological Sciences, vol. 155, 121-137 (1998). (pdf)

  • C. Bajaj, D. Schikore
    Topology Preserving Data Simplification with Error Bounds
    Journal on Computers and Graphics, vol. 22.1, pp. 3-12, 1998. (pdf)

  • C. Bajaj
    Visualization Paradigms
    Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998). (pdf) (ps)

  • C. Bajaj, V. Pascucci, D. Schikore
    Accelerated IsoContouring of Scalar Fields
    Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998). (pdf) (ps)

  • C. Bajaj, V. Pascucci, G. Ribbiolo, D. Schikore
    Hypervolume Visualization: A Challenge in Simplicity
    Proceeding of the IEEE/ACM 1998 Symposium on Volume Visualization pages 95-102 October 1998, Research Triangle Park, NC. (pdf) (ps) (pdf) (ps)">abstract)

  • C. Bajaj, V. Pascucci, D. Schikore
    Visualization of Scalar Topology for Structural Enhancement
    Proceeding of the IEEE Visualization, pages 51-58, October 1998, Research Triangle Park, NC. (pdf) (ps)

  • C. Bajaj, V. Pascucci, D.Schikore
    The Contour Spectrum
    Proceedings of the 1997 IEEE Visualization Conference,167-173, October 1997 Phoeniz, Arizona. (pdf)

  • C. Bajaj, V. Pascucci, D. Schikore
    Fast Isocontouring for Improved Interactivity
    Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, (1996), San Francisco, CA. Pages: 39-46 (text) 99 (color plate). (pdf) (ps)

  • C. Bajaj, F. Bernardini, V. Pascucci, D. Schikore
    Interrogative Visualization of the Visible Human Datasets
    The Visible Human Project Conference, 1996. (ps)

  • D. Schikore, C. Bajaj
    Visualization of Scalar Topology for Structural Enhancement
    Technical Report 96-006, Purdue University, Computer Sciences (1996). (pdf) (ps) (ps)(pdf), Color Plate page 8(ps)(pdf)">abstract)

  • C. Bajaj, V. Pascucci, D. Schikore
    Fast Isocontouring for Improved Interactivity
    Technical Report 96-024, Purdue University, Computer Sciences (1996). (ps)

  • C. Bajaj
    Interactive Visualization of Multidimensional Data
    Computer Graphics and Applications, edited by S. Y. Shin, T. Kunii, World Scientific Publishing, (Invited Paper), (1995), 63-77. (pdf) (ps)

  • C. Bajaj, M. Fields
    The VAIDAK Medical Image Model Reconstruction Toolkit
    Proceedings: The 1993 ACM/SIGAPP Symposium on Applied Computing, (1993), Indianapolis, Indiana, ACM Press, 28-35. (pdf) (ps)

Structural Analysis

  • Z. Yu, C. Bajaj, M. Hoshijima, M. Holst, T. Hayashi, M. Ellisman, J. McCammon
    Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation
    Journal of Structural Biology, 2008. Accepted. (pdf) (abstract)

  • Y. Cheng, J. Suen, D. Zhang, S. Bond, Y. Zhang, Y. Song, N. Baker, C. Bajaj, M. Holst, J. McCammon
    Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations
    Biophysical Journal, 92: 3397-3406 (2007). (pdf) (abstract)

  • D. Zhang, J. Seun, Y. Zhang, Y. Song, Z. Radic, P. Tylor, M. Holst, N. Baker, J. McCammon
    Continuum Diffusion Rate Calculations by Solving the Time Varying Smoluchowski Equation Using Finite Element Methods
    Biophyscial Journal 88, 1659-1665 (2007)

  • Y. Zhang, Y. Bazilives, S. Goswami, T. Hughes, C. Bajaj
    Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
    Computer Methods in Applied Mechanics and Engineering (CMAME), 196 (29-30) 2943-2959. 2007

  • J. Oden, K. Diller, J. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Prudhomme, M. Rylander, R. Stafford, Y. Zhang
    Dynamic Data-Driven Finite Element Models for Laser Treatment of Cancer
    Journal of Numerical Methods for Partial Differential Equations, 23 (4) 901-922, 2007

