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Publications

2010 -- 2009 -- 2008 -- 2007 -- 2006 -- 2005

    2010

  1. Adams, B., Wicke, M., Ovsjanikov, M., Wand, M., Seidel, H.-P., and Guibas, L.J. (2010). Meshless Shape and Motion Design for Multiple Deformable Objects. Computer Graphics Forum 29, 43-59.
    http://dx.doi.org/10.1111/j.1467-8659.2009.01536.x


  2. Agarwal-Harding, K.J., Schwartz, M.H., Delp, S.L. (2010). Variations of hamstrings lengths and velocities with walking speed. Journal of Biomechanics, 43(8), 1522-1526.
    PMID: 20381047


  3. Arnold, E.M., Ward, S.R., Lieber, R.L., and Delp, S.L. (2010). A model of the lower limb for analysis of human movement. Ann Biomed Eng, 38, 269-79.
    PMID: 19957039


  4. Bowman, G.R., Huang, X., and Pande, V.S. (2010). Network models for molecular kinetics and their initial applications to human health. Cell Res 20, 622-30.
    PMID: 20421891


  5. Chiang, T.H., Hsu, D., and Latombe, J.C. (2010). Markov Dynamic Models for Long-Timescale Protein Motion. ISMB 2010, Boston, July 2010. Bioinformatics 26, i269-77.
    PMID: 20529916, PMCID: 2881362


  6. Eastman, P. and Pande, V.S. (2010). Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulati ons. Journal of Chemical Theory and Computation, 6 (2), pp 434–437.
    PMID: 20563234, PMCID: 2885791 [Available on 2011/2/1]


  7. Eastman, P. and Pande, V.S. (2010). Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J Comput Chem, 31, 1268-72.
    PMID: 19847780, PMCID: 2841709 [Available on 2011/4/30]


  8. England, J.L. and Pande, V.S. (2010). Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework. Biochem Cell Biol 88, 359-69.
    PMID: 20453936


  9. Fenn, T.D., Schnieders, M.J., Brunger, A.T., and Pande, V.S. (2010). Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. Biophys J 98, 2984-92.
    PMID: 20550911

  10. Fleming, T.C., Shin, J.Y., Lee, S.H., Becker, E., Huang, K.C., Bustamante, C., and Pogliano, K. (2010). Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation. Genes Dev 24, 1160-72.
    PMID: 20516200, PMCID: 2878653 [Available on 2010/12/1]


  11. Flores, S.C., and Altman, R.B. (2010). Turning limited experimental information into 3D models of RNA. RNA, Epub ahead of print, July 22, 2010.
    PMID: 20651028


  12. Flores, S.C., Wan, Y., Russell, R., and Altman, R.B. (2010). Predicting RNA structure by multiple template homology modeling. Proceedings of the Pacific Symposium on Biocomputing, 15, 216-227.
    PMID: 19908374, PMCID: 2872935


  13. Fox, M.D. and Delp, S.L. (2010). Contributions of muscles and passive dynamics to swing initiation over a range of walking speeds. J Biomech, 43(8), 1450-1455.
    PMID: 20236644, PMCID: 2866832 [Available on 2011/5/28]


  14. Göktepe, S., Wong, J, and Kuhl, E. (2010). Atrial and ventricular fibrillation: computational simulation of spiral waves in cardiac tissue. Archive of Applied Mechanics, 80(5), 569-580.
    http://dx.doi.org/10.1007/s00419-009-0384-0


  15. Haque, I.S., Pande, V.S., and Walters, W.P. (2010). SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs. J Chem Inf Model 50, 560-4.
    PMID: 20218693


  16. Huang, K.C. and Ramamurthi, K. (2010). Macromolecules that like their membranes curvy. Molec Microbiol, 76(4), 822-832.
    http://dx.doi.org/10.1111/j.1365-2958.2010.07168.x


  17. Huang, X., Yao, Y., Sun, J., Bowman, G.R., Guibas, L., Carlsson, G., and Pande, V.S. (2010). Constructing Multi-resolution Markov State Models(MSMs) to elucidate RNA hairping folding mechanisms. Proceedings of the Pacific Symposium on Biocomputing, 228-239.
    PMID: 19908375


  18. Les, A.S., Shadden, S.C., Figueroa, C.A., Park, J.M., Tedesco, M.M., Herfkens, R.J., Dalman, R.L., and Taylor, C.A. (2010). Quantification of hemodynamics in abdominal aortic aneurysms during rest and exercise using magnetic resonance imaging and computational fluid dynamics. Ann Biomed Eng 38, 1288-313.
    PMID: 20143263


