CHANDRAJIT L. BAJAJ
`
`Professor of Computer Sciences,
`Computational Applied Mathematics Chair in Visualization,
`Director, Center for Computational Visualization,
`Institute for Computational Engineering and Sciences
`The University of Texas at Austin
`ACES 2.324, 201 East 24th Street, Austin, TX 78712
`
`Phone: (512) 471-8870
`
`bajaj@ices.utexas.edu
`
`
`
`Email: bajaj@cs.utexas.edu
`http://www.ices.utexas.edu/CCV
`
`Web: http://www.cs.utexas.edu/users/bajaj
`======================================================================
`PERSONAL
`Born April 19, 1958
`Married, 2 sons, 1 daughter
`United States Citizen
`
`EDUCATION
`1980 B.TECH. (Electrical Engineering), Indian Institute of Technology, Delhi
`1983 M.S. (Computer Science), Cornell University
`1984 Ph.D. (Computer Science), Cornell University
`
`PROFESSIONAL EXPERIENCE
`
`Fax: (512) 471-0982
`
` •
`
` Assistant Professor of Computer Sciences, Purdue University, 1984-89
`• Associate Professor of Computer Sciences, Purdue University, 1989-93
`• Visiting Associate Professor of Computer Sciences, Cornell University, 1990-91
`• Professor of Computer Sciences, Purdue University, 1993-97
`• Director of Image Analysis and Visualization Center, Purdue University, 1996-97
`• CAM (Comp. Appd. Math) Chair of Visualization, University of Texas at Austin, 1997- Present
`• Professor of Computer Sciences, University of Texas at Austin, 1997- Present
`• Director of Computational Visualization Center, University of Texas at Austin, 1997- Present
`
`HONORS, AWARDS & MEMBERSHIP IN PROFESSIONAL SOCIETIES
`
` •
`
` National Science Talent Scholarship, 1975. Dean's Honor Roll, IIT Delhi, 1975-1980
`• Scholastic Merit Award, (B. Tech. DGPA of 10.00/10.00)
`• Member of National Science Foundation (NSF) Panels on Advanced Computational Research, Geometric,
`Symbolic and Numeric Computing, Major Research Instrumentation, 1990 – 2006
`• Frame Technology Excellence in Publishing Award, 1993
`• Purdue University, Provost’s Research Center Initiation Award, 1994
`• Keynote Addresses at SIAM Computational Science (2000), Pacific Computer Graphics (2002), Volume Graphics
`(2004), EuroGraphics (2004), Computational Algebra (2004), Cyberworlds (2005), Institute of Mathematics and
`its Applications –IMA (2007), HSEMB Conference (2007), CAD conference (2009), Physics/Biology Interface
`(2009), CompImage (2010), ACM Solid Physical Modeling (2010), Symposium on Geometry Processing (2011),
`IEEE Pacific Vis (2012), Intl Conf. On Contemporary Computing (2012), Advances in Comp. Mechanics, (2013),
`22nd Meshing Roundtable (2013), NSF CyberBridges Workshop (2013), MBI-OSU Large Data Visualization
`Workshop (2014), Banff EM Workshop (BIRS) (2014)
`• Association of Computing Machinery, Student Chapter, Appreciation Certificate 2001
`• Member of National Institute of Health, Special Emphasis Study Sections, 2001, 2004
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`Petitioner Apple Inc. - Exhibit 1004, p. 1
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`• Association of Computing Machinery, Recognition of Service Award, 2002
`• University of Texas, Faculty Research Award 2004, Dean Research Assignment Award 2004
`• Member of the Austrian Science Foundation (FWF), Scientific Evaluation Committee 2005 - Present
`• Best paper award at Computer Aided Design (CAD) 2006
`•
`Invited Jacques Morgenstern Colloquium INRIA- Sophia Antipolis, France, April, 2006
`• Elected Member of Sigma Xi and Upsilon Pi Epsilon Honor Societies. Member of Association of Computing
`Machinery (ACM), Institute of Electrical and Electronic Engineers (IEEE), Biophysical Society, Society of
`Industrial and Applied Mathematics (SIAM), American Association for Advancement of Sciences (AAAS).