  • X. Zhang, C. Bajaj, B. Kwon, T. Dolinsky, J. Nielsen, N. Baker
    Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Structural Similarity
    Multiscale Modeling and Simulation, 5 (4), 1196-213, 2006. (pdf) (abstract)

  • J. T. Oden, K. R. Diller, C. Bajaj, J. C. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, Y. Feng, D. Fuentes, S. Prudhomme, M. N. Rylander, R. J. Stafford, Y. Zhang
    Development of a Computational Paradigm for Laser Treatment of Cancer
    Lecture Notes in Computer Science, 3993: 530-537, 2006. (pdf) (abstract) (Related CVC Project)

  • J. T. Oden, K. R. Diller, C. Bajaj, J. C. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, Y. Feng, D. Fuentes, S. Prudhomme, M. N. Rylander, R. J. Stafford, Y. Zhang
    Development of a Computational Paradigm for Laser Treatment of Cancer
    International Conference on Computational Science (3): 530-537, 2006. (pdf) (abstract) (Related CVC Project)

  • Y. Bazilevs, Y. Zhang, V. Calo, S. Goswami, C. Bajaj, T. Hughes
    Isogeometric Analysis of Blood Flow: a NURBS-based Approach
    CompIMAGE. Coimbra, Portugal. October 20-21, 2006.

  • W. Liu, Y. Liu, D. Farrell, L. Zhang, X. Wang, Y. Fukui, N. Patankar, Y. Zhang, C. Bajaj, J. Lee, J. Hong, X. Chen, H. Hsu
    Immersed finite element method and its applications to biological systems
    Comput. Methods Appl. Mech. Engrg. 195 (2006) 1722–1749. (pdf) (abstract)

  • D. Zhang, J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M. Holst, C. Bajaj, N. Baker, J. McCammon
    Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods
    Biophys. J. 88, 1659-1665 (2005). (pdf) (abstract)

  • B. Kang, I. Ihm, C. Bajaj
    Extending the Photon Mapping Method for Realistic Rendering of Hot Gaseous Fluids
    Computer Animation and Virtual Worlds (CASA 2005), 16, 3, 353-363. (pdf) (abstract)

  • Y. Song, Y. Zhang, C. Bajaj, N. Baker
    Continuum Diffusion Reaction Rate Calculations of Wild Type and Mutant Mouse Acetylcholinesterase: Adaptive Finite Element Analysis
    Biophysical Journal, 87(3):1558-1566, 2004. (pdf)

  • Y. Song, Y. Zhang, T. Shen, C. Bajaj, J. McCammon, N. Baker
    Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
    Biophysical Journal, 86(4):2017-2029, 2004. (pdf) (abstract)

  • Y. Shin, C. Bajaj
    Auralization I: Vortex Sound Synthesis
    Proceedings of Symposium on Visualization, Joint Eurographics - IEEE TCVG, VisSym 2004, Symposium on Visualization, pp. 193-200, Konstanz, Germany, May 19-21, 2004. Eurographics Association 2004, ISBN 3-905673-07-X. (pdf) (ps) (abstract)

  • Z. Yu, C. Bajaj
    A Segmentation-Free Approach for Skeletonization of Gray-Scale Images via Anisotropic Vector Diffusion
    Proceedings of 2004 IEEE International Conference on Computer Vision and Pattern Recognition (CVPR'04), Volume 1, Pages 415-420, Washington, DC. (pdf) (abstract)

  • C. Bajaj, I. Ihm, J. Min, J. Oh
    SIMD Optimization of Linear Expressions for Programmable Graphics Hardware
    Computer Graphics Forum, 23, 4(2004), 1-18. (pdf)

  • C. Bajaj, G. Xu
    Adaptive Surfaces Fairing by Geometric Diffusion
    Geometric Modeling: Techniques, Applications, Systems and Tools, 2004, M. Sarfraz(ed), Kluwer Academic Publishers, ISBN: 1-4020-1817-7, Pages 32-49. (pdf) (abstract)

  • C. Bajaj, G. Xu
    Anisotropic Diffusion of Surfaces and Functions on Surfaces
    ACM Transactions on Graphics, 22, 1, (2003), 4-32. (pdf)