  19. Saha, M., Levitt, M., and Chiu, W. (2010). MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in CryoEM Structures. ISMB 2010, Boston, July 2010. Bioinformatics 26, i301-9.
    PMID: 20529921, PMCID: PMC2881380


  20. Schröder, G.F., Levitt, M., Brunger, A.T. (2010). Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218-1222.
    http://dx.doi.org/10.1038/nature08892


  21. Seth, A., Sherman, M., Eastman, P., and Delp, S. (2010). Minimal formulation of joint motion for biomechanisms. Nonlinear Dynamics. Published on-line May 1, 2010.
    http://dx.doi.org/10.1007/s11071-010-9717-3


  22. Steele, K., Seth, A., Hicks, J.L., Schwartz, M.S., Delp, S.L. (2010). Muscle contributions to support and progression during single-limb stance in crouch gait. Journal of Biomechanics. (Epub ahead of print)
    PMID: 20493489


  23. Taylor, C.A. and Steinman, D.A. (2010). Image-based modeling of blood flow and vessel wall dynamics: applications, methods and future directions: Sixth International Bio-Fluid Mechanics Symposium and Workshop, March 28-30, 2008 Pasadena, California. Ann Biomed Eng 38, 1188-203.
    PMID: 20087775


  24. Voelz, V.A., Bowman, G.R., Beauchamp, K., and Pande, V.S. (2010). Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 132, 1526-8.
    PMID: 20070076, PMCID: 2835335 [Available on 2011/2/10]


  25. Voelz, V.A., Singh, V.R., Wedemeyer, W.J., Lapidus, L.J., and Pande, V.S. (2010). Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. J Am Chem Soc 132, 4702-9.
    PMID: 20218718, PMCID: 2853762 [Available on 2011/4/7]


  26. Wu, S., Liu, T., and Altman, R.B. (2010). Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. BMC Struct Biol 10, 4.
    PMID: 20122268, PMCID: 2833161


    27. 2009

  27. Besier TF, Fredericson M, Gold GE, Beaupre GS, Delp SL. (2009). Knee muscle forces during walking and running in patellofemoral pain patients and pain-free controls. J Biomech 42, 898-905.
    PMID: 19268945, PMCID: 2671570


  28. Bowman, G.R., Beauchamp, K.A., Boxer, G., and Pande, V.S. (2009). Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131, 124101.
    PMID: 19791846, PMCID: 2766407


  29. Bowman, G.R., Huang, X., and Pande, V.S. (2009). Using generalized ensemble simulations and Markov state models to identify conformational states. Methods. 49(2):197-201.
    PMID: 19410002, PMCID: 2753735


  30. Chazal, F., Cohen-Steiner, D., Guibas, L.G., Mémoli, F., and Oudot, S.Y. (2009). Gromov-Hausdorff Stable Signatures for Shapes using Persistence. Proc. Eurographics Symposium on Geometry Processing Berlin.
    http://dx.doi.org/10.1111/j.1467-8659.2009.01516.x


  31. Choi G, Cheng CP, Wilson NM, Taylor CA. (2009). Methods for quantifying three-dimensional deformation of arteries due to pulsatile and nonpulsatile forces: implications for the design of stents and stent grafts. Ann Biomed Eng 37, 14-33.
    PMID: 19002584


  32. Choi, G., Shin, L.K., Taylor, C.A., and Cheng, C.P. (2009). In vivo deformation of the human abdominal aorta and common iliac arteries with hip and knee flexion: implications for the design of stent-grafts. J Endovasc Ther 16, 531-8.
    PMID: 19842734, PMCID: 2793421


  33. Demircan, E., Khatib, O., Wheeler, J., and Delp, S. (2009). Reconstruction and EMG-informed control, simulation and analysis of human movement for athletics: performance improvement and injury prevention. Conf Proc IEEE Eng Med Biol Soc 2009, 6534-7.
    PMID: 19964175


  34. Draper, C.E., Besier, T.F., Santos, J.M., Jennings, F., Fredericson, M., Gold, G.E., Beaupre, G.S., and Delp, S.L. (2009). Using real-time MRI to quantify altered joint kinematics in subjects with patellofemoral pain and to evaluate the effects of a patellar brace or sleeve on joint motion. J Orthop Res 27, 571-7.
    PMID: 18985690