`• Panel Member of the National Academy of Sciences, Vietnam Education Foundation, 2006, 2007
`• Member of the NSF-CISE Board of Visitors, 2004, ETH Zurich, CS Dept Evaluation Committee (2004), INRIA
`Evaluation Committee 2007
`• King Abdullah University of Science and Technology (KAUST) Center Director Chair search committee, 2008
`• Member of Consolider Scientific Committee of the Spanish Ministerio de Ciencia e Innovacion, 2008, 2009
`• Member of the NIH-NCRR National Biomedical Computation Resource Advisory Committee, 2006 – Present
`• Member of Mol. Structure Function (MSFD), Study Section, National Institute of Health, 2008 – 2010
`• Chairperson of Mol. Structure Function (MSFD) Study Section, National Institute of Health, 2011 – 2014
`Invited Speaker at the 2010 Visions of Computing Lecture Series, UT-CS Austin, November 2010
`•
`• University of Texas-Moncrief Grand Challenge Faculty Research Award, 2009-2010
`• Fellow of The American Association for the Advancement of Science (AAAS), 2008 – Present
`• Fellow of the Association for Computing Machinery (ACM), 2009- Present
`• Fellow of University of Texas Institute for Cellular and Molecular Biology (ICMB), 2010
`• Best Paper Award at ACM Symposium on Solid and Physical Modeling, 2010, Haifa, Israel
`• University of Texas-Moncreif Grand Challenge Faculty Research Award – 2011, 2012
`• Program Co-Chair, SIAM/ACM Geometric and Physical Modeling Conference, Orlando, Florida – 2011
`•
`Invited William Mong Distinguished Colloquium, Hong Kong University, May, 2012
`•
`Invited Barrs Distinguished Colloquium, U of Florida, Oct 2013
`• Fellow of the Institute of Electrical and Electronic Engineers (IEEE), 2013 –
`
`RESEARCH ACTIVITIES
`
`My research interests span the theoretical and applied algorithmic mathematics underpinnings of Image Processing,
`Geometric Modeling, Computer Graphics, Visualization, Structural Biology and Bioinformatics. I analyze and apply
`these algorithms 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 for
`identifying energetically favorable molecular binding and related functional conformations , and (c) integrated
`approaches to multi-scale computational modeling, mathematical analysis and interrogative visualization of the
`dynamics of electrical signaling, and oscillations (3–10 Hz) amongst neurons, particularly in the hippocampus .
`I am on the faculty GSC of UT departments: CAM, BME, MATH, ICMB, and have been involved in several academic
`activities, including advising M.S and Ph.D. students from these programs.
`
`JOURNAL PUBLICATIONS (Current H-index = 59, I10-index = 191, Total Cites = 12,171)
`
`1. C. Bajaj (1985). “Geometric Optimization and the Polynomial Hierarchy”, Lecture Notes in Computer Science,
`176-195.
`2. C. Bajaj (1986). "Proving Geometric Algorithm Non-Solvability: An Application of Factoring Polynomials",
`Journal of Symbolic Computation, 2(1):99-102
`3. C. Bajaj, M. Kim. “Generation of Configuration Space Obstacles: The Case of Moving Algebraic Curves”,
`IEEE International Conference on Robotics and Automation, 4, 979-984
`4. S. Abhyankar, C. Bajaj (1987). "Automatic Parameterization of Rational Curves and Surfaces I: Conics and
`Conicoids", Computer Aided Design, 19(1):11-14
`5. S. Abhyankar, C. Bajaj (1987). "Automatic Parameterization of Rational Curves and Surfaces II: Cubics and
`Cubicoids", Computer Aided Design, 19(9):499-502
`6. M. Atallah, C. Bajaj (1987). "Efficient Algorithms for Common Transversals", Information Processing Letters,
`25(2):87-91
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`Petitioner Apple Inc. - Exhibit 1004, p. 2
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`7. C. Bajaj (1987). "Geometric Optimization and the Polynomial Hierarchy", Theoretical Computer Science,
`54(1):87-102
`8. S. Abhyankar, C. Bajaj (1988). "Automatic Parameterization of Rational Curves and Surfaces III: Algebraic Plane
`Curves", Computer Aided Geometric Design, 5(4):309-321
`9. M. Wu, C. Bajaj, C. Liu (1988). "Face Area Evaluation Algorithm for Solids", Computer Aided Design, 20(2):75-
`82
`10. C. Bajaj, T. Moh (1988). "Generalized Unfoldings for Shortest Paths in Euclidean 3-Space", International Journal
`of Robotics Research, 7(1):71-76
`11. C. Bajaj, M. Kim (1988). "Generation of Configuration Space Obstacles: The Case of Moving Spheres", IEEE
`Journal of Robotics and Automation, 4(1):94-99
`12. C. Bajaj (1988). "The Algebraic Degree of Geometric Optimization Problems", Discrete and Computational
`Geometry, 3(1):177-191
`13. C. Bajaj, C. Hoffmann, R. Lynch, J. Hopcroft (1988). "Tracing Surface Intersections", Computer Aided Geometric
`Design, 5(4):285-307
`14. S. Abhyankar, C. Bajaj (1989). "Automatic Parameterization of Rational Curves and Surfaces IV: Algebraic Space
`Curves", ACM Transactions on Graphics, 8(4):325-334
`15. C. Bajaj, M. Kim (1989). "Generation of Configuration Space Obstacles: The Case of Moving Algebraic Curves",
`Algorithmica, 4(1):157-172
`16. C. Bajaj, M. Li (1989). "Geometric Optimization and D^P -Completeness", Discrete and Computational Geometry,
`4(1):3-13. Abstract appears in Zentralblatt fur Mathematik.
