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Publications

    2008

  1. Adams B, Ovjanikovs M, Wang M, Seidel H-P., Guibas L. (2008). Meshless modeling of deformable shapes and their motion. Eurographics/ACM SIGGRAPH Symposium on Computer Animation 2008.
    http://graphics.stanford.edu/~barta/research/research.html


  2. Besier TF, Gold GE, Delp SL, Fredericson M, Beaupré GS. (2008). The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint. Journal of Orthopaedic Research. (Epub ahead of print, Jun 3, 2008)
    PMID: 18524000


  3. Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ., Pande VS. (2008). Structural Insight into RNA Hairpin Folding Intermediates. Journal of the American Chemical Society. (in press)
    PMID: 18593120


  4. Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. (2008). Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci. 18;105(11):4144-9.
    PMID: 18322008


  5. De Sapio V, Khatib O, Delp S. (2008). Least action principles and their application to constrained and task-level problems in robotics and biomechanics. Multibody System Dynamics. 19, 303-322, April 2008.
    http://dx.doi.org/10.1007/s11044-007-9097-8


  6. Demircan E, Sentis L, De Sapio V, Khatib O. (2008). Human Motion Reconstruction by Direct Control of Marker Trajectories. Advances in Robot Kinematics, Book Chapter, Pages 263-272.
    http://www.springerlink.com/content/q57606t83qr0j052/


  7. Dinov ID, Rubin DL, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. (2008). iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. PLoS ONE, 2008. 28;3(5):e2265.
    PMID: 18509477


  8. Draper CE, Santos J, Kourtis L, Besier T, Beaupré G, Gold GE, Delp SL. (2008). Feasibility of using real-time MRI to measure joint kinematics in 1.5T and open-bore 0.5T systems. Journal of Magnetic Resonance Imaging. 28(1):158-166.
    PMID: 18581329


  9. England JL, Pande VS, Haran G. (2008). Chemical denaturants inhibit the onset of dewetting. J Am Chem Soc 130, 11854-5.
    PMID: 18707183


  10. Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB. (2008). HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors. Proteins: Structure, Function, and Bioinformatics. Published Online: 23 Apr 2008.
    PMID: 18433058


  11. Glazer DS, Radmer RJ, Altman RB. (2008). Combining molecular dynamics and machine learning to improve protein function recognition. Pacific Symposium on Biocomputing 2008, 332-43.
    PMID: 18229697


  12. Hicks JL, Schwartz MH, Arnold AS, Delp SL. (2008). Crouched postures reduce the capacity of muscles to extend the hip and knee during the single-limb stance phase of gait. J Biomech. 41(5):960-7.
    PMID: 18291404


  13. Huang Q, Adams B, Wicke M, Guibas L. (2008). Non-Rigid Registration Under Isometric Deformations. Eurographics Symposium on Geometry Processing (SGP), Comp. Graphics Forum, 27(5), 1149-1458, 2008.
    http://graphics.stanford.edu/projects/lgl/papers/hawg-nrrid-08/hawg-nrrid-08.pdf


  14. Huang X, Bowman GR, Pande VS. (2008). Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. Journal of Chemical Physics. May 28;128(20):205106.
    PMID: 18513049


  15. Humphrey JD, Taylor CA. (2008). Intracranial and Abdominal Aortic Aneurysms: Similarities, Differences and Need for a New Class of Computational Models. Annual Review of Biomedical Engineering. 10:221–46.
    http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioeng.10.061807.160439?cookieSet=1


  16. Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. (2008). Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc 3, 1395-401.
    PMID: 18772866


  17. Lew A, Buscaglia G. (2008). A discontinuous-Galerkin-based immersed boundary method. International Journal for Numerical Methods in Engineering. (in press)
    http://dx.doi.org/10.1002/nme.2312


  18. Losasso F, Talton J, Kwatra N, Fedkiw R. (2008). Two-Way Coupled SPH and Particle Level Set Fluid Simulation. IEEE Trans Vis Comput Graph. 14, 797-804.
    PMID: 18467755


  19. Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. (2008). High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. Jun;36(11):e63.
    PMID: 18477638