  • C. Bajaj, G. Xu, J. Warren
    Acoustics Scattering on Arbitrary Manifold Surfaces
    Geometric Modeling and Processing, Theory and Application 2002, Japan, Pages 73-82. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Normalized Gradient Vector Diffusion and Image Segmentation
    Proceedings of the 7th European Conference on Computer Vision (LNCS 2352), vol. 3, pp. 517-530, (Published by Springer Press), Copenhagen, Denmark, May 28-31, 2002. (pdf)

  • Z. Yu, C. Bajaj
    Image Segmentation Using Gradient Vector Diffusion and Region Merging
    Proceedings of the 16th International Conference on Pattern Recognition, vol. 2, pp. 941-944, (Published by IEEE CS-Press), Quebec, Canada, August 11-15, 2002. (pdf)

  • Z. Yu, C. Bajaj
    Anisotropic Vector Diffusion in Image Smoothing
    Proceeding of the 9th IEEE International Conference on Image Processing, vol. 1, pp. 828-831, (Published by IEEE CS Press), Rochester, New York, September 22-25, 2002. (pdf)

  • C. Bajaj, G. Xu
    Anisotropic Diffusion of Noisy Surfaces and Noisy Functions on Surfaces
    Proc. of Information Visualization 2001, London, UK, 2001. (pdf)

  • C. Bajaj, G. Xu
    Adaptive fairing of surface meshes by geometric diffusion
    Proceedings of Fifth International Conference on Information Visualisation, 2001. 25-27 July 2001. Page(s):731 - 737. (pdf)

  • C. Bajaj, G. Xu
    Smooth Shell Construction with Mixed Prism Fat Surfaces
    Brunett, G., Bieri,H., Farin, G. (eds.), Geometric Modeling Computing Supplement, 14, (2001), 19-35. (pdf) (ps)

  • C. Bajaj, I. Ihm, S. Park
    Compression-Based 3D Texture Mapping for Real-Time Rendering
    Graphical Models, 62:6, (2000), 391-410. (pdf) (abstract)

  • C. Bajaj, F. Bernardini, S. Cutchin, K. Lin, E. Sacks, D. Schikore
    Comprehensive Analysis of Joints from Patient Clinical Data
    Technical Report 97-019, Purdue University, Computer Sciences, (1997). (pdf) (ps)

  • C. Bajaj, F. Bernardini, K. Lin, E. Sacks, D. Schikore
    Physical Simulation of the Visible Human Joints
    The Visible Human Project Conference, 1996. (ps)

  • C. Bajaj, D. Schikore
    Custom Prosthesis Design, Visualization, and Prototyping
    Proceedings of SPIE, Volume 2359. Visualization in Biomedical Computing 1994, Richard A. Robb, Editor, September 1994, pp. 504-510. (pdf) (ps)

  • C. Bajaj, D. Schikore
    Distributed Design of Hip Prosthesis using BHAUTIK
    Proceedings: The 1993 ACM/SIGAPP Symposium on Applied Computing, (1993), Indianapolis, Indiana, ACM Press, 36-39. (pdf)

  • V. Anupam, C. Bajaj, S. Cutchin, S. Evans, I. Ihm, J. Chen, A. Royappa, D. Schikore, G. Xu
    Scientific Problem Solving in a Distributed and Collaborative Geometric Environment
    3rd International Conference on Expert Systems for Numerical Computing, May 17-19, 1993, West Lafayette, IN.

  • C. Bajaj, W. Dyksen, C. Hoffmann, E. Houstis, T. Korb, J. Rice
    Computing About Physical Objects
    Proceedings: The 12th IMACS World Congress, Paris, (1988), 642-645.

Biophysics

  • L. Liu, C. Bajaj, J.O. Deasy, D.A. Low, T. Ju
    Surface Reconstruction From Non-parallel Curve Networks.
    Computer Graphics Forum (Proceedings of Eurographics 2008, Crete, Greece), Accepted for publication, 2008

  • C. Bajaj , A. DiCarlo and A. Paoluzzi
    PROTO-PLASM: Parallel Language for Adaptive and Scalable Modelling of Biosystems
    Philosophical Transactions of the Royal Society A, 2008 (to appear)

  • Z. Yu, C. Bajaj, M. Hoshijima, M. Holst, T. Hayashi, M. Ellisman, J. McCammon
    Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation
    Journal of Structural Biology, 2008. Accepted. (pdf) (abstract)

  • C. Bajaj, G. Xu, Q. Zhang
    A Fast Variational Method for the Construction of Smooth Molecular Surfaces
    Computer Methods in Applied Mechanics and Engineering, 2008. Accepted.

