Simbios
 
Literature

 

[1] Lew, A., Marsden, J., Ortiz, M., and West, M., Variational time integrators. To appear in International Journal for Numerical Methods in Engineering, 2004.

[2] Dingemans, K.P., Teeling, P., Lagendijk, J.H., and Becker, A.E., Extracellular Matrix of the Human Aortic Media: An Ultrastructural Histochemical and Immunohistochemical Study of the Adult Aortic Media. Anatomical Record, 2000. 258: p. 1-14.

[3] Houdusse, A., Kalabokis, V.N., Himmel, D., Szent-Gyorgyi, A.G., and Cohen, C., Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head. Cell, 1999 May 14. 97(4): p. 459-70.

[4] Gordon, A.M., Huxley, A.F., and Julian, F.J., Tension development in highly stretched vertebrate muscle fibres. J Physiol, 1966. 184(1): p. 143-69.

[5] DeLano, W.L., The PyMOL User's Manual. 2002, San Carlos, CA, USA: DeLano Scientific.

[6] Tsui, V. and Case, D.A., Molecular dynamics simulations of nucleic acids using a generalized Born solvation model. J. Am. Chem. Soc., 2000. 122: p. 2489-2498.

[7] Bashford, D. and Case, D.A., Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem., 2000. 51: p. 129-152.

[8] Clark, J.M. and Glagov, S., Transmural Organization of the Arterial Media. The Lamellar Unit Revisited. Arteriosclerosis, 1985. 5(1): p. 19-34.

[9] Anderson, F.C. and Pandy, M.G., Dynamic optimization of human walking. J Biomech Eng, 2001. 123(5): p. 381-90.

[10] Huxley, A.F., Muscle structure and theories of contraction. Prog Biophys Biophys Chem, 1957. 7: p. 255-318.

[11] Coureux, P.D., Wells, A.L., Menetrey, J., Yengo, C.M., Morris, C.A., Sweeney, H.L., and Houdusse, A., A structural state of the myosin V motor without bound nucleotide. Nature, 2003 Sep 25. 425(6956): p. 419-23.

[12] Anderson, F.C. and Pandy, M.G., Static and dynamic optimization solutions for gait are practically equivalent. Journal of Biomechanics, 2001. 34: p. 153-161.

[13] Anderson, F.C. and Pandy, M.G. Contributions of individual muscles to support during normal gait. in Submitted to the 6th Annual Meeting of the Gait and Clinical Movement Analysis Society. 2001. Sacramento, CA.

[14] O'Shea, E.K., Klemm, J.D., Kim, P.S., and Alber, T., X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science, 1991. 254(5031): p. 539-44.

[15] Bevilacqua, P.C., Kierzek, R., Johnson, K.A., and Turner, D.H., Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science, 1992. 258(5086): p. 1355-8.

[16] Cech, T.R., Herschlag, D., Piccirilli, J.A., and Pyle, A.M., RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. J. Biol. Chem., 1992. 267(25): p. 17479-82.

[17] Rock, R.S., Rice, S.E., Wells, A.L., Purcell, T.J., Spudich, J.A., and Sweeney, H.L., Myosin VI is a processive motor with a large step size. Proc Natl Acad Sci U S A, 2001. 98(24): p. 13655-9.

[18] Houdusse, A., Szent-Gyorgyi, A.G., and Cohen, C., Three conformational states of scallop myosin S1. Proc Natl Acad Sci U S A, 2000 Oct 10. 97(21): p. 11238-43.

[19] Trybus, K.M., Freyzon, Y., Faust, L.Z., and Sweeney, H.L., Spare the rod, spoil the regulation: necessity for a myosin rod. Proc Natl Acad Sci U S A, 1997. 94(1): p. 48-52.

[20] Sweeney, H.L., Rosenfeld, S.S., Brown, F., Faust, L., Smith, J., Xing, J., Stein, L.A., and Sellers, J.R., Kinetic tuning of myosin via a flexible loop adjacent to the nucleotide binding pocket. J Biol Chem, 1998. 273(11): p. 6262-70.

[21] Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M., CHARMM: a program for macromolecular energy minimization and dynamics. J. Comp. Chem., 1983. 4: p. 187-217.

[22] Keasar, C. and Rosenfeld, R., Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations. Fold Des, 1998. 3(5): p. 379-88.

[23] Delp, S.L. and Loan, J.P., A Computational Framework for Simulation and Analyzing Human Movement. IEEE Computing in Science and Engineering, 2000. 2(5): p. 46-55.

[24] Puso, M.A., Maker, B.N., Ferencz, R.M., and Hallquist, J.O., Nike3d: A Nonlinear, Implicit, Three-Dimensional Finite Element Code for Solid and Structural Mechanics. 2002, Lawrence Livermore National Lab Technical Report.

[25] Williams, G.A., Dugan, J.M., and Altman, R.B., Constrained global optimization for estimating molecular structure from atomic distances. J Comput Biol, 2001. 8(5): p. 523-47.

[26] Nilges, M., Habazettl, J., Brunger, A.T., and Holak, T.A., Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J Mol Biol, 1991. 219(3): p. 499-510.

[27] Holtje, H.-D., Folkers, G., Sippl, W., and Rognan, D., Molecular Modeling: Basic Principles and Applications. 2003, New York: John Wiley & Sons.

[28] Schlick, T., Molecular Modeling and Simulation. 2002, New York: Springer Verlag.

[29] Bathe, K.J., Finite element procedures. 1996, Englewood Cliffs, N.J.: Printice Hall.

[30] Belytschko, T., Nonlinear finite elements for continua and structures. 2000, New York: John Wiley.

[31] Kane, T.R. and Levison, D.A., Dynamics: Theory and Applications. 1985, New York: McGraw-Hill.

[32] Fung, Y.C., Biomechanics: Mechanical Properties of Living Tissues. 1981, New York: Springer-Verlag.

[33] Yamaguchi, G., Dynamic Modeling of Musculoskeletal Motion. 2001, Boston: Kluwer Publishers.

[34] Kass, M., Witkin, A., and Terzopoulos, D., Snakes: Active contour models. International Journal of Computer Vision, 1987. 1(4): p. 321–331.

[35] Kimmel, R., V., C., and Sapiro, G., Geodesic active contours. International Journal of Computer Vision, 1997. 22(1): p. 61-79.

[36] Paragios, N. and Deriche, R., Geodesic Active Contours and Level Sets for the Detection and Tracking of Moving Objects. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2000. 22: p. 266-280.

[37] Osher, S. and Sethian, J., Front propagation with curvature dependent speed: Algorithms based on Hamilton-Jacobi formulations. Journal of Computational Physics, 1988. 79: p. 12-49.

[38] Sethian, J., A fast marching level set method for monotonically advancing fronts. Proceedings of the National Academy of Sciences, 1996. 93(4): p. 1951-5.

[39] Chan, T. and Vese, L., An Active Contour Model without Edges. Proceedings of International Conference on Scale Space Theories in Computer Vision, 1999: p. 141-51.