  20. O'Connell MK, Murthy S, Phan S, Xu C, Buchanan J, Spilker R, Dalman RL, Zarins CK, Denk W, Taylor CA. (2008). The three-dimensional micro- and nanostructure of the aortic medial lamellar unitmeasured using 3D confocal and electron microscopy imaging. Matrix Biol. 2008 Apr;27(3):171-81.
    PMID: 18248974


  21. Ovjanikovs M, Sun J, Guibas L. (2008). Global Intrinsic Symmetries of Shapes. Proc. Eurographics Symposium on Geometry Processing (SGP). Best Student Paper Award.
    http://www.stanford.edu/~sunjian/paper_ppt/global_symmetry.pdf


  22. Pauly M, Mitra NJ, Wallner J, Pottmann H, Guibas LJ. (2008). Discovering structural regularity in 3D geometry. ACM Transactions on Graphics (Proceedings of SIGGRAPH), 27(3) Artilce 43.
    http://portal.acm.org/citation.cfm?doid=1360612.1360642


  23. Petrone P, Snow C, Lucent D, Pande V. (2008). Side-chain recognition and gating in the ribosome exit tunnel. PNAS. (In press)


  24. Reinbolt JA, Fox MD, Arnold AS, Õunpuu S, Delp SL. (2008). Importance of preswing rectus femoris activity in stiff-knee gait. Journal of Biomechanics. 41(11):2362-9. Epub 2008 Jul 9.
    PMID: 18617180


  25. Robinson-Mosher A, Shinar T, Gretarsson J, Su J, Fedkiw R. (2008). Two-way Coupling of Fluids to Rigid and Deformable Solids and Shells. SIGGRAPH 2008, 27(3) Article 46.
    http://portal.acm.org/citation.cfm?doid=1360612.1360645


  26. Schmidt JP, Delp SL, Sherman, MA, Taylor CA, Pande VS, Altman RB. (2008). The Simbios National Center: Systems Biology in Motion. Proceedings of the IEEE, special issue on Computational System Biology. Volume 96,  Issue 8,  Aug. 2008 Page(s):1266 - 1280.
    http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4567420


  27. Selle A, Fedkiw R, Kim B-M, Liu Y, Rossignac J. (2008). An Unconditionally Stable MacCormack Method. J. Sci. Comput. (in press).
    http://www.springerlink.com/content/9252536103441187/fulltext.pdf


  28. Selle A, Lentine M, Fedkiw R. (2008). A Mass Spring Model for Hair Simulation. SIGGRAPH 2008, ACM TOG, 27(3) Article 64.
    http://portal.acm.org/citation.cfm?doid=1360612.1360663


  29. Selle A, Su J, Irving G, Fedkiw R. (2008). Highly Detailed Folds and Wrinkles for Cloth. IEEE TVCG. (in press)


  30. Shadden SC, Taylor CA. (2008). Characterization of Coherent Structures in the Cardiovascular System. Annals of Biomedical Engineering. Jul;36(7):1152-62.
    PMID: 18437573


  31. Sherbondy AJ, Dougherty RF, Ben-Shachar M, Cheung S-H, Napel S, Wandell BA. (2008). ConTrack: Finding the Most Likely Pathways Between Brain Regions. Journal of Vision. Volume 8, Number 9, Article 15, Pages 1-16.
    PMID: 18831651


  32. Shinar T, Schroeder C, Fedkiw R. (2008). Two-way Coupling of Rigid and Deformable Bodies. ACM SIGGRAPH/Eurographics Symposium on Computer Animation (SCA). Edited by Doug James and Markus Gross.
    http://physbam.stanford.edu/~fedkiw/papers/stanford2008-03.pdf


  33. Sivaramakrishnan S, Spink BJ, Sim AY, Doniach S, Spudich JA. (2008). Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif. Proc Natl Acad Sci USA 105, 13356-61.
    PMID: 18768817


  34. Sundaram P, Zamorodian AJ, Beaulieu CF, Napel S. (2008). Colon Polyp Detection Using Smoothed Shape Operators: Preliminary Results. Medical Image Analysis. 12(2):99-119.
    PMID: 17910934