`17. C. Bajaj (1990). “Rational Hypersurface Display”, Computer Graphics, 24(2), 117-127
`18. C. Bajaj, M. Kim (1990). "Convex Hulls of Objects bounded by Algebraic Curves", Algorithmica, 6(1):533-553
`19. C. Bajaj, M. Kim (1990). "Generation of Configuration Space Obstacles: The Case of Moving Algebraic Surfaces",
`International Journal of Robotics Research, 9(1):92-112
`20. C. Bajaj, T. Dey (1990). "Polygon Nesting and Robustness", Information Processing Letters, 35(1):23-32
`21. C. Bajaj, T. Dey (1990). “Robust Computations of Polygon Nesting”, International Workshop on Discrete
`Algorithms and Complexity, 33-40
`22. J. Johnstone, C. Bajaj (1990). "Sorting Points along an Algebraic Curve", Siam Journal on Computing, 19(5):925-
`967
`23. C. Bajaj, I. Ihm (1992). "Algebraic Surface Design with Hermite Interpolation", ACM Transactions on Graphics,
`11(1):61-91
`24. C. Bajaj, T. Dey (1992). "Convex Decomposition of Polyhedra and Robustness", Siam Journal on Computing,
`21(2):339-364
`25. T. Dey, K. Sugihara, C. Bajaj (1992). "Delaunay Triangulations in Three Dimensions with Finite Precision
`Arithmetic", Computer Aided Geometric Design, 9(6):457-470
`26. T. Dey, C. Bajaj, K. Sugihara (1991). "On Good Triangulations in Three Dimensions", International Journal of
`Computational Geometry and Applications, 2(1):75-95
`27. C. Bajaj, I. Ihm (1992). "Smoothing Polyhedra using Implicit Algebraic Splines", Computer Graphics, 26(2):79-88.
`28. C. Bajaj, J. Canny, T. Garrity, J. Warren (1993). "Factoring Rational Polynomials over the Complexes", Siam
`Journal on Computing, 22(2):318-331
`29. C. Bajaj, I. Ihm, J. Warren (1993). "Higher-Order Interpolation and Least-Squares Approximation Using Implicit
`Algebraic Surfaces", ACM Transactions on Graphics, 12(4):327-347
`30. V. Anupam, C. Bajaj, D. Schikore, M. Schikore (1994). "Distributed and Collaborative Visualization", IEEE
`Computer, 27(7)37-43
`31. C. Bajaj, G. Xu (1994). "NURBS Approximation of Surface/Surface Intersection Curves", Advances in
`Computational Mathematics, 2(1):1-21
`32. V. Anupam, C. Bajaj (1994). "SHASTRA - An Architecture for Development of Collaborative Applications",
`International Journal of Intelligent and Cooperative Information Systems, 3(2):155-166
`33. V. Anupam, C. Bajaj (1994). "SHASTRA: Multimedia Collaborative Design Environment", IEEE Multimedia,
`1(2):39-49
`34. C. Bajaj, F. Bernardini, G. Xu (1995). "Automatic Reconstruction of Surfaces and Scalar Fields from 3D Scans",
`Computer Graphics, pp 109-118
`35. C. Bajaj, A. Royappa (1995). "Finite Representations of Real Parametric Curves and Surfaces", International
`Journal of Computational Geometry and Applications, 5(3):313-326
`36. C. Bajaj, J. Chen, G. Xu (1995). "Modeling with Cubic A-patches", ACM Transactions on Graphics, 14(2):103-
`133
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`37. C. Bajaj, E. Coyle, K. Lin (1996). "Arbitrary Topology Shape Reconstruction from Planar Cross Sections",
`Graphical Models and Image Processing, 58(6):524-543
`38. C. Bajaj, G. Xu (1997). "Piecewise Rational Approximation of Real Algebraic Curves", Journal of Computational
`Mathematics, vol. 15(1):55-71
`39. C. Bajaj, F. Bernardini, G. Xu (1997). "Reconstructing Surfaces and Functions on Surfaces from Unorganized
`Three-Dimensional Data", Algorithmica, 19(1):243-261
`40. C. Bajaj, G. Xu (1997). "Spline Approximations of Real Algebraic Surfaces", Journal of Symbolic Computation,
`Special Isssue on Parametric Algebraic Curves and Applications, 23(23):315-333
`41. C. Bajaj, G. Xu (1997). “Modeling and Visualization of C1 and C2 Scattered Function Data on Curved Surfaces”,
`Proc. of 2nd Pacific Conference on Computer Graphics and Applications, 19-29
`42. C. Bajaj, R. Holt, A. Netravali (1998). "Rational Parameterizations of Nonsingular Real Cubic Surfaces", ACM
`Transactions on Graphics, 17(1):1-31
`43. E. Sacks, C. Bajaj (1998). "Sliced Configuration Spaces for Curved Planar Bodies", International Journal Of
`Robotics Research, 17(6):639-651
`44. C. Bajaj, D. Schikore (1998). "Topology Preserving Data Simplification with Error Bounds", Journal on
`Computers and Graphics, 22(1):3-12
`45. L. Moriarty, B. Duerstock, C. Bajaj, K. Lin, R. Borgens (1998). "Two and Three Dimensional Computer Graphics
`the Subacute Spinal Cord Injury", Journal of Neurological Sciences, 155(2):121-137
`Evaluation of