  35. Ensign DL, Pande VS. (2009). The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophys J 96, L53-5.
    PMID: 19383445, PMCID: 2718323


  36. Figueroa CA, Baek S, Taylor CA, Humphrey JD. (2009). A computational framework for fluid–solid-growth modeling in cardiovascular simulations. Comput. Methods Appl. Mech. Engrg. (In press).
    http://dx.doi.org/10.1016/j.cma.2008.09.013


  37. Fox MD, Reinbolt JA, Ounpuu S, Delp SL. (2009). Mechanisms of improved knee flexion after rectus femoris transfer surgery. J Biomech 42, 614-9.
    PMID: 19217109


  38. Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS. (2009). Accelerating molecular dynamic simulation on graphics processing units. J Comput Chem 30, 864-72.
    PMID: 19191337, PMCID: 2724265


  39. Glazer, D.S., Radmer, R.J., and Altman, R.B. (2009). Improving structure-based function prediction using molecular dynamics. Structure 17, 919-29.
    PMID: 19604472, PMCID: 2748254


  40. Hicks, J.L., Schwartz, M.H., and Delp, S.L., Modeling and Simulation of Walking, in In Diagnosis and Management of Movement Abnormalities in Cerebral Palsy, J.R. Gage and M. Schwartz, Editors. 2009, Cambridge Press. p. 285-305.
    http://web.stanford.edu/group/nmbl/publications/pdf/Hicks2009.pdf


  41. Huang Q, Wicke M, Adams B, Guibas L. (2009). Shape Decomposition Using Modal Analysis. Computer Graphics Forum 28 (2) [Eurographics 2009 Proceedings].
    http://dx.doi.org/10.1111/j.1467-8659.2009.01380.x


  42. Huang, X., Bowman, G.R., Bacallado, S., and Pande, V.S. (2009). Adaptive Seeding Method: Rapid Equilibrium Sampling Initiated from Non-equilibrium Data. Proc. Nat. Acad. Sci. U.S.A. 106, 47: 19765-19769
    PMID: 19805023, PMCID: 2785240

  43. Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. (2009). Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15, 189-99.
    PMID: 19144906, PMCID: 2648710


  44. Jonikas MA, Radmer RJ, Altman RB. (2009). Knowledge-Based Instantiation of Full Atomic Detail into Coarse Grain RNA 3D Structural Models. Bioinformatics (Epub October 7, 2009)
    PMID: 19812110, PMCID: 2788923


  45. Kasson PM, Pande VS. (2009). Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. Pac Symp Biocomput, 492-503.
    PMID: 19209725, PMCID: 2811693


  46. Keating KS, Flores SC, Gerstein MB, Kuhn LA. (2009). StoneHinge: hinge prediction by network analysis of individual protein structures. Protein Sci 18, 359-71.
    PMID: 19180449, PMCID: 2708048


  47. Keenan, K.E., Kourtis, L.C., Besier, T.F., Lindsey, D.P., Gold, G.E., Delp, S.L., and Beaupre, G.S. (2009). New resource for the computation of cartilage biphasic material properties with the interpolant response surface method. Comput Methods Biomech Biomed Engin 12, 415-22.
    PMID: 19675978, PMCID: 2858459


  48. Kelley NW, Huang X, Tam S, Spiess C, Frydman J, Pande VS. (2009). The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. J Mol Biol 388, 919-27.
    PMID: 19361448, PMCID: 2677131


  49. Khatib, O., Demircan, E., De Sapio, V., Sentis, L., Besier, T., and Delp, S. (2009). Robotics-based synthesis of human motion. J Physiol Paris 103, 211-219
    PMID: 19665552, PMCID: 2782476 [Available on 2010/9/1]


  50. Kwatra, N., Su, J., Grétarssonand, J.T., Fedkiw, R. (2009). A method for avoiding the acoustic time step restriction in compressible flow. Journal of Computational Physics
 28, 4146-4161.
    http://dx.doi.org/10.1016/j.jcp.2009.02.027


  51. Li, H., Adams, B., Guibas, L.J., and Pauly, M. (2009). Robust single-view geometry and motion reconstruction. ACM SIGGRAPH Asia 2009 papers. ACM Transactions on Graphics (TOG),
    Volume 28 , Issue 5 (December 2009), Proceedings of ACM SIGGRAPH Asia 2009,
    SESSION: Reconstruction & modeling, Article No.: 175
    http://doi.acm.org/10.1145/1661412.1618521