  35. Sweet CR, Petrone P, Pande VS, Izaguirre JA. (2008). Normal mode partitioning of Langevin dynamics for biomolecules. J Chem Phys. 14;128(14):145101.
    PMID: 18412479


  36. Ten Eyck A, Celiker F, Lew A. (2008). Adaptive stabilization of discontinuous Galerkin methods for nonlinear elasticity: Motivation, formulation and numerical examples. Computer Methods in Applied Mechanics and Engineering. (in press)
    http://dx.doi.org/10.1016/j.cma.2008.02.020


  37. Ten Eyck A, Celiker F, Lew A. (2008). Adaptive stabilization of discontinuous Galerkin methods for nonlinear elasticity: Analytical estimates. Computer Methods in Applied Mechanics and Engineering. (in press)
    http://dx.doi.org/10.1016/j.cma.2008.02.022


  38. Weinstein R, Guendelman E, Fedkiw R. (2008). Impulse-Based Control for Joints and Muscles. IEEE Transactions on Visualization and Computer Graphics, Volume 14 , Issue 1, 37-46, 2008.
    PMID: 17993700


  39. Weiss DR, Raschke TM, Levitt M. How Hydrophobic Buckminsterfullerence Affects Surrounding Water Structure. Journal of Physical Chemistry B. Mar 13;112(10):2981-90.
    PMID: 18275178


  40. Yao, P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin Landsbergz I, Altman RB. (2008). Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. IEEE/ACM Trans. on Computational Biology and Bioinformatics. (Accepted).

    41. 2007

  41. Adams B, Pauly M, Keiser R, Guibas L. (2007). Adaptively Sampled Particle Fluids. ACM SIGGRAPH, 2007.
    http://portal.acm.org/citation.cfm?id=1276437


  42. Arnold AS, Schwartz MH, Thelen DG, Delp SL. (2007). Contributions of muscles to terminal-swing knee motions vary with walking speed. J Biomech. 2007;40(16):3660-71. Epub 2007 Jul 19.
    PMID: 17659289


  43. Arnold AS, Thelen DT, Schwartz MH, Anderson FC, Delp SL. (2007). Muscular Coordination of Knee Motion During the Terminal Swing Phase of Gait. J. Biomechanics. 2007, 40(15):3314-24.
    PMID: 17572431

  44. Bai Y, Greenfeld M, Travers K, Chu VB, Lipfert J, Doniach S, Herschlag D. (2007). Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids. Journal of the American Chemical Society. 129(48):14981-14988.
    PMID: 17990882


  45. Bao Z, Hong JM, Teran J, Fedkiw R. (2007). Fracturing rigid materials. IEEE Trans Vis Comput Graph. 2007 Mar-Apr;13 (2):370-8.
    PMID: 17218752


  46. Blemker SS, Asakawa D, Gold G, Delp SL. (2007). Image-Based Musculoskeletal Modeling: Applications, Advances, and Future Opportunities. J of Magnetic Resonance Imaging. 25:441–451, 2007.
    PMID: 17260405


  47. Boissonnat JD, Guibas LJ, Steve YO. (2007). Manifold Reconstruction in Arbitrary Dimensions using Witness Complexes. Proceedings of the 23rd ACM Sympos. on Comput. Geom. 2007.
    http://portal.acm.org/citation.cfm?id=1247106


  48. Delp SL, Anderson FC, Arnold AS, Loan P, Habib A, John C, Guendelman E, Thelen DG. (2007). OpenSim: Open-source software to create and analyze dynamic simulations of movement. IEEE Transactions on Biomedical Engineering, 54:11,1940-1950.
    PMID: 18018689


  49. Dugan JM, Altman RB. (2007). Using surface envelopes to constrain molecular modeling. Protein Sci. Jul; 16(7):1266-73.
    PMID: 17586766


  50. Goergen CJ, Johnson BL, Greve JM, Taylor CA, Zarins CK. (2007). Increased Anterior Abdominal Aortic Wall Motion: Possible Role in Aneurysm Pathogenesis and Design of Endovascular Devices. (2007). Journal of Endovascular Therapy. 2007.
    PMID: 17696635