`http://tinyurl.com/PMID9562256, PMID: 9562256, PMC Journal in Process
`46. C. Bajaj, C. Baldazzi, S. Cutchin, A. Paoluzzi, V. Pascucci, M. Vicentino (1999). "A programming approach for
`complex animations. Part I. Methodology", Computer Aided Design, 31(11):695-710
`47. C. Bajaj, G. Xu (1999). "A-Splines: Local Interpolation and Approximation Using Gk- Continuous Piecewise Real
`Algebraic Curves", Computer Aided Geometric Design, 16(6):557-578
`48. F. Bernardini, C. Bajaj, J. Chen, D. Schikore (1999). "Automatic Reconstruction of 3D CAD Models from Digital
`Scans", International Journal on Computational Geometry and Applications, 9(4-5):327-369
`49. C. Bajaj, J. Chen, R. Holt, A. Netravali (1999). "Energy Formulations of A-Splines", Computer Aided Geometric
`Design, 16(1):39-59
`50. C. Bajaj, V. Pascucci, G. Zhuang (2002). "Single Resolution Compression of Arbitrary Triangular Meshes with
`Properties", Computational Geometry: Theory and Applications, 14(1-3):167-186
`51. C. Bajaj, E. Coyle, K. Lin (1999). "Tetrahedral Meshes from Planar Cross Sections", Computer Methods in
`Applied Mechanics and Engineering, 179(1-2):31-52
`52. B. Duerstock, C. Bajaj, V. Pascucci, D. Schikore. K. Lin, R. Borgens (2000). "Advances in three-dimensional
`reconstruction of the experimental spinal cord injury", Computerized Medical Imaging and Graphics, 24(6):389-
`406, http://tinyurl.com/PMID11008186, PMID: 11008186, PMC Journal in Process
`53. C. Bajaj, I. Ihm, S. Park (2000). "Compression-Based 3D Texture Mapping for Real-Time Rendering", Graphical
`Models, 62(6):391-410
`54. C. Bajaj, A. Royappa (2000). "Parameterization in Finite Precision", Algorithmica, 27(1):100-114
`55. G. Xu, C. Bajaj, W. Xue (2000). "Regular algebraic curve segments (I)-Definitions and characteristics", Computer
`Aided Geometric Design, 17(6):485-501
`56. G. Xu, C. Bajaj, C. Chu (2000). "Regular Algebraic Curve Segments (II) - Interpolation and Approximation",
`Computer Aided Geometric Design, 17(6):503-519
`57. C. Bajaj, I. Ihm, S. Park (2001). “3D RGB Image Compression for Interactive Applications”, ACM Transactions
`on Graphics, 20(1):10-38
`58. G. Xu, H. Huang, C. Bajaj (2001). "C1 Modeling with A-patches from Rational Trivariate Functions", Computer
`Aided Geometric Design, 18(3):221-243
`59. C. Bajaj, G. Xu (2001). "Regular Algebraic Curve Segments (III) - Applications in Interactive Design and Data
`Fitting", Computer Aided Geometric Design, 18(3):149-173
`60. H. Pfister, B. Lorenson, C. Bajaj, G. Kindlmann, W. Schroeder, L. Avila, K. Raghu, R. Machiraju, J. Lee (2002).
`"The Transfer Function Bake-off", IEEE Computer Graphics and Applications, 21(3):16-22
`61. C. Bajaj, S. Schaefer, J. Warren, G. Xu (2002). "A Subdivision Scheme for Hexahedral Meshes", The Visual
`Computer, 18(5):343-356
`62. G. Xu, C. Bajaj, S. Evans (2002). "C1 Modeling with Hybrid Multiple-sided A-patches", Special issue on Surface
`and Volume Reconstructions in the International Journal of Foundations of Computer Science, 13(2):261-284
`63. C. Bajaj, G. Xu, R. Holt, A. Netravali (2002). "Hierarchical Multiresolution Reconstruction of Shell Surfaces",
`Computer Aided Geometric Design, 19(2):89-112
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`64. B. Duerstock, C. Bajaj, R. Borgens (2003). "A Comparative Study of the Quantitative Accuracy of Three-
`Dimensional Reconstructions of Spinal Cord from Serial Histological Sections", Journal of Microscopy,
`210(2):138-148, http://tinyurl.com/PMID12753096, PMID: 12753096, PMC Journal In Process
`65. W. Blanke, C. Bajaj (2003). "Active Visualization in a Multidisplay Immersive Environment", Computers &
`Graphics, 27(5):681-691
`66. C. Bajaj, G. Xu (2003). "Anisotropic Diffusion of Surfaces and Functions on Surfaces", ACM Transactions on
`Graphics, 22(1):4-32
`67. W. Jiang, M. Baker, Q. Wu, C. Bajaj, W. Chiu (2003). "Applications of Bilateral Denoising Filter in Biological
`Electron Microscopy", Journal of Structural Biology, 144(1-2):114-122, doi:10.1016/j.jsb.2003.09.028,
`http://tinyurl.com/PMID14643214, PMID: 14643214, PMC Journal In Process
`68. G. Xu, C. Bajaj (2003). "Curvature Computations of 2-manifolds in R^k", Journal of Computational Mathematics,
`21(5):681-688
`69. C. Bajaj, V. Pascucci, A. Shamir, R. Holt, A. Netravali (2003). "Dynamic Maintenance and Visualization of
`Molecular Surfaces", Discrete Applied Mathematics, 127(1):23-51 doi: 10.1016/S0166-218X(02)00283-4.