  52. Liao, J.C., Elting, M.W., Delp, S.L., Spudich, J.A., and Bryant, Z. (2009). Engineered Myosin VI Motors Reveal Minimal Structural Determinants of Directionality and Processivity. J Mol Biol.
    PMID: 19631216


  53. Liu, T. and Altman, R.B. (2009). Prediction of calcium-binding sites by combining loop-modeling with machine learning. BMC Struct Biol 9, 72.
    PMID: 20003365, PMCID: 2808310


  54. Luttmann E, Ensign DL, Vaidyanathan V, Houston M, Rimon N, Oland J, Jayachandran G, Friedrichs M, Pande VS. (2009). Accelerating molecular dynamic simulation on the cell processor and Playstation 3. J Comput Chem 30, 268-74.
    PMID: 18615421


  55. Miao Y, Ortoleva PJ. (2009). Molecular dynamics/order parameter extrapolation for bionanosystem simulations. J Comput Chem 30, 423-37.
    PMID: 18636559


  56. Morrison TM, Choi G, Zarins CK, Taylor CA. (2009). Circumferential and longitudinal cyclic strain of the human thoracic aorta: age-related changes. J Vasc Surg 49, 1029-36.
    PMID: 19341890, PMCID: 2695673


  57. Parker, D., Bryant, Z., and Delp, S.L. (2009). Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics. Cellular and Molecular Bioengineering 2:3, 366-374.
    PMID: 20428469, PMCID: 2860290


  58. Rangarajan, R., Lew, A., and Buscaglia, G.C. (2009). A discontinuous-Galerkin-based immersed boundary method with non-homogeneous boundary conditions and its application to elasticity. Computer Methods in Applied Mechanics and Engineering. 198, 1513-1534.
    http://dx.doi.org/10.1016/j.cma.2009.01.018


  59. Reinbolt JA, Fox MD, Schwartz MH, Delp SL. (2009). Predicting outcomes of rectus femoris transfer surgery. Gait Posture. Jul;30(1):100-5. Epub 2009 May 2.
    PMID: 19411175, PMCID: 2747373


  60. Remy CD, Thelen DG. (2009). Optimal estimation of dynamically consistent kinematics and kinetics for forward dynamic simulation of gait. J Biomech Eng 131, 031005.
    PMID: 19154064


  61. Selle, A., Su, J., Irving, G., and Fedkiw, R. (2009). Robust high-resolution cloth using parallelism, history-based collisions, and accurate friction. IEEE Trans Vis Comput Graph 15, 339-50.
    PMID: 19147895


  62. Sun, J., Ovsjanikov, M., and Guibas, L.G. (2009). A Concise and Provably Informative Multi-scale Signature Based on Heat Diffusion. Proc. Eurographics Symposium on Geometry Processing (SGP). Best Paper Award.
    http://dx.doi.org/10.1111/j.1467-8659.2009.01515.x

  63. Tawhai, M., Bischoff, J., Einstein, D., Erdemir, A., Guess, T., and Reinbolt, J. (2009). Multiscale modeling in computational biomechanics. IEEE Eng Med Biol Mag 28, 41-9.
    PMID: 19457733, PMCID: 2854014


  64. Taylor, C.A. and Figueroa, C.A. (2009). Patient-specific modeling of cardiovascular mechanics. Annu Rev Biomed Eng 11, 109-34.
    PMID: 19400706


  65. Taylor, C.A., Humphrey, J.D. (2009). Open problems in computational vascular biomechanics: Hemodynamics and arterial wall mechanics. Computer Methods in Applied Mechanics and Engineering
198(45-46), 3514-3523
    PMID: 20161129, PMCID: 2743020 [Available on 2010/9/15]


  66. Ten Eyck, A. and Lew, A. (2009). An adaptive stabilization strategy for enhanced strain methods in nonlinear elasticity. International Journal for Numerical Methods in Engineering 81, 1387-1416.
    http://www3.interscience.wiley.com/journal/122594634/abstract


  67. Voelz, V.A., Luttmann, E., Bowman, G.R., and Pande, V.S. (2009). Probing the nanosecond dynamics of a designed three-stranded Beta-sheet with a massively parallel molecular dynamics simulation. Int J Mol Sci 10, 1013-30.
    PMID: 19399235, PMCID: 2672016


  68. Voelz VA, Petrone P, Pande VS. (2009). A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. Pac Symp Biocomput, 340-52.
    PMID: 19209713