[40] Tsai, A., Yezzi, A., Wells, W., Tempany, C., Tucker, D., Fan, A., E. Grimson, E., and A. Willsky, A., A shape based approach to curve evolution for segmentation of medical imagery. IEEE Transactions on Medical Imaging, 2003. 22(2): p. 137 - 154.

[41] Leventon, M., Statistical Models for Medical Image Analysis. 2000, Massachussetts Insitute of Technology, Ph.D. Thesis.

[42] Lorigo, L.M., Faugeras, O., Grimson, W.E.L., Keriven, R., Kikinis, R., Nabavi, A., and Westin, C.F., CURVES: Curve evolution for vessel segmentation. Medical Image Ananysis, 2001. 5(3): p. 195–206.

[43] van Donkelaar, C.C., Kretzers, L.J.G., Bovendeerd, P.H.M., Lataster, L.M.A., Nicolay, K., Janssen, J.D., and Drost, M.R., Diffusion tensor imaging in biomechanical studies of skeletal muscle function. Journal of Anatomy, 1999. 194(79-88).

[44] Sherbondy, A., Houston, M., and Napel, S. Interactively Guided Volumetric Segmentation using Programmable Graphics Hardware. in Radiological Society of North America 89th Scientific Sessions. 2003. Chicago.

[45] Sherbondy, A., Houston, M., and Napel, S. Fast Volume Segmentation with Simultaneous Visualization Using Programmable Graphics Hardware. in Proceedings: IEEE Visualization. 2003. Seattle, WA.

[46] Shiffman, S. and Napel, S., Object Segregation in Images. 2002.: US.

[47] Shiffman, S., Rubin, G.D., and Napel, S., Medical Image Segmentation Using Analysis of Isolabel Contour Maps. IEEE Transactions on Medical Imaging, 2000. 19(11): p. 1064-74.

[48] Shiffman, S., Rubin, G.D., Schraedley-Desmond, P., and Napel, S., Semiautomated Segmentation of Blood Vessels using Ellipse Overlap Criteria: Method and Comparison to Manual Editing. Medical Physics, 2003. 30(10): p. 2572-83.

[49] Zhuge, F., Napel, S., Paik, D., and Rubin, G.D. Automatic Detection and Quantification of Abdominal Aortic Thrombus in CT Angiograms Based on Clustering and Global Geometric Information. in Radiological Society of North America 86th Scientific Sessions,. 2000. Chicago.

[50] Zhuge, F., Napel, S., Shiffman, S., and Rubin, G.D. Automated Aortic Flow-channel Segmentation: Method and Comparison with Manual Segmentation. in Radiological Society of North America 87th Scientific Sessions. 2001. Chicago.

[51] Zhuge, F., Napel, S., Raman, R., Raman, B., and Rubin, G.D. A Discrete Deformable Contour Model for Segmentation of Abdominal Aortic Thrombus. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[52] Wang, K.C., Dutton, R.W., and Taylor, C.A., Improving geometric model construction for blood flow modeling. IEEE Eng Med Biol Mag, 1999. 18(6): p. 33-9.

[53] Wang, K.C.-Y., Level set methods for computational prototyping with application to hemodynamic modeling, in Electrical Engineering. 2001, Stanford University: Stanford, CA. p. 210.

[54] Gordon, A.M., Huxley, A.F., and Julian, F.J., The variation in isometric tension with sarcomere length in vertebrate muscle fibres. J Physiol, 1966. 184(1): p. 170-92.

[55] Denoth, J., Stussi, E., Csucs, G., and Danuser, G., Single muscle fiber contraction is dictated by inter-sarcomere dynamics. J Theor Biol, 2002. 216(1): p. 101-22.

[56] Humphrey, J.D., Cardiovascular Solid Mechanics. Cells, Tissues, and Organs. 2002: Springer.

[57] Zajac, F.E., Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. Critical Reviews in Biomedical Engineering, 1989. 17: p. 359-411.

[58] Pappas, G.P., Asakawa, D.S., Delp, S.L., Zajac, F.E., and Drace, J.E., Nonuniform shortening in the biceps brachii during elbow flexion. J Appl Physiol, 2002. 92(6): p. 2381-9.

[59] Gielen, A.W., Oomens, C.W., Bovendeerd, P.H., Arts, T., and Janssen, J.D., A Finite Element Approach for Skeletal Muscle using a Distributed Moment Model of Contraction. Comput Methods Biomech Biomed Engin, 2000. 3(3): p. 231-244.

[60] Johansson, T., Meier, P., and Blickhan, R., A finite-element model for the mechanical analysis of skeletal muscles. J Theor Biol, 2000. 206(1): p. 131-49.

[61] Martins, J.A.C., Pires, E.B., Salvado, R., and Dinis, P.B., A numerical model of passive and active behavior of skeletal muscles. Computer Methods in Applied Mechanics and Engineering, 1998. 151: p. 419-433.

[62] Oomens, C.W., Maenhout, M., van Oijen, C.H., Drost, M.R., and Baaijens, F.P., Finite element modelling of contracting skeletal muscle. Philos Trans R Soc Lond B Biol Sci, 2003. 358(1437): p. 1453-60.

[63] Yucesoy, C.A., Koopman, B.H., Huijing, P.A., and Grootenboer, H.J., Three-dimensional finite element modeling of skeletal muscle using a two-domain approach: linked fiber-matrix mesh model. J Biomech, 2002. 35(9): p. 1253-62.

[64] Jenkyn, T.R., Koopman, B., Huijing, P., Lieber, R.L., and Kaufman, K.R., Finite element model of intramuscular pressure during isometric contraction of skeletal muscle. Phys Med Biol, 2002. 47(22): p. 4043-61.

[65] Criscione, J.C., Douglas, A.S., and Hunger, W.C., Physically based strain invariant set for materials exhibiting transversely isotropic behavior. Journal of the Mechaincs and Physics of Solids, 2001. 49: p. 871-897.

[66] Blemker, S.S. and Delp, S.L. A 3D of muscle reveals the causes of nonuniform strains in the biceps brachii. in Prooceedings of the American Society of Biomechanics Meeting. 2003. Toledo, OH.

[67] Johnson, M. and Tarbell, J.M., A Biphasic, Anisotropic Model of the Artery Wall. J. Biomechanical Engrg., 2001. 123( ): p. 52-57.

[68] Simon, B.R., Multiphase Poroelastic Finite Element Models for Soft Tissue Structures. Appl Mech Rev, 1992. 45(6): p. 191-218.

[69] Simon, B.R., Kaufmann, M.V., McAfee, M.A., and Baldwin, A.L., Finite Element Models for Arterial Wall Mechanics. J. Biomechanical Engrg., 1993. 115( ): p. 489-496.

[70] Simon, B.R., Kaufmann, M.V., McAfee, M.A., and Baldwin, A.L., Porohyperelastic theory and finite element models for soft tissue with application to arterial mechanics, in Mechanics of Poroelastic Media, A.P.S. Selvadurai, Editor. 1996, Kluwer Academic Publishers. p. 245-261.