`70. C. Bajaj, A. Netravali (2003). "NURBS Approximation of A-splines and A-patches", International Journal of
`Computational Geometry and Applications, 13(5):359-390
`71. C. Bajaj, Z. Yu, M. Auer (2003). "Volumetric Feature Extraction and Visualization of Tomographic Molecular
`Journal
`of
`Structural
`Biology,
`Imaging",
`144(1-2):132-143,
`doi:10.1016/j.jsb.2003.09.037,
`http://tinyurl.com/PMID14643216, PMID: 14643216, PMC Journal In Process
`72. C. Bajaj, G. Xu (2004). “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, 32-49,
`doi: 10.1109/IV.2001.942137
`73. Y. Zhu, B. Carragher, R. Glaeser, D. Fellmann, C. Bajaj, M. Bern, F. Mouche, F. Haas, R. Hall, D. Kriegman, et al
`(2004). "Automatic Particle Selection: Results of a Comparative Study, Journal of Structural Biology, 145(1-2):3-
`14, doi: 10.1016/j.jsb.2003.09.033, http://tinyurl.com/PMID15065668, PMID: 15065668, PMC Journal In Process
`74. Y. Song, Y. Zhang, C. Bajaj, N. Baker (2004). "Continuum Diffusion Reaction Rate Calculations of Wild-Type
`and Mutant Mouse Acetylcholinesterase: Adaptive Finite Element Analysis", Biophysical Journal, 87(3):1558-
`1566, doi: 10.1529/biophysj.104.041517, http://tinyurl.com/PMC1304562, PMCID: PMC1304562
`75. Z. Yu, C. Bajaj (2004). "Detecting Circular and Rectangular Particles Based on Geometric Feature Detection in
`Electron Micrographs", Journal of Structural Biology, 145(1-2):168-180, doi: 10.1016/j.jsb.2003.10.027,
`http://tinyurl.com/PMID15065684, PMID: 15065684, PMC Journal In Process
`76. Y. Song, Y. Zhang, T. Shen, C. Bajaj, J. McCammon, N. Baker (2004). "Finite Element Solution of the Steady-
`State Smoluchowski Equation for Rate Constant Calculations", Biophysical Journal, 86(4):2017-2029, doi:
`10.1529/biophysj.106.102533, http://tinyurl.com/PMC1304055, PMCID: PMC1304055
`77. C. Bajaj, I. Ihm, J. Min, J. Oh (2004). "SIMD Optimization of Linear Expressions for Programmable Graphics
`Hardware", Computer Graphics
`Forum,
`23(4):697-714,
`doi:
`10.1111/j.1467-8659.2004.00803.x,
`http://tinyurl.com/PMC2782869, PMCID: PMC2782869.
`78. C. Bajaj, B. Sohn, V. Siddavanahalli (2004). "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):435-452, http://tinyurl.com/PMC2805201a, PMCID:
`PMC2805201
`79. Y. Zhang, C. Bajaj, B. Sohn (2005). "3D Finite Element Meshing from Imaging Data", Computer Methods in
`Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194(48-49):5083-5106,
`doi:10.1016/j.cma.2004.11.026, http://tinyurl.com/PMC2748876, PMCID: PMC2748876
`80. C. Bajaj (2005). "A Laguerre Voronoi Based Scheme for Meshing Particle Systems", Japan Journal of Industrial
`and Applied Mathematics, (JJIAM), 22(2):167-177, doi: 10.1.1.73.9956, http://tinyurl.com/PMC2865151a ,
`PMC2865151
`81. Z. Yu, C. Bajaj (2005). "Automatic Ultrastructure Segmentation of Reconstructed CryoEM Maps of Icosahedral
`Viruses", IEEE Transactions on Image Processing: Special Issue on Molecular and Cellular Bioimaging, 14(9):
`1324-37, doi: 10.1109/TIP.2005.852770, http://tinyurl.com/PMID16190468, PMID16190468, PMC Journal in
`Process
`82. C. Bajaj, J. Castrillon-Candas, V. Siddavanahalli, Z. Xu (2005). "Compressed Representations of Macromolecular
`Structure,
`Structures
`and
`Properties",
`13(3):463-471,
`doi:10.1016/j.str.2005.02.004
`,
`http://tinyurl.com/PMID15766547, PMID15766547, PMC Journal in Process
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`83. Y. Zhang, G. Xu, C. Bajaj (2005). “Surface Smoothing and Quality Improvement of Quadrilateral/Hexahedral
`Meshes with Geometric Flow”, Comm. in Numerical Methods in Engineering, 24, doi:10.1002/cnm.1067, PMCID:
`PMC2761001
`84. D. Zhang, J. Suen, Y. Zhang, Y. Song, Z. Radic, P. Taylor, M. Holst, C. Bajaj, N. Baker, J. McCammon (2005).