  69. Wand, M., Adams, B., Ovsjanikov, M., Berner, A., Bokeloh, M., Jenke, P., Guibas, L. Seidel, H.-P. and Schilling A. (2009). Efficient Reconstruction of Non-rigid Shape and Motion from Real-Time 3D Scanner Data. In: ACM Transactions on Graphics 28(2), April 2009.
    70. http://doi.acm.org/10.1145/1516522.1516526


  70. Wang, D., Bushnell, D.A., Huang, X., Westover, K.D., Levitt, M., and Kornberg, R.D. (2009). Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 324, 1203-6.
    PMID: 19478184, PMCID: 2718261


  71. Weiss DR, Levitt M. (2009). Can Morphing Methods Predict Intermediate Structures? J Mol Biol. 385, 665–674.
    PMID: 18996395, PMCID: 2691871


  72. Wiard, R.M., Kim, H.J., Figueroa, C., Kovacs, G.T., Taylor, C.A., and Giovangrandi, L. (2009). Estimation of central aortic forces in the ballistocardiogram under rest and exercise conditions. Conf Proc IEEE Eng Med Biol Soc 2009, 2831-4.
    PMID: 19964271


  73. Yao, Y., Sun, J., Huang, X., Bowman, G.R., Singh, G., Lesnick, M., Guibas, L.J., Pande, V.S., and Carlsson, G. (2009). Topological methods for exploring low-density states in biomolecular folding pathways. J Chem Phys 130, 144115.
    PMID: 19368437, PMCID: PMC2719471

    2008

  74. 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://portal.acm.org/citation.cfm?id=1632605


  75. Besier TF, Gold GE, Delp SL, Fredericson M, Beaupre GS. (2008). The influence of femoral internal and external rotation on cartilage stresses within the patellofemoral joint. J Orthop Res 26, 1627-35.
    PMID: 18524000


  76. Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS. (2008). Structural insight into RNA hairpin folding intermediates. J Am Chem Soc 130, 9676-8.
    PMID: 18593120, PMCID: 2652247


  77. 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    , PMCID: 2393762


  78. 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


  79. 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/


  80. 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, PMCID: 2386255


  81. 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


  82. England JL, Pande VS, Haran G. (2008). Chemical denaturants inhibit the onset of dewetting. J Am Chem Soc 130, 11854-5.
    PMID: 18707183, PMCID: 2637366


  83. 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. 73, 299-319.
    PMID: 18433058


  84. 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, PMCID: 2459243


  85. Halperin I, Glazer DS, Wu S, Altman RB. (2008). The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications. BMC Genomics 9 Suppl 2, S2.
    PMID:18831785, PMCID: 2559884


  86. 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, PMCID: 2443703


  87. 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


  88. 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, PMCID: 2809694


  89. Humphrey, J.D. and Taylor, C.A. (2008). Intracranial and abdominal aortic aneurysms: similarities, differences, and need for a new class of computational models. Annu Rev Biomed Eng 10, 221-46.
    PMID: 18647115, PMCID: 2742216


  90. Kelley NW, Vishal V, Krafft GA, Pande VS. (2008). Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. J Chem Phys 129, 214707.
    PMID: 19063575, PMCID: 2674793


  91. 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, PMCID: 2652576


  92. Lew A, Buscaglia G. (2008). A discontinuous-Galerkin-based immersed boundary method. International Journal for Numerical Methods in Engineering 76, 427-454.
    http://dx.doi.org/10.1002/nme.2312


  93. Lew, A., Ten Eyck, A., and Rangarajan, R. (2008). Some Applications of Discontinuous Galerkin Methods in Solid Mechanics. IUTAM Symposium on Theoretical, Computational and Modelling Aspects of Inelastic Media, 227-236.
    http://dx.doi.org/10.1007/978-1-4020-9090-5


  94. Liu MQ, Anderson FC, Schwartz MH, Delp SL. (2008). Muscle contributions to support and progression over a range of walking speeds. J Biomech. 41, 3243-3252.
    PMID: 18822415


  95. 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


  96. 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, PMCID: 2441812


  97. 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, PMCID: 2679973


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


  99. 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


  100. Petrone PM, Snow CD, Lucent D, Pande VS. (2008). Side-chain recognition and gating in the ribosome exit tunnel. Proc Natl Acad Sci U S A 105, 16549-54.
    PMID: 18946046, PMCID: 2575457