  • X. Yan, Z. Yu, P. Zhang, A. Batistti, P. Chipman, C.Bajaj, M. Bergoin, M. Rossman and T. Baker
    The Capsid Proteins of a Large, Icosahedral dsDNA Virus?
    Journal of Molecular Biology, October 2008. Available online from doi:10.1016/j.jmb.2008.11.002

  • W. Zhao, G. Xu, C. Bajaj
    An algebraic spline model of molecular surfaces
    Proceedings of the 2007 ACM symposium on Solid and physical modeling, pp. 297-302, 2007. (pdf) (abstract)

  • X. Zhang, C. Bajaj
    Extraction, Visualization and Quantification of Protein Pockets
    International Conference on Computational Systems Bioinformatics CSB2007, Vol 6, pp. 275-286

  • D. Zhang, J. Seun, Y. Zhang, Y. Song, Z. Radic, P. Tylor, M. Holst, N. Baker, J. McCammon
    Continuum Diffusion Rate Calculations by Solving the Time Varying Smoluchowski Equation Using Finite Element Methods
    Biophyscial Journal 88, 1659-1665 (2007)

  • J. Oden, K. Diller, J. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Prudhomme, M. Rylander, R. Stafford, Y. Zhang
    Dynamic Data-Driven Finite Element Models for Laser Treatment of Cancer
    Journal of Numerical Methods for Partial Differential Equations, 23 (4) 901-922, 2007

  • C. Bajaj, G. Xu, Q. Zhang
    Bio-Molecule Surfaces Construction Via a Higher-Order Level Set Method
    Proceedings of the 14th CAD/CG International Conference, 2007, Beijing, China

  • C. Bajaj
    Automatic Structure Interpretation of Single Particle Cryo-Electron Microscopy: From Images To Pseudo-Atomic Models
    2007 IEEE International Symposium on Biomedical Imaging, from Nano to Macro, Washington, DC, March 2007.

  • Y. Zhang, G. Xu, C. Bajaj
    Quality Meshing of Implicit Solvation Models of Biomolecular Structures
    The special issue of Computer Aided Geometric Design (CAGD) on Applications of Geometric Modeling in the Life Sciences, Volume 23, Issue 6, August 2006, Pages 510-530. (pdf) (abstract)

  • X. Zhang, C. Bajaj, B. Kwon, T. Dolinsky, J. Nielsen, N. Baker
    Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Structural Similarity
    Multiscale Modeling and Simulation, 5 (4), 1196-213, 2006. (pdf) (abstract)

  • C. M. Shepherd, I. A. Borelli, G. Lander, P. Natarajan, V. Siddavanahalli, C. Bajaj, J. E. Johnson, C. L. Brooks, III, V. S. Reddy
    VIPERdb: a relational database for structural virology
    Nucleic Acids Res. 2006 Jan 1; 34 (Database Issue), D386-9, 2006 (pdf) (abstract)

  • Y. Zhang, Y. Bazilevs, S. Goswami, C. Bajaj, T. Hughes
    Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
    Proceedings of 15th International Meshing Roundtable, pp. 73-92. Birmingham, AL. September 17-20, 2006.

  • M. Baker, Z. Yu, W. Chiu, C. Bajaj
    Automated Segmentation of Molecular Subunits in Electron Cryomicroscopy Density Maps
    Journal of Structural Biology, 2006. Accepted. (pdf)

  • J. T. Oden, K. R. Diller, C. Bajaj, J. C. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, Y. Feng, D. Fuentes, S. Prudhomme, M. N. Rylander, R. J. Stafford, Y. Zhang
    Development of a Computational Paradigm for Laser Treatment of Cancer
    International Conference on Computational Science (3): 530-537, 2006. (pdf) (abstract) (Related CVC Project)

  • C. Bajaj, S. Goswami, Z. Yu, Y. Zhang, Y. Bazilevs, T. Hughes
    Patient Specific Heart Models from High Resolution CT
    CompIMAGE. Coimbra, Portugal. October 20-21, 2006.

