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Journal Publications C. Bajaj, G. Xu, Q. Zhang
A Fast Variational Method for the Construction of Adaptive Resolution C^2 Smooth Molecular Surfaces
Computer Methods in Applied Mechanics and Engineering, volume 198, p1684-1690 (2009) Special Issue in Honor of Professor J. T. Oden’s 70th Birthday, http://dx.doi.org/10.1016/j.cma.2008.12.042, http://tinyurl.com/PMC2755577, PMCID: PMC2755577 (pdf) W. Zhao, G. Xu, C. Bajaj
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, Accepted for publication, http://dx.doi.org/10.1145/1236246.1236288, NIHMSID153456, PMC Journal in Process (pdf) (abstract) C. Bajaj, R. Chowdhury, V. Siddahanavalli
F2Dock: Fast Fourier Protein-Protein Docking
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, Accepted for publication, NIHMSID153460, http://tinyurl.com/NIHMSID153460, PMC Journal in Process (pdf) C. Bajaj, W. Zhao
Fast Molecular Solvation Energetics and Force Computation
SIAM Journal on Scientific Computing, 31(6): 4524-4552, January 2010, http://tinyurl.com/PMC2830669, PMCID: PMC2830669 (pdf) (abstract) 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
2009, http://dx.doi.org/10.1016/j.jmb.2008.11.002, http://tinyurl.com/PMID19027752, PMID: 19027752, PMC Journal in Process C. Bajaj , A. DiCarlo and A. Paoluzzi
Proto-Plasm: Parallel Language for Adaptive and Scalable Modeling of Biosystems
Philosophical Transactions of the Royal Society A, 2008 Sep 13;366(1878):3045-65, http://tinyurl.com/PMID18559320, PMID: 18559320, PMC Journal in Process 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, 164(3):304-13, 2008, http://tinyurl.com/PMC2790379, PMCID: PMC2790379 (pdf) (abstract) 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
Dynamic Data-Driven Finite Element Models for Laser Treatment of Cancer
Journal of Numerical Methods for Partial Differential Equations, 23 (4) 901-922, 2007, doi: 10.1002/num.20251, http://tinyurl.com/NIHMS92557, PMCID: PMC2850081 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, 2006, 5 (4), 1196-1213, doi: 10.1137/050647670, http://tinyurl.com/PMC2561295, PMCID: PMC2561295 (pdf) (abstract) M. Baker, Z. Yu, W. Chiu, C. Bajaj
Automated Segmentation of Molecular Subunits in Electron Cryomicroscopy Density Maps
Journal of Structural Biology, 2006, Dec;156(3):432-41, doi: 10.1016/j.jsb.2006.05.013, PMID: 16908194, http://tinyurl.com/PMID16908194, PMC Journal in Process (pdf) 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
Computer Methods In Applied Mechanics and Engineering (CMAME), 195: 1722-1749, 2006, doi:10.1016/j.cma.2005.05.049, http://tinyurl.com/PMC2830735, PMCID: PMC2830735 (pdf) (abstract) 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, doi: 10.1016/j.cagd.2006.01.008, http://tinyurl.com/PMC2756697, PMCID: PMC2756697 (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, http://tinyurl.com/PMC134735, PMCID: PMC1347395 (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, doi:10.1016/j.cma.2004.11.026, http://tinyurl.com/PMC2748876, PMCID: PMC2748876 (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, doi: 10.1109/TIP.2005.852770, http://tinyurl.com/PMID16190468, PMID16190468, PMC Journal in Process 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, doi:10.1016/j.str.2005.02.004 , http://tinyurl.com/PMID15766547, PMID15766547, PMC Journal in Process (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), doi: 10.1529/biophysj.104.053850, http://tinyurl.com/PMC1305222, PMCID: PMC1305222 (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, doi: 10.1016/j.jsb.2003.09.033, http://tinyurl.com/PMID15065668, PMID15065668, PMC Journal In Process (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, doi: 10.1529/biophysj.104.041517, http://tinyurl.com/PMC1304562, PMCID: PMC1304562 (pdf) 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, doi: 10.1016/j.jsb.2003.10.027, http://tinyurl.com/PMID15065684, PMID15065684, PMC Journal In Process (pdf) (abstract) 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, doi: 10.1529/biophysj.106.102533, http://tinyurl.com/PMC1304055, PMCID: PMC1304055 (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, http://tinyurl.com/PMID12753096, PMID12753096, PMC Journal In Process (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, doi:10.1016/j.jsb.2003.09.028, http://tinyurl.com/PMID14643214, PMID14643214, PMC Journal In Process (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) C. Bajaj, Z. Yu, M. Auer
Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging
Journal of Structural Biology, Volume 144, Issues 1-2, Oct. 2003, Pages 132-143, doi:10.1016/j.jsb.2003.09.037, http://tinyurl.com/PMID14643216, PMID14643216, PMC Journal In Process (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, http://tinyurl.com/PMID11008186, PMID11008186, PMC Journal in Process (pdf) 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) Conference Presentations & Publications A. Gillette and C. Bajaj
A Generalization for Stable Mixed Finite Elements
Proceedings of the ACM Symposium on Solid and Physical Modeling, Sept. 2010, Accepted for Publication. C. Bajaj and R. Chowdhury
Multi-level Grid Algorithms for Faster Molecular Energetics
Proceedings of the ACM Symposium on Solid and Physical Modeling, Sept. 2010, Accepted for Publication J. Edwards and C. Bajaj
Topologically correct reconstruction of tortuous contour forests
Proceedings of the ACM Symposium on Solid and Physical Modeling, accepted, September 2010 C. Bajaj, R. Chowdhury, M. Rasheed
A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics
Proceedings of the 2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling, San Francisco, CA, 2009, NIHMSID193756, PMC Journal in Process (pdf) C. Bajaj, A. Chen, G. Xu, Q. Zhang, W. Zhao
Hierarchical Molecular Interfaces and Solvation Electrostatics
Proceedings of the 2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling, San Francisco, CA, 2009, NIHMSID193754, PMC Journal in Process (pdf) W. Zhao, G. Xu, C. Bajaj
An algebraic spline model of molecular surfaces
Proceedings of the 2007 ACM Symposium on Solid and Physical Modeling, 2007, pp. 297-302, NIHMSID194067, PMC Journal in Process (pdf) (abstract) 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, PubMed ID: 19424455, PMCID: 2678009, NIHMSID: 87373 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 (pdf) X. Zhang, C. Bajaj
Extraction, Visualization and Quantification of Protein Pockets
Proc. of the 6th Annual International Conference on Computational Systems Bioinformatics, CSB2007, vol 6, pp. 275 – 286, http://tinyurl.com/PMID17951831PMID, : 17951831 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, NIHMSID194039, PMC Journal in Process (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, NIHMSID194017, PMC Journal in Process (pdf) 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. (pdf) 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, http://tinyurl.com/PMC2860966, PMCID: PMC2860966 (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, 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
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) Book Chapters 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, 2007, pp. 115-137 (pdf) 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, 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.
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