[71] Simon, B.R., Kaufmann, M.V., McAfee, M.A., and Baldwin, A.L., Porohyperelastic finite element analysis of large arteries using ABAQUS. J. Biomechanical Engrg., 1998. 120: p. 296-298.

[72] Simon, B.R., Kaufman, M.V., Liu, J., and Baldwin, A.L., Porohyperelastic-transport-swelling theory, material properties and finite element models for large arteries. Int. J. Solids and Structures, 1998. 35(34-45): p. 5021-5031.

[73] Vorp, D.A., Raghavan, M.L., and Webster, M.W., Mechanical Wall Stress in Abdominal Aortic Aneurysm: Influence of Diameter and Asymmetry. Journal of Vascular Surgery, 1998. 27(4): p. 632-639.

[74] Delfino, A., Stergiopulos, N., Jr., J.E.M., and Meister, J.-J., Residual strain effects on the stress fields in a thick wall finite elemetn model of the human carotid bifurcation. J. Biomechanics, 1997. 30(8): p. 777-786.

[75] Chuong, C.J. and Fung, Y.C., Three-dimensional stress distribution in arteries. J. Biomechanical Engrg., 1983. 105: p. 268-274.

[76] Holzapfel, G.A., Gasser, T.C., and Ogden, R.W., A new constitutive framework for arterial wall mechanics and a comparative study of material models. J. Elasticity, 2000. 61: p. 1-48.

[77] Daggett, V. and Levitt, M., Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct, 1993. 22: p. 353-80.

[78] Lin, M. and Gottschalk, S., Collision detection between geometric models: A survey. In Proceedings of IMA Conference on Mathematics of Surfaces, 1992. 37-56(1): p. 1998.

[79] Lin, M.C. and F, J., Canny, A fast algorithm for incremental distance calculation, Proc. International Conference on Robotics and Automation IEEE ICRA ", 1992. 1008-1014(1): p. 1991.

[80] Hubbard, P.M., Collision detection for interactive graphics applications. IEEE Trans 1992. 218-230(1): p. 1995.

[81] Lin, M. and Gottschalk, S., Collision detection between geometric models: A survey. Proc. of IMA Conference on Mathematics of Surfaces, 1998: p. 37-56.

[82] Guibas, L., Nguyen, A., Russel, D., and Zhang, L., Collision detection for deforming necklaces. Proc. 18th ACM Symposium on Computational Geometry, 2002: p. 33-42.

[83] Agarwal, P.K., Basch, J., Guibas, L.J., Hershberger, J., and Zhang, L., Deformable free-space tilings for kinetic collision detection. Int. J. Robotics Research, 2002. 21(3): p. 179-198.

[84] Basch, J., Guibas, L., and Hershberger, J., Data structures for mobile data. J. Algorithms, 1999. 31(1): p. 1-28.

[85] Guibas, L.J., Kinetic data structures --- a state of the art report. Proc. Workshop Algorithmic Foundations of Robotics, 1998: p. 191-209.

[86] Guendleman, E., Bridson, R., and Fedkiw, R., Nonconvex Rigid Bodies with Stacking. SIGGRAPH, ACMTOG, 2003. 22: p. 871-878.

[87] Adalsteinsson, D. and Sethian, J., The Fast Construction of Extension Velocities in Level Set Methods. J. Comput. Phys., 1999. 148: p. 2-22.

[88] Levin, D., Mesh-independent surface interpolation, in To appear in Geometric Modeling for Scientific Visualization, Brunnett, Hamann, and Mueller, Editors. 2003, Springer-Verlag.

[89] Bridson, R., Fedkiw, R., and Anderson, J., Robust Treatment of Collisions, Contact and Friction for Cloth Animation. SIGGRAPH, ACMTOG, 2002. 21: p. 594-603.

[90] Teran, J., Irving, G., Hauser, K., and Fedkiw, R., Robust Simulation of Large Muscle Groups with Connective Tissue. Submitted to SIGGRAPH, ACMTOG, 2004.

[91] Klein, T.E., Huang, C.C., Pettersen, E.F., Couch, G.S., Ferrin, T.E., and Langridge, R., A real-time malleable molecular surface. J Mol Graph, 1990. 8(1): p. 16-24, 26.

[92] Owen, S.J., A Survey of Unstructured Mesh Generation Technology. Proceedings 7th International Meshing Roundtable, 1998.

[93] Lee, C.K. and Lo, S.H., Automatic Adaptive 3-D Finite Element Refinement Using Different-Order Tetrahedral Elements. International Journal for Numerical Methods in Engineering, 1997. 40: p. 2195-2226.

[94] Molino, N., Bridson, R., and Fedkiw, R., Tetrahedral Mesh Generation for Deformable Bodies. International Meshing Roundtable, 2003.

[95] Taylor, C.A., A Computational Framework for Investigating Hemodynamic Factors in Vascular Adaptation and Disease, in PhD Dissertation, Department of Mechanical Engineering. 1996, Stanford University: Stanford, CA.

[96] Taylor, C.A., Draney, M.T., Ku, J.P., Parker, D., Steele, B.N., Wang, K., and Zarins, C.K., Predictive Medicine: Computational Techniques in Therapeutic Decision-Making. Computer Aided Surgery, 1999. 4: p. 231-247.

[97] Wilson, N.M., Geometric Algorithms and Software Architecture for Computational Prototyping: Applications in Vascular Surgery and MEMS, in PhD Dissertation, Department of Mechanical Engineering. 2002, Stanford University: Stanford, CA.

[98] Ku, J.P., Draney, M.T., Arko, F.R., Lee, W.A., Chan, F.P., Pelc, N.J., Zarins, C.K., and Taylor, C.A., In Vivo Validation of Numerical Predication of Blood Flow in Arterial Bypass Grafts. Annals of Biomedical Engineering, 2002. 30: p. 743-752.

[99] Blemker, S.S. and Delp, S.L. 3D Modeling of Complex Muscle Geometry. in To be presented that the upcoming Orthopaedic Research Society Symposium on Computer Simulation in Biomechanics. 2004. San Francisco, CA.

[100] Shephard, M.S., Meshing environment for geometry-based analysis. International Journal for Numerical Methods in Engineering, 2000. 47: p. 169-190.

[101] Bekkers, E. and Taylor, C.A., Image Based Analytic Surface Representation and Mesh Generation. 7th National Congress on Computational Mechanics, 2003.

[102] Eck, M. and Hoppe, H., Automatic Reconstruction of B-spline Surfaces of Arbitrary Topological Type. ACM SIGGRAPH, 1996: p. 325-334.

[103] Peters, J., Patching Catmull-Clark Meshes. ACM SIGGRAPH, 2000: p. 255-258.

[104] Kimmel, R. and Sethian, J., Fast Marching Methods on Triangulated Domains. Proc. Nat. Acad. Sci., 1998. 95: p. 8341-8345.

[105] Ortiz, J.K.a.M., An analysis of the Quasicontinuum Method. Journal of the Mechanics and Physics of Solids, 2001. 49(9): p. 1899-1923.