  • C. Bajaj, S. Goswami
    Secondary and Tertiary Structural Fold Elucidation from 3D EM Maps of Macromolecules
    Proceedings of the Fifth Indian Conference on Computer Vision, Graphics & Image Processing, ICVGIP 2006, LNCS 4338, Springer Verlag, 2006, 264 - 275. (abstract)

  • W. Liu, Y. Liu, D. Farrell, L. Zhang, X. Wang, Y. Fukui, N. Patankar, Y. Zhang, C. Bajaj, J. Lee, J. Hong, X. Chen, H. Hsu
    Immersed finite element method and its applications to biological systems
    Comput. Methods Appl. Mech. Engrg. 195 (2006) 1722–1749. (pdf) (abstract)

  • Y. Zhang, C. Bajaj, B. Sohn
    3D Finite Element Meshing from Imaging Data
    Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194, 48-49, 5083-5106, 2005. (pdf) (abstract)

  • D. Zhang, J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M. Holst, C. Bajaj, N. Baker, J. McCammon
    Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods
    Biophys. J. 88, 1659-1665 (2005). (pdf) (abstract)

  • J. Castrillon-Candas, C. Bajaj, V. Siddavanahalli
    An Adaptive Irregularly Spaced Fourier Method for Protein-Protein Docking
    Technical Report TR-05-34, Department of Computer Sciences, The University of Texas at Austin, July 11, 2005. (pdf) (abstract)

  • C. Bajaj, J. Castrillon-Candas, V. Siddavanahalli, Z. Xu
    Compressed Representations of Macromolecular Structures and Properties
    Structure, Volume 13, Issue 3, March 2005, Pages 463-471. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Automatic Ultrastructure Segmentation of Reconstructed CryoEM Maps of Icosahedral Viruses
    IEEE Transactions on Image Processing: Special Issue on Molecular and Cellular Bioimaging, 2005 Sep;14(9):1324-37. (pdf) (abstract)

  • C. Bajaj, Z. Yu
    Geometric and Signal Processing of Reconstructed 3D Maps of Molecular Complexes
    Handbook of Computational Molecular Biology, Edited by S. Aluru, Chapman & Hall/CRC Press, Computer and Information Science Series, December 21, 2005, ISBN: 1584884061. (pdf) (abstract)

  • C. Bajaj
    Geometric Modeling and Quantitative Visualization of Virus Ultrastructure
    Modeling Biology: Structures, Behaviors, Evolution, Edited L. da Fontoura Costa and M. Laublichler, MIT Press, 2005, (to appear). (pdf)

  • Y. Song, Y. Zhang, C. Bajaj, N. Baker
    Continuum Diffusion Reaction Rate Calculations of Wild Type and Mutant Mouse Acetylcholinesterase: Adaptive Finite Element Analysis
    Biophysical Journal, 87(3):1558-1566, 2004. (pdf)

  • Y. Song, Y. Zhang, T. Shen, C. Bajaj, J. McCammon, N. Baker
    Finite Element Solution of the Steady-State Smoluchowski Equation for Rate Constant Calculations
    Biophysical Journal, 86(4):2017-2029, 2004. (pdf) (abstract)

  • Y. Zhu, B. Carragher, R. Glaeser, D. Fellmann, C. Bajaj, M. Bern, F. Mouche, F. Haas, R. Hall, D. Kriegman, S. Ludtke, S. Mallick, P. Penczek, A. Roseman, F. Sigworth, N. Volkmann, C. Potter
    Automatic Particle Selection: Results of a comparative study
    Journal of Structural Biology, Volume 145, 2004, Pages 3-14. (pdf) (abstract)

  • Z. Yu, C. Bajaj
    Detecting Circular and Rectangular Particles Based on Geometric Feature Detection in Electron Micrographs
    Journal of Structural Biology, Volume 145, 2004, Pages 168-180. (pdf) (abstract)

  • C. Bajaj, P. Djeu, V. Siddavanahalli, A. Thane
    TexMol: Interactive Visual Exploration of Large Flexible Multi-component Molecular Complexes
    Proc. of the Annual IEEE Visualization Conference, October 2004, Austin, Texas, IEEE Computer Society Press, pp. 243-250. (pdf)

  • C. Bajaj, Z. Yu, M. Auer
    Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143. (pdf)