  51. Guibas LJ, Oudot SY. (2007). Reconstruction using Witness Complexes. Proc. 18th ACM-SIAM Sympos. on Discrete Algorithms. 1076-1085, 2007. Full version invited for publication in Discrete and Computational Geometry.
    http://portal.acm.org/citation.cfm?id=1283499


  52. Guibas LJ, Wang Y. (2007). Toward Unsupervised Segmentation of Semi-Rigid Low-Resolution Molecular Surfaces. Algorithmica. 48(4):433-438, Aug 2007.
    DOI: 10.1007/s00453-007-0151-y


  53. Hicks J, Arnold A, Anderson F, Schwartz M, Delp S. (2007). The effect of excessive tibial torsion on the capacity of muscles to extend the hip and knee during single-limb stance. Gait Posture, 26(4):546-52, 2007.
    PMID: 17229573


  54. Hong, J., Shinar, T., Kang, M., and Fedkiw, R. (2007). On Boundary Condition Capturing for Multiphase Interfaces. J. Sci. Comput. 31, 1-2 (May. 2007), 99-125.
    http://portal.acm.org/citation.cfm?id=377456.377480


  55. Irving G, Schroeder C, Fedkiw R. (2007). Volume Conserving Finite Element Simulations of Deformable Models. ACM Trans. Graph, Volume 26 , Issue 3 (July 2007).
    http://portal.acm.org/citation.cfm?id=1275808.1276394


  56. Kasson P, Zomorodian A, Park S, SInghal N, Guibas L, Pande V. (2007). Persistent voids: a new structural metric for membrane fusion. Bioinformatics, 2007, Jul 15;23(14):1753-9.
    PMID: 17488753


  57. Laederach A. Informatics challenges in structured RNA. (2007). Brief Bioinform. 2007 Sep;8(5):294-303.
    PMID: 17611237


  58. Laederach A, Chan JM, Schwartzman A, Willgohs E, Altman RB. (2007). Coplanar and coaxial orientations of RNA bases and helices. RNA. May;13(5):643-50, 2007.
    PMID: 17339576


  59. Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. (2007). Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci USA. Apr 24;104(17):7045-50, 2007.
    PMID: 17438287


  60. Liao JC, Spudich JA, Parker D, Delp SL. (2007). Extending the absorbing boundary method to fit dwell-time distributions of molecular motors with complex kinetic pathways. Proc Natl Acad Sci USA. Feb 27;104(9):3171-6, 2007.
    PMID: 17360624


  61. Mitra, N. J., Flöry, S., Ovsjanikov, M., Gelfand, N., Guibas, L., and Pottmann, H. (2007). Dynamic geometry registration. In Proceedings of the Fifth Eurographics Symposium on Geometry Processing (Barcelona, Spain, July 04 - 06, 2007). ACM International Conference Proceeding Series, vol. 257. Eurographics Association, Aire-la-Ville, Switzerland, 173-182.
    http://portal.acm.org/citation.cfm?id=1281991.1282015


  62. Mitra NJ, Guibas L, Pauly M. (2007). Symmetrization. ACM SIGGRAPH 2007, Volume 26 , Issue 3 July 2007
    http://portal.acm.org/citation.cfm?id=1275808.1276456


  63. Russel D, Karavelas M, Guibas L. (2007). A package for exact kinetic data structures and sweepline algorithms. Computational Geometry, Theory and Applications, Volume 38, Issues 1-2:111-127, 2007.
    http://portal.acm.org/citation.cfm?id=1248143


  64. Schröder GF, Brunger AT, Levitt M. (2007). Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure. Dec;15(12):1630-41, 2007
    PMID: 18073112


  65. Shi R, Napel S, Rosenberg JK, Shin LK, Walsh CF, Mogensen MA, Joshi AJ, Pankhudi P, Beaulieu CF. (2007). Transparent rendering of intraluminal contrast for 3D polyp visualization at CT colonography. J Comput Assist Tomogr. 2007 Sep-Oct;31 (5):773-9.
    PMID: 17895791


  66. Sifakis E, Shinar T, Irving G, Fedkiw R. (2007). Hybrid Simulation of Deformable Solids. In Proc. Of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (SCA) 2007, 81-90.
    http://portal.acm.org/citation.cfm?id=1272702