[106] McCammon, J.A., Gelin, B.R., and Karplus, M., Dynamics of Folded Proteins. Nature 1977. 267(1): p. 585-590.

[107] Levitt, M., Computer Studies of Protein Molecules. In Protein Folding, 1980. Elsevier/North Holland(1): p. pp.

[108] Levitt, M., Molecular Dynamics of Native Protein: I. Computer Simulation of Trajectories J Mol Biol 1983. 168(1): p. 595-620.

[109] Levitt, M., Computer Simulation of DNA Double Helix Dynamics. Cold Spring Harbor Symp Quant Biol 1983. 47(1): p. 251-261.

[110] Levitt, M., Molecular Dynamics of Macromolecules in Water. Chemica Scripta, 1989. 29A(1): p. 197-203.

[111] Bushnell, D.A. and Kornberg, R.D., Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A, 2003 Jun 10. 100(12): p. 6969-73.

[112] Cramer, P., Bushnell, D.A., Fu, J., Gnatt, A.L., Maier-Davis, B., Thompson, N.E., Burgess, R.R., Edwards, A.M., David, P.R., and Kornberg, R.D., Architecture of RNA polymerase II and implications for the transcription mechanism. Science, 2000 Apr 28. 288(5466): p. 640-9.

[113] Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A., High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell, 2001 Nov 30. 107(5): p. 679-88.

[114] Yonath, A., The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states. Annu Rev Biophys Biomol Struct, 2002. 31: p. 257-73.

[115] Noller, H.F. and Baucom, A., Structure of the 70 S ribosome: implications for movement. Biochem Soc Trans, 2002 Nov. 30(Pt 6): p. 1159-61.

[116] Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A., The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 2000 Aug 11. 289(5481): p. 905-20.

[117] Wimberly, B.T., Brodersen, D.E., Clemons, W.M.J., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V., Structure of the 30S ribosomal subunit. Nature, 2000 Sep 21. 407(6802): p. 327-39.

[118] Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F., Crystal structure of the ribosome at 5.5 A resolution. Science, 2001 May 4. 292(5518): p. 883-96.

[119] Warshel, A., Molecular dynamics simulations of biological reactions. Acc Chem Res, 2002 Jun. 35(6): p. 385-95.

[120] Simonson, T., Archontis, G., and Karplus, M., Free energy simulations come of age: protein-ligand recognition. Acc Chem Res, 2002 Jun. 35(6): p. 430-7.

[121] Giudice, E. and Lavery, R., Simulations of nucleic acids and their complexes. Acc Chem Res, 2002 Jun. 35(6): p. 350-7.

[122] Daggett, V., Molecular dynamics simulations of the protein unfolding/folding reaction. Acc Chem Res, 2002 Jun. 35(6): p. 422-9.

[123] Carloni, P., Rothlisberger, U., and Parrinello, M., The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc Chem Res, 2002 Jun. 35(6): p. 455-64.

[124] Meiler, J. and Baker, D., Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci U S A, 2003 Oct 14. 100(21): p. 12105-10.

[125] Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., and Baker, D., Design of a novel globular protein fold with atomic-level accuracy. Science, 2003 Nov 21. 302(5649): p. 1364-8.

[126] Altman, R. and Jardertzky, O., New strategies for the determination of macromolecular structure in solution. Journal of Biochemistry, 1986. 100(6): p. 1403-1423.

[127] Edelsbrunner, H. and Koehl, P., The weighted-volume derivative of a space-filling diagram. Proc Natl Acad Sci U S A, 2003. 100(5): p. 2203-8.

[128] Shrake, A. and Rupley, J.A., Environment and exposure to solvent of protein atoms in lyzyzyme and insulin. J Mol Biol 1973. 79(1): p. 351-371.

[129] Legrand, S.M. and Merz, K.M., Rapid approximation to molecular surface area via the use of Boolean logic and lookup tables. J Comp Chem 1993. 14(1): p. 349-352.

[130] Wodak, S.J. and Janin, J., Analytical approximation to the accessible surface area of proteins. Proc Natl Acad Sci USA 1979. 77(1): p. 1736-1740.

[131] Hasel, W., Hendrikson, T.F., and Still, W.C., A rapid approximation to the solvent accessible surface areas of atoms. Tetrahed Comp Method 1988. 1(1): p. 103-116.

[132] Street, A.G. and Mayo, S.L., Pairwise calculation of protein solvent-accessible surface areas. Folding & Design 1998. 3(1): p. 253-258.

[133] Connolly, M., Analytical molecular surface calculation. J Appl Cryst 1983. 16(1): p. 548-558.

[134] Richmond, T.J., Solvent accessible surface area and excluded volume in proteins. J Mol Biol 1984. 178(1): p. 63-89.

[135] Von Freyberg, B., Richmond, T.J., and Braun, W., Surface area included in energy refinements of proteins: a comparative study on atomic solvation parameters. J Mol Biol 1993. 233(1): p. 275-292.

[136] Fraczkiewicz, R. and Braun, W., Exact and efficient analytical calculation of the accessible surface area and their gradient for macromolecules. J Comput Chem 1998. 19(1): p. 319-333.

[137] Eisenhaber, F. and Argos, P., Improved strategy in analytic surface calculation for molecular systems: handling of singularities and computational efficiency. J Comput Chem 1993. 14(1): p. 1272-1280.

[138] Gogonea, V. and Osawa, E., An improved algorithm for the analytical computation of solvent-excluded volume: The treatment of singularities in solvent accessible surface area and volume functions. J Comput Chem 1995. 7(1): p. 817-842.

[139] Kratky, K.W., The area of the intersection of n equal cicular disks. J Phys A: Math Gen 1978. 11(1): p. 1017-1024.

[140] Gibson, K.D. and Scheraga, H.A., Exact calculation of the volume and surface area of fused hard sphere molecule with unequal atomic radii. Mol Phys 1987. 62(1): p. 1247-1265.

[141] Edelsbrunner, H., The union of balls and its dual shape. Discrete Comput Geom 1995. 13(1): p. 415-440.

[142] Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., and Subramaniam, S., Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins, 1998. 33(1): p. 18-29.

[143] Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V., and Subramaniam, S., Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins, 1998. 33(1): p. 1-17.

[144] Featherstone, R., Robot Dynamic Algorithms. 1987: Kluwer Academic Publishers.

[145] Chang, K.S. and Khatib, O., Operational Space Dynamics: Efficient Algorithms for Modeling and Control of Branching Mechanisms. Proc. IEEE International Conference on Robotics and Automation, 2000: p. 850-856.

[146] Ruspini, D. and Khatib, O., Collision/Contact Models for Dynamic Simulation and Haptic Interaction. Proc. ISRR'99, the Ninth International Symposium of Robotics Research, 1999: p. 185-194.

[147] Khatib, O., A Unified Approach to Motion and Force Control of Robot Manipulators: The Operational Space Formulation. IEEE Journal on Robotics and Automation, 1987. 3(1): p. 43-53.