  • W. Jiang, M. Baker, Q. Wu, C. Bajaj, W. Chiu
    Applications of Bilateral Denoising Filter in Biological Electron Microscopy
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 114-122. (pdf)

  • C. Bajaj, V. Pascucci, A. Shamir, R. Holt, A. Netravali
    Dynamic Maintenance and Visualization of Molecular Surfaces
    Discrete Applied Mathematics 127 (2003). Pages 23-51. (pdf) (ps) (abstract)

  • B. Duerstock, C. Bajaj, R. Borgens
    A Comparative Study of the Quantitative Accuracy of Three-Dimensional Reconstructions of Spinal Cord from Serial Histological Sections
    Journal of Microscopy, 210:2, (2003), 138-148. (pdf)

  • B. Duerstock, C. Bajaj, V. Pascucci, D. Schikore. K. Lin, R. Borgens
    Advances in three-dimensional reconstruction of the experimental spinal cord injury
    Computerized Medical Imaging and Graphics, Volume 24, Issue 6, November 2000, Pages 389-406. (pdf)

  • C. Bajaj, H. Lee, R. Merkert, V. Pascucci
    NURBS based B-rep Models from Macromolecules and their Properties
    In Proceedings of Fourth Symposium on Solid Modeling and Applications, Atlanta,Georgia, 1997, C. Hoffmann and W. Bronsvort Eds., ACM Press. pp. 217-228. (pdf) (ps)

  • C. Bajaj, E. Coyle, K. Lin
    Arbitrary Topology Shape Reconstruction from Planar Cross Sections
    Graphical Models and Image Processing, 58:6, (1996), 524-543. (pdf)

  • C. Bajaj, V. Anupam, D. Schikore
    Custom Prosthesis Design and Prototyping Using Multimedia
    Multimedia Medical Education, edited by Roy Rada and Claude Ghaoui, Intellect Books, Oxford, England, (1995), chapter 3, 39-47, ISBN 1-871516-63-3.

  • C. Bajaj
    Distributed Medical Modeling, Design Prototyping and Collaborative Visualization
    Proceedings: Applications of Computer Vision in Medical Image Processing, AAAI 1994 Spring Symposium, AIM-94, Stanford, CA, (1994).

  • C. Bajaj
    Electronic Skeletons: Modeling Skeletal Structures with Piecewise Algebraic Surfaces
    Curves and Surfaces in Computer Vision and Graphics 2: Proceedings of the Symposium on Electronic Imaging Science and Technology, volume 1610, pages 230-237, Boston, MA, 1991. (pdf) (abstract)

Computational (Algebraic) Geometry

  • C. Bajaj, G. Xu, Q.Zhang
    Bio-Molecule Surfaces Construction Via a Higher-Order Level Set Method
    accepted for publication in Journal of Computational Science and Technology, 2008

  • C. Bajaj, A. Paoluzzi, S. Portuesi, N. Lei and W. Zhao
    Boolean Set Operations with Cubic Algebraic Patches
    Computer-Aided Design and Applications, 2008 (to appear)

  • C. Bajaj , A. DiCarlo and A. Paoluzzi
    PROTO-PLASM: Parallel Language for Adaptive and Scalable Modelling of Biosystems
    Philosophical Transactions of the Royal Society A, 2008 (to appear)

  • C.Bajaj, S. Goswami
    Multi-Component Heart Reconstruction from Volumetric Imaging
    Proc. of the ACM Solid and Physical Modeling Symposium, Stony Brook, NY, 2008, (to appear)

  • Z. Yu, C. Bajaj, M. Hoshijima, M. Holst, T. Hayashi, M. Ellisman, J. McCammon
    Three-Dimensional Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between Microscopic Imaging and Mathematical Simulation
    Journal of Structural Biology, 2008. Accepted. (pdf) (abstract)

  • C. Bajaj, G. Xu, Q. Zhang
    A Fast Variational Method for the Construction of Smooth Molecular Surfaces
    Computer Methods in Applied Mechanics and Engineering, 2008. Accepted.