  67. Sifakis, E., Der, KG., and Fedkiw, R. (2007). Arbitrary cutting of deformable tetrahedralized objects. Proceedings of the 2007 ACM Siggraph/Eurographics Symposium on Computer Animation (San Diego, California, August 02 - 04, 2007). Symposium on Computer Animation. Eurographics Association, Aire-la-Ville, Switzerland, 73-80.
    http://portal.acm.org/citation.cfm?id=1272701


  68. Tang S, Liao JC, Dunn A, Spudich JA, Altman RB, Schmidt J. (2007). Predicting allosteric communication in myosin via a pathway of conserved residues. Journal of Molecular Biology 373, 1361-1373, 2007.
    PMID: 17900617


  69. Vicens Q, Gooding AR, Laederach A, Cech TR. (2007). Local RNA structural changes induced by crystallization are revealed by SHAPE. RNA, Apr;13(4):536-48, 2007.
    PMID: 17299128


  70. Zheng W, Liao JC, Brooks BR, Doniach S. (2007). Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins. 67(4):886-96, 2007.
    PMID: 17373706


  71. Wand, M., Jenke, P., Huang, Q., Bokeloh, M., Guibas, L., and Schilling, A. (2007). Reconstruction of deforming geometry from time-varying point clouds. Proceedings of the Fifth Eurographics Symposium on Geometry Processing (Barcelona, Spain, July 04 - 06, 2007). ACM International Conference Proceeding Series, vol. 257. Eurographics Association, Aire-la-Ville, Switzerland, 49-58.
    http://portal.acm.org/citation.cfm?id=1281991.1281998

    72. 2006

  72. Blemker SS and Delp SL. (2006). Rectus femoris and vastus intermedius fiber excursions predicted by three-dimensional muscle models. Journal of Biomechanics, 39:1383-1391, 2006.
    PMID: 15972213


  73. De Sapio V, Khatib O, Delp S. (2006). Task-level approaches for the control of constrained multibody systems. (2006). Multibody System Dynamics. 16:73-102, 2006.
    http://dx.doi.org/10.1007/s11044-006-9017-3


  74. Gao J, L Guibas and A Nguyen. (2006). Deformable spanners and applications. Journal Computational Geometry: Theory and Applications, 35: 1-2, 2-19, 2006.
    http://dx.doi.org/10.1016/j.comgeo.2005.10.001


  75. Higginson JS, Zajac FE, Neptune RR, Kautz SA, Delp SL. (2006). Muscle contributions to support during gait in an individual with post-stroke hemiparesis. J Biomech. 39(10):1769-77, 2006.
    PMID: 16046223


  76. Irving G, Teran J and Fedkiw R. (2006). Tetrahedral and Hexahedral Invertible Finite Elements. Graphical Models, 68:66-89, 2006.
    http://dx.doi.org/10.1016/j.gmod.2005.03.007


  77. Irving G, Guendelman E, Losasso F and Fedkiw R. (2006). Efficient Simulation of Large Bodies of Water by Coupling Two and Three Dimensional Techniques. SIGGRAPH 2006, ACM TOG 25, 805-811. 2006
    http://portal.acm.org/citation.cfm?id=1179352.1141959


  78. Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. (2006). Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol. May 12;358(4):1179-90, 2006.
    PMID: 16574145


  79. Losasso F, R Fedkiw and S Osher. (2006). Spatially Adaptive Techniques for Level Set Methods and Incompressible Flow. Computers and Fluids. 35, 995-1010, 2006.
    http://physbam.stanford.edu/~fedkiw/papers/stanford2004-07.pdf


  80. Losasso F, Shinar T, Selle A and Fedkiw R. (2006). Multiple Interacting Liquids. SIGGRAPH 2006, ACM TOG 25, 812-819, 2006.
    http://portal.acm.org/citation.cfm?id=1179352.1141960


  81. Mitra NJ, Guibas L, Giesen J, Pauly M. (2006). Probabilistic Fingerprints for Shapes. Symposium on Geometry Processing. 121-130, 2006.
    http://portal.acm.org/citation.cfm?id=1281973