[148] Shea, J. and Brooks, C., From Folding Thories to Folding Proteins A Review and Assessment of Simulation Studies of Protein Folding and Unfolding., in Annual Review of Physical Chemistry, H. Strauss, Editor. 2001, Annual Reviews: Palo Alto. p. 499-535.

[149] Shea, J. and Brooks, C., Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist beta-Barrel Model. J. Chem. Phys., 1998. 109: p. 2895-2903.

[150] Clementi, C., Jennings, P., and Onuchic, J., Prediction of Folding Mechanism for cirrcularpremuted protien. J. Mol. Biol., 2001. 311: p. 879-890.

[151] Clementi, C., Jennings, P., and Onuchicn, J., How Native State Topology Affects Dihydrofolate Reductase And Interleukin-1 beta. Proc. Nat. Acad. Sci., 2000. 97: p. 5871-5876.

[152] Clementi, C., Nymeyer, H., and Onuchic, J., Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding? An investigation for small globbular proteins. J. Mol. Biol., 2000. 298: p. 937-953.

[153] Shimada, J. and Shakhnovich, E.I., The Ensemble Folding Kinetics Of Protei G From An All-Atom Monte Carlo Simulation. Proc. Nat. Acad. Sci., 2002. 99: p. 11175-11180.

[154] Li, L. and Shakhnovich, E.I., Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl. Acad. Sci., 2001. 98: p. 13014-13018.

[155] Plaxco, K., Simons, K., and Baker, D., Contact Order, Transition State Placement and the Refolding Rates of Single Domain Proteins folding. J. Mol. Biol., 1998. 277: p. 985-994.

[156] Duan, Y. and Kollman, P., Pathways to a protein folding intermediate observed in a l-microsecond simulation in aqueous solution. Science, 1998. 282: p. 740-744.

[157] Jordan, B.W. and Polak, E., Theory of a class of discrete optimal control systems. J. Electron. Control, 1964. 17: p. 697-711.

[158] Lew, A., Marsden, J., Ortiz, M., and West, M., Asynchronous variational integrators. Archive for Rational Mechanics & Analysis, 2003. 167(2): p. 85-146.

[159] Marsden, J.E. and Ratiu, T., Introduction to Mechanics and Symmetry. Texts in Applied Mathematics. Vol. 17. 1994: Springer-Verlag.

[160] Lew, A., Marsden, J., Ortiz, M., and West, M., Variational time integrators in computational solid mechanics, in Dept of Aeronautics. 2003, Caltech: Pasadena.

[161] Marsden, J.E. and West, M., eds. Discrete mechanics and variational integrators. Acta Numerica. Vol. 10. 2001, Cambridge University Press.

[162] Newmark, N., A method of computation for structural dynamics. ASCE Journal of the Engineering Mechanics Division, 1959. 85(EM3): p. 67-94.

[163] Hairer, E. and Lubich, C., Long-time energy conservation of numerical methods for oscillatory differential equations. SIAM J Numer Anal, 2000. 38(2): p. 414-41.

[164] Lew, A., Radovitzky, R., and Ortiz, M., An artificial viscosity, Lagrangian finite element method for capturing shocks in largely-deforming elastic-plastic materials. Journal of Computer-Aided Materials Design, 2002. 8(2-3): p. 213-231.

[165] Tuckerman, M., Berne, B.J., and Martyna, G.J., Reversible multiple time scale molecular dynamics. Journal of Chemical Physics, 1992. 97: p. 1990-2001.

[166] Grubmüller, H., Heller, H., Windemuth, A., and Schulten, K., Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Molecular Simulations, 1991. 6: p. 121-142.

[167] Cho, A.E., Doll, J.D., and Freeman, D.L., The construction of double-ended classical trajectories. Chemical Physics Letter, 1994. 229: p. 218-224.

[168] Olender, R. and Elber, R., Calculation of classical trajectories with a very large time step: Formalism and numerical examples. Journal of Chemical Physics, 1996. 105: p. 9299-9315.

[169] Passerone, D. and Parrinello, M., A concerted variational strategy for investigating rare events. Journal of Chemical Physics, 2003. 118: p. 2025-2032.

[170] Passerone, D. and Parrinello, M., Action-derived molecular dynamics in the study of rare events. Phsical Review Letters, 2001. 87: p. 108302(1).

[171] Crehuet, R. and Field, M., Comment on “Action-derived molecular dynamics in the study of rare events”. Physical Review Letters, 2003. 90: p. 089801(1).

[172] Passerone, D. and Parrinello, M., Passerone and Parrinello reply. Phsical Review Letters, 2003. 90: p. 089802(1).

[173] Radovitzky, R. and Ortiz, M., Error estimation and adaptive meshing in strongly nonlinear dynamic problems. Computer Methods in Applied Mechanics and Engineering, 1999. 172: p. 203-240.

[174] Molinari, J.F. and Ortiz, M., Three-dimensional adaptive meshing by subdivision and edge-collapse in finite-deformation dynamic-plasticity problems with application to adiabatic shear banding. International Journal for Numerical Methods in Engineering, 2002. 53(5): p. 1101-1126.

[175] Hughes, T.J.R., Franca, L.P., and Hulbert, G.M., A new finite element formulation for computational fluid dynamics: VIII The Galerkin/least squares method for advective-diffusive equations. Comp. Methods Appl. Mech. Eng., 1989. 73: p. 173-89.

[176] Steele, B.N., Wan, J., Ku, J.P., Hughes, T.J.R., and Taylor, C.A., In vivo validation of a one-dimensional finite-element method for predicting blood flow in cardiovascular bypass grafts. IEEE Transactions on Biomedical Engineering, 2003. 50(6): p. 649-656.

[177] Donea, J. and Giulian, S., An Arbitrary Lagrangian-Eulerian finite element method for transient fluid-structure interactions. Computer Methods in Applied Mechanics and Engineering, 1982. 33: p. 689-723.

[178] Fedkiw, R., Coupling an Eulerian fluid calculation to a Lagrangian solid calculation with the Ghost Fluid Method. Journal of Computational Physics, 2002. 175: p. 200-224.

[179] Arienti, M., Hung, P., Morano, E., and Shepherd, J.E., A level set approach to Eulerian-Lagrangian coupling. Journal of Computational Physics, 2003. 185(1): p. 213-251.

[180] Zajac, F.E., Muscle coordination of movement: a perspective. J Biomech, 1993. 26(Suppl 1): p. 109-24.

[181] Yamaguchi, G.T. and Zajac, F.E., Restoring unassisted natural gait to paraplegics via functional neuromuscular stimulation: a computer simulation study. IEEE Trans Biomed Eng, 1990. 37(9): p. 886-902.

[182] Riley, P.O. and Kerrigan, D.C., Torque action of two-joint muscles in the swing period of stiff-legged gait: a forward dynamic model analysis. J Biomech, 1998. 31(9): p. 835-40.