`"Tetrameric Mouse Acetylcholinesterase: Continuum Diffusion Rate Calculations by Solving the Steady-State
`Smoluchowski Equation Using Finite Element Methods", Biophys.
`J.
`88(3):1659-1665,
`doi:
`10.1529/biophysj.104.053850, http://tinyurl.com/PMC1305222, PMCID: PMC1305222
`85. Y. Zhang, C. Bajaj (2006). "Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data",
`Computer Methods in Applied Mechanics and Engineering, 195(9-12):942-960, doi:10.1016/j.cma.2005.02.016,
`http://tinyurl.com/PMC2740490, PMCID: PMC2740490
`86. X. Zhang, C. Bajaj, B. Kwon, T. Dolinsky, J. Nielsen, N. Baker (2006). "Application of New Multiresolution
`Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Structural Similarity",
`Multiscale Modeling and Simulation, 5(4):1196-1213, doi: 10.1137/050647670, http://tinyurl.com/PMC2561295,
`PMCID: PMC2561295
`87. M. Baker, Z. Yu, W. Chiu, C. Bajaj (2006). "Automated Segmentation of Molecular Subunits in Electron
`Cryomicroscopy Density Maps", Journal of Structural Biology, 156(3):432-441, doi: 10.1016/j.jsb.2006.05.013,
`http://tinyurl.com/PMID16908194, PMID: 16908194, PMC Journal in Process
`88. G. Xu, Q. Pan, C. Bajaj (2006). "Discrete Surface Modeling Using Partial Differential Equations", Computer Aided
`Geometric Design, 23(2):125-145, doi:10.1016/j.cagd.2005.05.004, http://tinyurl.com/PMC2760856, PMCID:
`PMC2760856
`89. W. Liu, Y. Liu, D. Farrell, L. Zhang, X. Wang, Y. Fukui, N. Patankar, C. Bajaj, Y. Zhang, J. Lee, J. Hong, X.
`Chen, H. Hsu (2006). “Immersed Finite Element Method and Its Applications to Biological Systems”, Computer
`Methods
`In
`Applied
`Mechanics
`and
`Engineering
`(CMAME),
`195(13-16):1722-1749,
`doi:10.1016/j.cma.2005.05.049, http://tinyurl.com/PMC2830735, PMCID: PMC2830735
`90. C. Bajaj, A. Paoluzzi, G. Scorzelli (2006). "Progressive Conversion from B-rep to BSP for Streaming Geometric
`Modeling", Computer-Aided Design
`and Applications,
`3(5):577-586,
` PMCID:
`PMC3077047,
`http://tinyurl.com/PMC3077047
`91. Y. Zhang, G. Xu, C. Bajaj (2006). "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, 23(6):510-530, doi: 10.1016/j.cagd.2006.01.008, http://tinyurl.com/PMC2756697, PMCID:
`PMC2756697
`92. B. Sohn, C. Bajaj (2006). "Time-Varying Contour Topology", IEEE Transactions on Visualization and Computer
`Graphics (TVCG), 12(1):14-25, doi: 10.1109/TVCG.2006.16, http://tinyurl.com/PMC2703823, PMCID:
`PMC2703823.
`93. C. M. Shepherd, I. A. Borelli, G. Lander, P. Natarajan, V. Siddavanahalli, C. Bajaj, J. E. Johnson, C. L. Brooks, III,
`V. S. Reddy (2006). "VIPERdb: a relational database for structural virology", Nucleic Acids Res. 34(1):D386,
`http://tinyurl.com/PMC134735, PMCID: PMC1347395.
`94. 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 (2006). “Development of a Computational Paradigm for
`Lecture
`Notes
`in
`Computer
`Science,
`Laser
`Treatment
`of
`Cancer”,
`3993:
`530-537,
`http://dx.doi.org/10.1007/11758532_70, PMCID: PMC2676779.
`95. S. Park, C. Bajaj (2007). "Feature Selection of 3D Volume Data through Multi-Dimensional Transfer Functions",
`Pattern Recognition Letters, 28(3):367-374, doi: 10.1016/j.patrec.2006.04.008, http://tinyurl.com/PMC2743423,
`PMCID: PMC2743423.