  101. 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


  102. 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.
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  103. 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.
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  104. Selle A, Fedkiw R, Kim B-M, Liu Y, Rossignac J. (2008). An Unconditionally Stable MacCormack Method. J. Sci. Comput. 35, 350-371.
    http://dx.doi.org/10.1007/s10915-007-9166-4


  105. Selle A, Lentine M, Fedkiw R. (2008). A Mass Spring Model for Hair Simulation. SIGGRAPH 2008, ACM TOG, 27(3) Article 64.
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  106. Shadden SC, Taylor CA. (2008). Characterization of Coherent Structures in the Cardiovascular System. Annals of Biomedical Engineering. Jul;36(7):1152-62.
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  107. 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, PMCID: 2696074


  108. 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


  109. 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.
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  110. Sweet CR, Petrone P, Pande VS, Izaguirre JA. (2008). Normal mode partitioning of Langevin dynamics for biomolecules. J Chem Phys. 14;128(14):145101.
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  111. 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.
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  112. Spink BJ, Sivaramakrishnan S, Lipfert J, Doniach S, Spudich JA. (2008). Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. Nat Struct Mol Biol 15, 591-7.
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  113. 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)
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  114. 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


  115. 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


  116. Weiss DR, Raschke TM, Levitt M. How Hydrophobic Buckminsterfullerence Affects Surrounding Water Structure. Journal of Physical Chemistry B. Mar 13;112(10):2981-90.
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  117. Xiao M, Higginson JS. (2008). Muscle function may depend on model selection in forward simulation of normal walking. J Biomech 41, 3236-42.
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  118. Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Halperin-Landsberg I, Altman RB. (2008). Efficient algorithms to explore conformation spaces of flexible protein loops. IEEE/ACM Trans Comput Biol Bioinform 5, 534-45.
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    119. 2007

  119. Adams B, Pauly M, Keiser R, Guibas L. (2007). Adaptively Sampled Particle Fluids. ACM SIGGRAPH, 2007 papers 26.
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  120. 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.
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  121. 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, PMCID: 2795578

  122. 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


  123. 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


  124. 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.
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  125. 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.
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  126. 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.
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  127. Dugan JM, Altman RB. (2007). Using surface envelopes to constrain molecular modeling. Protein Sci. Jul; 16(7):1266-73.
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  128. Dunn AR, Spudich JA. (2007). Dynamics of the unbound head during myosin V processive translocation. Nat Struct Mol Biol 14, 246-8.
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  129. 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.
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  130. Guibas LJ, Oudot SY. (2007). Reconstruction using Witness Complexes. Proc. 18th ACM-SIAM Sympos. on Discrete Algorithms. 1076-1085, 2007. Full version in Discrete Comput Geom (2008) 40: 325–356 .
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  131. Guibas LJ, Wang Y. (2007). Toward Unsupervised Segmentation of Semi-Rigid Low-Resolution Molecular Surfaces. Algorithmica. 48(4):433-438, Aug 2007.
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  132. 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, PMCID: 2443695


  133. 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


  134. Irving G, Schroeder C, Fedkiw R. (2007). Volume Conserving Finite Element Simulations of Deformable Models. ACM Trans. Graph, Volume 26 , Issue 3 (July 2007).
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  135. 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.
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  136. Laederach A. Informatics challenges in structured RNA. (2007). Brief Bioinform. 2007 Sep;8(5):294-303.
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  137. 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.
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  138. 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.
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  139. 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.
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  140. 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.
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  141. Mitra NJ, Guibas L, Pauly M. (2007). Symmetrization. ACM SIGGRAPH 2007, Volume 26 , Issue 3 July 2007
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  142. 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.
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  143. 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
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  144. 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


  145. 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.
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  146. 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.
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  147. 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.
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  148. 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.
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  149. 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.
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  150. 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.
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    151. 2006

  151. 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.
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  152. 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


  153. 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


  154. 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


  155. 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


  156. 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


  157. 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, PMCID: 2621361


  158. 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


  159. 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


  160. Mitra NJ, Guibas L, Giesen J, Pauly M. (2006). Probabilistic Fingerprints for Shapes. Symposium on Geometry Processing. 121-130, 2006.
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  161. Petrone P and Pande V. (2006). Can Conformational Change Be Described by Only a Few Normal Modes? Biophysical Journal, 90:1583-1593, March 2006.
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  162. 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
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  163. 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


  164. 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


  165. 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


  166. 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


  167. 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.
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    168. 2005

  168. 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.
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  169. 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.
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  170. 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.
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  171. 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.
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  172. 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


  173. 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


  174. 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