[183] Piazza, S.J. and Delp, S.L., Three-Dimensional Dynamic Simulation of Total Knee Replacement Motion During a Step-Up Task. Journal of Biomechanical Engineering, 2001. 123: p. 599-606.

[184] Winter, D., Kinetics: Forces and Moments of Force, in Biomechanics and Motor Control of Human Movement. 1990, Wiley & Sons: Waterloo, Ontario, Canada.

[185] Khatib, O., A Unified Approach for Motion and Force Control of Robot Manipulators: The Operational Space Formulation. IEEE Journal of Robotics and Automation, 1987. RA-3(1): p. 43-53.

[186] Havel, T.F., Kuntz, I.D., and Crippen, G.M., The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. J Theor Biol, 1983. 104(3): p. 359-81.

[187] Havel, T.F., Crippen, G.M., Kuntz, I.D., and Blaney, J.M., The combinatorial distance geometry method for the calculation of molecular conformation. II. Sample problems and computational statistics. J Theor Biol, 1983. 104(3): p. 383-400.

[188] Bayley, M.J., Jones, G., Willett, P., and Williamson, M.P., GENFOLD: a genetic algorithm for folding protein structures using NMR restraints. Protein Sci, 1998. 7(2): p. 491-9.

[189] Wagner, G., Braun, W., Havel, T.F., Schaumann, T., Go, N., and Wuthrich, K., Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol, 1987. 196(3): p. 611-39.

[190] Arrowsmith, C., Pachter, R., Altman, R., and Jardetzky, O., The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution. Eur J Biochem, 1991. 202(1): p. 53-66.

[191] Arrowsmith, C.H., Pachter, R., Altman, R.B., Iyer, S.B., and Jardetzky, O., Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor. Biochemistry, 1990. 29(27): p. 6332-41.

[192] Schmidt, J.P., Chen, C.C., Cooper, J.L., and Altman, R.B., A surface measure for probabilistic structural computations. Proc Int Conf Intell Syst Mol Biol, 1998. 6: p. 148-56.

[193] Chen, C.C., Chen, R.O., and Altman, R.B., Constraining volume by matching the moments of a distance distribution. Comput Appl Biosci, 1996. 12(4): p. 319-26.

[194] Chen, C.C., Singh, J.P., and Altman, R.B., Using imperfect secondary structure predictions to improve molecular structure computations. Bioinformatics, 1999. 15(1): p. 53-65.

[195] Altman, R.B. and Brinkley, J.F., Probabilistic constraint satisfaction with structural models: application to organ modeling by radial contours. Proc Annu Symp Comput Appl Med Care, 1993: p. 492-6.

[196] Davy, D.T. and Audu, M.L., A dynamic optimization technique for predicting muscle forces in the swing phase of gait. J Biomech, 1987. 20(2): p. 187-201.

[197] Kaplan, M.L. and Heegaard, J.H., Predictive algorithms for neuromuscular control of human locomotion. Journal of Biomechanics, 2001. 34(8): p. 1077-1083.

[198] Neptune, R.R. and Hull, M.L., Evaluation of performance criteria for simulation of submaximal steady-state cycling using a forward dynamic model. J Biomech Eng, 1998. 120(3): p. 334-41.

[199] Raasch, C.C., Zajac, F.E., Ma, B., and Levine, W.S., Muscle coordination of maximum-speed pedalling. Journal of Biomechanics, 1997. 30: p. 595-602.

[200] Levitt, M. and Lifson, S., Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure. J Mol Biol 1969. 46(1): p. 269-279.

[201] Levitt, M., Energy Refinement of Hen Egg-White Lysozyme. J Mol Biol 1974. 82(1): p. 393-420.

[202] Levitt, M., Hydrogen Bond and Internal Solvent Dynamics of BPTI Protein. Ann N Y Acad Sci 1981. 367(1): p. 162-181.

[203] Koehl, P. and Delarue, M., Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol, 1994 Jun 3. 239(2): p. 249-75.

[204] Snow, C.D., Nguyen, H., Pande, V.S., and Gruebele, M., Absolute comparison of simulated and experimental protein-folding dynamics. Nature, 2002. 420(6911): p. 102-6.

[205] Levitt, M., Sander, C., and Stern, P.S., Protein Normal-Mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease and Lysozyme. J Mol Biol 1985. 181(1): p. 423-447.

[206] Tirion, M.M., Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. PHYSICAL REVIEW LETTERS, 1996 Aug 26. 77(9): p. 1905-1908.

[207] Delarue, M. and Sanejouand, Y.H., Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J Mol Biol, 2002 Jul 26. 320(5): p. 1011-24.

[208] Zheng, W. and Doniach, S., A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci U S A, 2003 Nov 11. 100(23): p. 13253-8.

[209] Tama, F., Gadea, F.X., Marques, O., and Sanejouand, Y.H., Building-block approach for determining low-frequency normal modes of macromolecules. Proteins, 2000 Oct 1. 41(1): p. 1-7.

[210] McCammon, J.A., Deutch, J.M., and Felderhof, B.U., Frictional Properties of Multisubunit Structures. Biopolymers 1975. 14(1): p. 2613-2623.

[211] Ermak, D.L. and McCammon, J.A., Brownian Dynamics with Hydrodynamic Interactions. J Chem Phys 1978. 69(1): p. 1352-1360.

[212] Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A., Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A, 2001 Aug 28. 98(18): p. 10037-41.

[213] Zhang, Q., Beard, D.A., and Schlick, T., Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm. J Comput Chem, 2003 Dec. 24(16): p. 2063-74.

[214] Das, R., Kwok, L.W., Millett, I.S., Bai, Y., Mills, T.T., Jacob, J., Maskel, G.S., Seifert, S., Mochrie, S.G., Thiyagarajan, P., Doniach, S., Pollack, L., and Herschlag, D., The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J Mol Biol, 2003. 332(2): p. 311-9.

[215] Russell, R., Millett, I.S., Tate, M.W., Kwok, L.W., Nakatani, B., Gruner, S.M., Mochrie, S.G., Pande, V., Doniach, S., Herschlag, D., and Pollack, L., Rapid compaction during RNA folding. Proc Natl Acad Sci U S A, 2002. 99(7): p. 4266-71.

[216] Grant, J.A., Pickup, B.T., and Nicholls, A., A smooth permittivity function for Poisson-Boltzmann Solvation Methods. Journal of Computational Chemistry, 2000. 22(6): p. 608-640.

[217] Qiu, D., Shenkin, P.S., Hollinger, F.P., and Still, W.C., The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. Journal Of Physical Chemistry A, 1997. 101: p. 3005-3014.

[218] Zagrovic, B., Snow, C., Shirts, M., and Pande, V.S., Folding the villin headpiece in atomistic detail. Journal of Molecular Biology, 2002. 323.

[219] Snow, C., Zagrovic, B., and Pande, V.S., Folding simulations of the Trp Cage. Journal American Chemical Society, 2002.

[220] Snow, C., Nguyen, H., Pande, V.S., and Gruebele., M., Folding of a bba protein: simulation and theory. Nature, 2002. 420: p. 102-106.