`96. Z. Yu, C. Bajaj (2008). “Computational Approaches for Automatic Structural Analysis of Large Bio-molecular
`IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(4):568-582,
`Complexes”,
`http://tinyurl.com/PMID18989044, PMID: 18989044, PMC Journal in Process
`97. Y. Cheng, J. Suen, D. Zhang, S. Bond, Y. Zhang, Y. Song, N. Baker, M. Holst, C. Bajaj, J. McCammon (2007).
`“Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate
`Biophysical
`Journal,
`Calculations”,
`92:
`3397-3406,
`doi:10.1529/biophysj.106.102533,
`http://tinyurl.com/PMC1853150, PMCID: PMC1853150.
`98. Y. Zhang, Y. Bazilevs, S. Goswami, C. Bajaj, T. Hughes (2007). “Patient-Specific Vascular NURBS
`Modeling for Isogeometric Analysis of Blood Flow”, Computer Methods in Applied Mechanics and
`Engineering
`(CMAME),
`196(29-30):2943-2959,
`doi:
`10.1007/978-3-540-34958-7,
`http://tinyurl.com/PMC2839408, PMCID: PMC2839408.
`
`6
`
`Petitioner Apple Inc. - Exhibit 1004, p. 6
`
`

`
`99. J. Oden, K. Diller, C. Bajaj, J. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, A. Elliott, Y. Feng,
`D. Fuentes, S. Prudhomme, M. Rylander, R. Stafford, Y. Zhang (2007). “Dynamic Data-Driven Finite
`Element Models for Laser Treatment of Cancer”, Journal of Numerical Methods for Partial Differential
`Equations, 23 (4) 901-922, doi: 10.1002/num.20251, PMCID: PMC2850081.
`100. Y. Zhang, C. Bajaj, G. Xu (2007). "Surface Smoothing and Quality Improvement of Quadrilateral/Hexahedral
`Meshes using Geometric Flow", Comm.
`in Numerical Methods
`in Engineering, 25(1):1-18, DOI:
`10.1002/cnm.1067, http://tinyurl.com/PMC2761001, PMCID: PMC2761001.
`101. C. Bajaj, A. Paoluzzi, S. Portuesi, N. Lei, W. Zhao (2008). “Boolean Set Operations with Prism Algebraic
`Patches”, Computer-Aided Design and Applications, 5(5):730-742, PMCID: PMC3080140.
`102. C. Bajaj, A. DiCarlo, A. Paoluzzi (2008). “Proto-Plasm: Parallel Language for Adaptive and Scalable Modeling of
`Biosystems”, Philosophical Transactions of the Royal Society A, 13;366(1878):3045-65, PMCID: PMC3342764.
`103. M. Auer, A. Koster, U. Ziese, C. Bajaj, N. Volkmann, D-N. Wang, J. Hudspeth (2008). “Th ree-Dimensional
`Architecture of Hair-Bundle Linkages Revealed by Electron-Microscopic Tomography”, Journal of the
`Association for Research in Otolaryngology, 9(2):215-24, PMCID: PMC2504599.
`104. L. Liu, C. Bajaj, J.O. Deasy, D.A. Low, T. Ju (2008). “Surface Reconstruction From Non-parallel Curve
`Networks”, Computer Graphics Forum, 27(2):155-163, , http://dx.doi.org/10.1111/j.1467-8659.2008.01112.x.,
`PMCID: PMC2733791.
`105. C. Bajaj, G. Xu, Q. Zhang (2008). “Bio-Molecule Surfaces Construction Via a Higher-Order Level Set Method”,
`Journal of Computational Science and Technology, 23(6): 1026-1036, PMCID: PMC2873780.
`106. Z. Yu, C. Bajaj, M. Hoshijima, M. Holst, T. Hayashi, M. Ellisman, J. McCammon (2008). “Three-Dimensional
`Geometric Modeling of Membrane-bound Organelles in Ventricular Myocytes: Bridging the Gap between
`Microscopic Imaging and Mathematical Simulation”, Journal of Structural Biology, 164(3):304-13, 2008,
`doi:10.1016/j.jsb.2008.09.004, PMCID: PMC2790379.
`107. X. Zhang, C. Bajaj (2009). “Scalable Isosurface Visualization of Massive Datasets on Commodity off-the-shelf
`Journal
`of
`Parallel
`and
`Distributed
`Computing,
`Clusters”,
`69(1):39-53,
`http://dx.doi.org/10.1016/j.jpdc.2008.07.006, http://tinyurl.com/PMC2743442, PMCID: PMC2743442
`108. C. Bajaj, G. Xu, Q. Zhang (2009). “A Fast Variational Method for the Construction of Smooth Molecular
`Surfaces”, Computer Methods in Applied Mechanics and Engineering, 198(21-26):1684-1690, Special Issue in
`http://dx.doi.org/10.1016/j.cma.2008.12.042,
`70th Birthday,
`Honor
`of Professor
`J.