  • C. Bajaj, S. Goswami
    Modeling Cardiovascular Anatomy from Patient-Specific Imaging Data
    Advances in Computational Vision and Medical Image Processing: Methods and Applications, ed. Joao Manuel R.S.Tavares and R.M. Natal Jorge, Chapter 1, pg 1 - 28, Springer, 2008

  • X. Yan, Z. Yu, P. Zhang, A. Batistti, P. Chipman, C.Bajaj, M. Bergoin, M. Rossman and T. Baker
    The Capsid Proteins of a Large, Icosahedral dsDNA Virus?
    Journal of Molecular Biology, October 2008. Available online from doi:10.1016/j.jmb.2008.11.002

  • W. Zhao, G. Xu, C. Bajaj
    An algebraic spline model of molecular surfaces
    Proceedings of the 2007 ACM symposium on Solid and physical modeling, pp. 297-302, 2007. (pdf) (abstract)

  • S. Goswami, A. Gillette, C. Bajaj
    Efficient Delaunay Mesh Generation From Sampled Scalar Functions
    Proceedings of the 16th International Meshing Roundtable, Seattle, WA, October 2007. pages 495 - 511

  • C. Bajaj, A. Gillette, S. Goswami
    Topology Based Selection and Curation of Level Sets
    Accepted as a Book Chapter in Topology-in-Visualization, Topo-in-Vis'07, ed. A. Wiebel, H. Hege, K. Polthier, G. Scheuermann, 2007

  • C. Bajaj
    Automatic Structure Interpretation of Single Particle Cryo-Electron Microscopy: From Images To Pseudo-Atomic Models
    2007 IEEE International Symposium on Biomedical Imaging, from Nano to Macro, Washington, DC, March 2007.

  • Y. Zhang, C. Bajaj
    Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
    Computer Methods in Applied Mechanics and Engineering, Volume 195, Issues 9-12, 1 February 2006, Pages 942-960. (pdf) (abstract) (Related CVC Project)

  • G. Xu, Q. Pan, C. Bajaj
    Discrete Surface Modelling Using Partial Differential Equations
    Computer Aided Geometric Design, Volume 23/2, pp 125-145, 2006. (pdf) (abstract)

  • Y. Zhang, C. Bajaj, B. Sohn
    3D Finite Element Meshing from Imaging Data
    Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194, 48-49, 5083-5106, 2005. (pdf) (abstract)

  • C. Bajaj
    A Laguerre Voronoi Based Scheme for Meshing Particle Systems
    Japan Journal of Industrial and Applied Mathematics, (JJIAM), vol. 22, No. 2, Pages 167-177, June 2005. (pdf) (abstract)

  • D. Zhang, J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M. Holst, C. Bajaj, N. Baker, J. McCammon
    Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State Smoluchowski Equation Using Finite Element Methods
    Biophys. J. 88, 1659-1665 (2005). (pdf) (abstract)

  • C. Bajaj
    Geometric Modeling and Quantitative Visualization of Virus Ultrastructure
    Modeling Biology: Structures, Behaviors, Evolution, Edited L. da Fontoura Costa and M. Laublichler, MIT Press, 2005, (to appear). (pdf)

  • Y. Zhang, C. Bajaj
    Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Imaging Data
    In Proceedings of 13th International Meshing Roundtable, pp. 365-376. Willamsburg, VA. September 19-22, 2004. (pdf)

  • M. van Kreveld, R. van Oostrum, C. Bajaj, V. Pascucci, D. Schikore
    Contour Trees and Small Seed Sets for Isosurface Generation
    Topological Data Structures for Surfaces
    Chap5, pp. 71-86, 2004. ed. by S. Rana, John Wiley & Sons, Ltd, 2004.

  • C. Bajaj
    A Laguerre Voronoi Based Scheme for Meshing Particle Systems
    Proc. of International Symposium on Voronoi Diagrams in Science and Engineering, VD2004, University of Tokyo, Japan, Sep 2004, pp. 115 -122. (pdf) (abstract)

  • C. Bajaj, G. Xu, R. Holt, A. Netravali
    NURBS Approximation of A-splines and A-patches
    International Journal of Computational Geometry and Applications, 13, 5, (2003), 359-389. (pdf)

  • C. Bajaj, V. Pascucci, A. Shamir, R. Holt, A. Netravali
    Dynamic Maintenance and Visualization of Molecular Surfaces
    Discrete Applied Mathematics 127 (2003). Pages 23-51. (pdf) (