[221] Pande, V.S., Baker, I., Chapman, J., Elmer, S., Kaliq, S., Larson, S., Rhee, Y.M., Shirts, M.R., Snow, C., Sorin, E.J., and Zagrovic, B., Atomistic Protein Folding Simulations on the Submillisecond Timescale Using Worldwide Distributed Computing. Biopolymers, 2003. 68: p. 91-109.

[222] Sorin, E.J., Engelhardt, M.A., Herschlag, D., and Pande, V.S., RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop. Journal of Molecular Biology, 2002. 317: p. 493-506.

[223] Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A., Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A, 2001. 98(18): p. 10037-41.

[224] Bryngelson, J., Onuchic, J., Socci, N., and Wolynes, P., Funnels, Pathway, and the energy landscape of protein folding. Struct. Funct. Genet., 1995. 21: p. 167-195.

[225] Chandler, D., Statistical mechanics of isomerization dynamics in liquids and the transition state approximation. J. Chem. Phys., 1978. 68: p. 2959-2970.

[226] Pande, V. and Rokhsar, D., Molecular dynamics simulations of unfolding and refolding of a ß-hairpin fragment of protein G. Proc. Natl. Acad. Sci., 1999. 96(16): p. 9062-9067.

[227] Dellago, C., Bolhuis, P., Csajka, F.S., and Chandler, D., Transition path sampling and the calculations of rate constants. J. Chem. Phys., 1998. 17(5): p. 1964-1977.

[228] Pande, V. and Rokhsar, D., Folding Pathway of a lattice model for proteins. Proc. Natl. Acad. Sci., 1999. 96: p. 1273-1278.

[229] Pande, V., Grosberg, A., Tanaka, T.a., and Rokhsar, D., Pathways for protein folding: Is a new view needed? Current Opinion in Structual Biology, 1999. 8: p. 68-79.

[230] Snow, C. and Ngyen, H., Folding of a bba protien: simulation and theory. Nature, 2002. 420: p. 102-106.

[231] Bolhuis, P.G., Transition-path sampling of B-hairpin folding. Proc. Natl. Acad. Sci., 2003. 100(21): p. 12129-12134.

[232] Chandler, D., Introduction to Modern Statistical Mechanics. 1987, New York: Oxford University Press.

[233] van Erp, T., Moroni, D.a., and PG, B., A novel path sampling method for the calculation of rate constants. J. Chem. Phys., 2003. 118(17): p. 7762-7774.

[234] Apaydin, M., Brutlag, D., Guestrin, C., Hsu, D., and Latombe, J., Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion. Proc. RECOMB'02, 2002: p. 12-21.

[235] Song, G., Thomas, S., Dill, K., Scholtz, J., and Amato, N., A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L. Proc. of the Pacific Symposium on Biocomputing, 2003.

[236] Raman, R., Raman, B., Hundt, W., Chow, L., Napel, S., and Rubin, G.D. Improved Speed of Bone Removal in CT Angiography (CTA) using Automated Targeted Morphological Separation: Method and Evaluation in CTA of the Lower Extremity Occlusive Disease (LEOD). in 88th RSNA. 2002. Chicago.

[237] Raman, R., Napel, S., Beaulieu, C.F., Bain, E.S., Jeffrey, R.B., Jr., and Rubin, G.D., Automated generation of curved planar reformations from volume data: method and evaluation. Radiology, 2002. 223(1): p. 275-80.

[238] Raman, R., Napel, S., and Rubin, G.D., Curved-slab maximum intensity projection: method and evaluation. Radiology, 2003. 229(1): p. 255-60.

[239] Paik, D.S., Beaulieu, C.F., Jeffrey, R.B., Rubin, G.D., and Napel, S., Automated flight path planning for virtual endoscopy. Med Phys, 1998. 25(5): p. 629-37.

[240] Beaulieu, C.F., Jeffrey, R.B., Jr., Karadi, C., Paik, D.S., and Napel, S., Display modes for CT colonography. Part II. Blinded comparison of axial CT and virtual endoscopic and panoramic endoscopic volume-rendered studies. Radiology, 1999. 212(1): p. 203-12.

[241] Paik, D.S., Beaulieu, C.F., Jeffrey, R.B., Jr., Karadi, C.A., and Napel, S., Visualization modes for CT colonography using cylindrical and planar map projections. J Comput Assist Tomogr, 2000. 24(2): p. 179-88.

[242] Teran, J., Irving, G., Hauser, K., and Fedkiw, R. Robust Simulation of Large Muscle Groups with Connective Tissue. in submitted to SIGGRAPH. 2004.

[243] Lorensen, W.E. and Cline, H.E., Marching cubes: a high resolution 3D surface construction system. Computer Graphics, 1987. 21(3): p. 163-169.

[244] Bekkers, E.a.T., C. A. Image Based Analytic Surface Representation and Mesh Generation. in 7th National Congress on Computational Mechanics. 2003.

[245] Pelc, N.J., Herfkens, R.J., Shimakawa, A., and Enzmann, D.R., Phase Contrast Cine Magnetic Resonance Imaging. Magnetic Resonance Quarterly, 1991. 7(4): p. 229-254.

[246] Pelc, N.J., Sommer, F.G., Li, K.C.P., Brosnan, T.J., Herfkens, R.J., and Enzmann, D.R., Quantitative Magnetic Resonance Flow Imaging. Magnetic Resonance Quarterly, 1994. 10(3): p. 125-147.

[247] Markl, M., Chan, F.P., Alley, M.T., Wedding, K.L., Draney, M.T., Elkins, C.J., Parker, D.W., Wicker, R., Taylor, C.A., Herfkens, R.J., and Pelc, N.J., Time Resolved Three Dimensional Phase Contrast MRI (4D-Flow). Journal of Magnetic Resonance Imaging, 2002. 17(4): p. 499-506.

[248] Spicer, S.A. and Taylor, C.A., Simulation-Based Medical Planning for Cardiovascular Disease: Visualization System Foundations. Computer Aided Surgery, 2000. 5: p. 82-89.

[249] Spicer, S.A., Taylor, C.A., Wang, K.C., and Dutton, R.W., Time-dependent volume rendering of unsteady advection-diffusion in computational hemodynamics Improving geometric model construction for blood flow modeling. American Society of Mechanical Engineers, Bioengineering Division, 1999. 42(6): p. 509-510.

[250] Cheng, C.P., Parker, D., and Taylor, C.A., Quantification of Wall Shear Stress in Large Blood Vessels Using Lagrangian Interpolation Functions with Cine Phase-Contrast Magnetic Resonance Imaging. Annals of Biomedical Engineering, 2002. 30: p. 1020-1032.

[251] Draney, M.T., Herfkens, R.J., Hughes, T.J.R., Pelc, N.J., Wedding, K.L., Zarins, C.K., and Taylor, C.A., Quantification of vessel wall cyclic strain using cine phase contrast magnetic resonance imaging. Annals of Biomedical Engineering, 2002. 30(8): p. 1033-1045.