`T. Oden’s
`http://tinyurl.com/PMC2755577, PMCID: PMC2755577.
`109. Z. Yu, M. Hoshijima, M. Holst, T. Haysashi, C. Bajaj, M. Ellisman, J.A. McCammon (2008). “Three-Dimensional
`Geometric Modeling of Membrane-Bound Organelles in Ventricular Myocytes: Bridging the Gap Between
`Imaging and Mathematical Simulation”, Journal of Structural Biology, 164(3):304-13,
`Microscopic
`http://tinyurl.com/PMC2790379, PMCID: PMC2790379
`110. X. Yan, Z. Yu, P. Zhang, A. Batistti, P. Chipman, C. Bajaj, M. Bergoin, M. Rossman, T. Baker (2009). “The
`Capsid Proteins of a Large, Icosahedral dsDNA Virus”, Journal of Molecular Biology, 385(4):1287-1299,
`http://dx.doi.org/10.1016/j.jmb.42008.11.002, http://tinyurl.com/PMID19027752, PMC2911444
`111. Y. Zhang, T.J.R. Hughes, C. Bajaj (2010). “An Automatic 3D Mesh Generation Method for Domains with
`Multiple Materials”, Computer Methods in Applied Mechanics and Engineering (CMAME), 199(5-8): 405-415,
`http://tinyurl.com/PMC2805160, PMCID: PMC2805160.
`112. C. Bajaj, W. Zhao (2010). “Fast Molecular Solvation Energetics and Force Computation”, SIAM Journal on
`Scientific Computing, 31(6): 4524-4552, http://tinyurl.com/PMC2830669, PMCID: PMC2830669
`113. Q. Zhang, C. Bajaj (2010). “Cryo-Electron Microscopy Data Denoising Based on the Generalized Digitized Total
`Variation Method”, Far East Journal of Applied Mathematics, 45(2):83-99, http://tinyurl.com/PMC3106423,
`PMCID: PMC3106423.
`114. C. Bajaj, R. Chowdhury, V. Siddahanavalli (2011). “F2Dock: Fast Fourier Protein-Protein Docking”, IEEE/ACM
`Transactions on Computational Biology and Bioinformatics, 8(1):45-58, http://tinyurl.com/NIHMSID153460,
`NIHMSID153460, doi: 10.1109/TCBB.2009.57, January – February 2011. PMCID: PMC3058388.
`115. W. Zhao, G. Xu, C. Bajaj (2011). “An Algebraic Spline Model of Molecular Surfaces for Energetic
`Computations”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(6);1458-1467,
`http://dx.doi.org/10.1145/1236246.1236288, NIHMSID153456,
`http://tinyurl.com/clzwrs6, November
`–
`December 2011. PMCID: PMC3153597.
`116. G. Xu, C. Bajaj (2011). “Regularization of B-Spline Objects”, Computer Aided Geometric Design, 258(1):38-49,
`doi:10.1016/j.cagd.2010.039008, http://tinyurl.com/PMC3016058, January 2011. PMCID: PMC3016058.
`
`7
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`Petitioner Apple Inc. - Exhibit 1004, p. 7
`
`

`
`117. C. Bajaj, R.A. Chowdhury, M. Rasheed (2011). “A Dynamic Data Structure for Flexible Molecular Maintenance
`and Informatics”, Bioinformatics, 27(1):55-62; doi: 10.1093/bioinformatics/btq627, January 2011. PMCID:
`PMC3008647.
`118. G. Xu, M. Li, A. Gopinath, C. Bajaj (2011). “Computational Inversion of Electron Tomography Images Using
`L2-Gradient Flows”, Journal of Computational Mathematics, 2011,V29(5): 501-525, NIHMSID# 266229, PMC
`Journal in Process, September 2011
`119. C. Bajaj, S-C Chen, A. Rand (2011). “An Efficient Higher-Order Fast Multipole Boundary Element Solution for
`Poisson-Boltzmann Based Molecular Electrostatics”, SIAM Journal on Scientific Computing, 33(2): 826-848,
`http://tinyurl.com/PMC3110014, June 2011. PMCID: PMC3110014.
`120. R. Khan, Q. Zhang, S. Darayan, S. Dhandapani, S. Katyal, C. Greene, C. Bajaj, D. Ress (2011). “Surface-Based
`Imaging Methods for High-Resolution Functional Magnetic Resonance Imaging”, Graphical Models, 73(6): 313-
`322 , NIHMSID# 268212, doi: 10.1016/j.gmod.210.11.002, November 2011. PMCID: PMC19036544.
`121. O. Sharma, Q. Zhang, F. Anton, C. Bajaj (2011). “Fast Streaming 3D Level set Segmentation on the GPU for
`Smooth Multi-phase Segmentation”, Transactions on Computational Sciences XIII, Lecture Notes in Computer
`Science, (6750): 72-91; # 282367, PMC Journal in Process, doi: 10.1007/978-3-642-22619-9_4
`122. A