  82. Petrone P and Pande V. (2006). Can Conformational Change Be Described by Only a Few Normal Modes? Biophysical Journal, 90:1583-1593, March 2006.
    PMID: 16361336


  83. Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. (2006). The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J Mol Biol. Oct 20;363(2):531-44, 2006
    PMID: 16963081


  84. Shi R, Schraedley-Desmond P, Napel S, Olcott E, Jeffrey RB Jr., Yee J, Zalis ME, Margolis D, Paik DS, Sherbondy A, Sundaram P and Beaulieu CF. (2006). CT Colonography: Influence of 3D Viewing and Polyp Candidate Features on Interpretation with Computer-aided Detection. Radiology, 239(3):768-776, 2006.
    PMID: 16714460


  85. Sifakis E, Selle A, Robinson-Mosher A, Fedkiw R. (2006). Simulating Speech with a Physics-Based Facial Muscle Model. ACM SIGGRAPH/Eurographics Symposium on Computer Animation (SCA), edited by M.-P. Cani and J. O’Brien, 261-270, 2006.
    http://portal.acm.org/citation.cfm?id=1218100


  86. TenEyck A and Lew A. (2006). Discontinuous Galerkin Methods for Nonlinear Elasticity. International Journal for Numerical Methods in Engineering. 67, 1204-1243, 2006.
    http://dx.doi.org/10.1002/nme.1667


  87. Weinstein R, Teran J and Fedkiw R. (2006). Dynamic Simulation of Articulated Rigid Bodies with Contact and Collision. IEEE Transactions on Visualization and Computer Graphics, 12(3):365-374, May/June 2006.
    PMID: 16640250


  88. Won JH, Rubin GD, Napel S. (2006). Flattening the abdominal aortic tree for effective visualization. Conf Proc IEEE Eng Med Biol Soc 1, 3345-8.
    PMID: 17946176


    89. 2005

  89. Adams B, Keiser R, Pauly M, Guibas L, Gross M and Dutre P. (2005). Efficient Raytracing of Deformable Point-Sampled Surfaces. Proc. Eurographics Symposium, pp. 677-684, 2005.
    http://graphics.stanford.edu/projects/lgl/paper.php?id=akpggd-erdpss-05


  90. Das R, Travers KJ, Bai Y and Herschlag D. (2005). Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core. J. Am. Chem. Soc., 127(23):8272-8273, 2005.
    PMID: 15941246


  91. Holzbaur KRS, Murray WM and Delp SL. (2005). A Model of the Upper Extremity for Simulating Musculoskeletal Surgery and Analyzing Neuromuscular Control. Annals of Biomedical Engineering, 33:829–840, 2005.
    PMID: 16078622


  92. Pauly M, Keiser R, Adams B, Dutre P, Gross M and Guibas L. (2005). Meshless Animation of Fracturing Solids. ACM SIGGRAPH Symposium 2005, ACM Transactions on Graphics (TOG), 24(3):957-964, Aug 2005.
    http://portal.acm.org/citation.cfm?id=1073204.1073296


  93. Sherman MA, JL Middleton, JP Schmidt, DS Paik, SS Blemker, AW Habib, FC Anderson, SL Delp and RB Altman. (2005). The SimTK Framework for physics-based simulation of biological structures: preliminary design. Proceedings of the Workshop on Component Models and Frameworks in High Performance Computing, June 22-25, 2005, Atlanta, GA (CompFrame 2005)
    http://www.compframe.org/compframe2005/CompFrame05_Program


  94. Sifakis E, Neverov I and Fedkiw R. (2005). Automatic Determination of Facial Muscle Activations from Sparse Motion Capture Marker Data. SIGGRAPH 2005, ACM TOG 24:417-425, Aug 2005.
    http://portal.acm.org/citation.cfm?id=1073208


  95. Teran J, Sifakis E, Irving G and Fedkiw R. (2005). Robust quasistatic finite elements and flesh simulation. Proceedings of the 2005 ACM Siggraph/Eurographics Symposium on Computer Animation, Los Angeles, California, July 29-31, SCA '05 ACM Press, New York, NY, 181-190.
    http://portal.acm.org/citation.cfm?id=1073368.1073394