[252] Altman, R.B., Hughes, C., and Gerstein, M.B., Methods for displaying macromolecular structural uncertainty: application to the globins. J Mol Graph, 1995. 13(3): p. 142-52, 109-2.

[253] Wilson, N.M., Geometric algorithms and software architecture for computational prototyping: Applications in vascular surgery and MEMS, in Mechanical Engineering. 2003, Stanford University: Stanford, CA. p. 254.

[254] Wilson, N.M., Wang, K.C., Dutton, R.W., and Taylor, C.A., A Software Framework for Creating Patient Specific Geometric Models from Medical Imaging Data for Simulation Based Medical Planning of Vascular Surgery. Lecture Notes in Computer Science, 2001. 2208: p. 449-456.

[255] Taylor, C., Hughes, T., and Zarins, C., Finite Element Modeling of Blood Flow in Arteries. Comp Meth Appl Mech Eng, 1998. 158: p. 155-196.

[256] Schmidt, R., Gerstein, M., and Altman, R.B., LPFC: an Internet library of protein family core structures. Protein Sci, 1997. 6(1): p. 246-8.

[257] Taylor, C.A., Cheng, C.P., Espinosa, L.A., Tang, B.T., Parker, D., and Herfkens, R.J., In vivo quantification of blood flow and wall shear stress in the human abdominal aorta during lower limb exercise. Annals of Biomedical Engineering, 2002. 30(3): p. 402-408.

[258] Ku, J.P., Draney, M.T., Arko, F.R., Lee, W.A., Chan, F.P., Pelc, N.J., Zarins, C.K., and Taylor, C.A., In vivo validation of numerical prediction of blood flow in arterial bypass grafts. Ann Biomed Eng, 2002. 30(6): p. 743-52.

[259] Nishikawa, R.M., Giger, M.L., Doi, K., Vyborny, C.J., and Schmidt, R.A., Computer-aided detection of clustered microcalcifications on digital mammograms. Med Biol Eng Comput, 1995. 33(2): p. 174-8.

[260] Doi, K., Giger, M.L., Nishikawa, R.M., and Schmidt, R.A., Computer-Aided Diagnosis of Breast Cancer on Mammograms. Breast Cancer, 1997. 4(4): p. 228-233.

[261] Summers, R.M., Beaulieu, C.F., Pusanik, L.M., Malley, J.D., Jeffrey Jr., R.B., Glazer, D.I., and Napel, S., Automated polyp detector for CT colonography: feasibility study. Radiology, 2000. 216(1): p. 284-90.

[262] Summers, R.M., Jerebko, A.K., Franaszek, M., Malley, J.D., and Johnson, C.D., Colonic polyps: complementary role of computer-aided detection in CT colonography. Radiology, 2002. 225(2): p. 391-9.

[263] Jerebko, A.K., Summers, R.M., Malley, J.D., Franaszek, M., and Johnson, C.D., Computer-assisted detection of colonic polyps with CT colonography using neural networks and binary classification trees. Med Phys, 2003. 30(1): p. 52-60.

[264] Jerebko, A.K., Malley, J.D., Franaszek, M., and Summers, R.M., Multiple neural network classification scheme for detection of colonic polyps in CT colonography data sets. Acad Radiol, 2003. 10(2): p. 154-60.

[265] Yoshida, H., Nappi, J., MacEneaney, P., Rubin, D.T., and Dachman, A.H., Computer-aided diagnosis scheme for detection of polyps at CT colonography. Radiographics, 2002. 22(4): p. 963-79.

[266] Yoshida, H., Masutani, Y., MacEneaney, P., Rubin, D.T., and Dachman, A.H., Computerized Detection of Colonic Polyps at CT Colonography on the Basis of Volumetric Features: Pilot Study. Radiology, 2002. 222(2): p. 327-36.

[267] Yoshida, H. and Nappi, J., Three-dimensional computer-aided diagnosis scheme for detection of colonic polyps. IEEE Trans Med Imaging, 2001. 20(12): p. 1261-74.

[268] Paik, D.S., Beaulieu, C.F., Jeffrey Jr., R.B., Yee, J., Steinauer-Gebauer, A., and Napel, S., Computer aided detection of polyps in CT colonography: method and free-response ROC evaluation of performance. Radiology, 2000. 217 (P): p. 370.

[269] Paik, D.S., Beaulieu, C.F., Mani, A., Prokesch, R., Yee, J., and Napel, S., Evaluation of computer-aided detection in CT colonography: potential applicability to a screening population. Radiology, 2001. 221(P): p. 332.

[270] Paik, D.S., Beaulieu, C.F., Rubin, G.D., Acar, B., Jeffrey Jr., R.B., and Napel, S., Optimization and evaluation of a computer aided detection (CAD) algorithm for both colonic polyps and lung nodules in CT. Radiology, 2002. 225(P): p. 256.

[271] Paik, D.S., Beaulieu, C.F., Rubin, G.D., Acar, B., Jeffrey Jr., R.B., Yee, J., Dey, J., and Napel, S., Surface normal overlap: a computer-aided detection algorithm with application to colonic polyps and lung nodules in helical CT. IEEE Trans Med Imaging, 2003: p. accepted pending revision 12/03.

[272] Paik, D.S., Napel, S., Rubin, G.D., and Beaulieu, C.F., Method For Characterizing Shapes In Medical Images. 2002: US.

[273] Paik, D.S., Rubin, G.D., Beaulieu, C.F., Napel, S., and Jeffrey Jr., R.B., Method For Detecting Shapes In Medical Images. 2002: US.

[274] Acar, B., Beaulieu, C.F., Paik, D.S., Yee, J., Tomasi, C., and Napel, S., Computer-aided detection of polyps in CT colonography using optical flow fields. Radiology, 2001. 221(P): p. 331.

[275] Acar, B., Beaulieu, C.F., Paik, D.S., Gokturk, S.B., Tomasi, C., Yee, J., and Napel, S. Assessment of an optical flow field-based polyp detector for CT colonography. in IEEE Engineering in Medicine and Biology Society, 23rd International Conference. 2001. Istanbul, Turkey.

[276] Acar, B., Napel, S., Paik, D.S., Gokturk, S.B., Tomasi, C., and Beaulieu, C.F. Using optical flow fields for polyp detection in virtual colonoscopy. in MICCAI (Medical Image Computing and Computer-aided Intervention). 2001. Utrecht, The Netherlands.

[277] Acar, B., Beaulieu, C.F., Gokturk, S.B., Tomasi, C., Paik, D.S., Jeffrey Jr., R.B., Yee, J., and Napel, S., Edge displacement field-based classification for improved detection of polyps in CT colonography. IEEE Trans Med Imaging, 2002. 21(12): p. 1461-7.

[278] Acar, B., Beaulieu, C.F., Paik, D.S., Yee, J., Jeffrey Jr., R.B., and Napel, S., 3D differential descriptors for improved computer-aided detection (CAD) of colonic polyps in computed tomography colonography (CTC). Radiology, 2002. 225(P): p. 405.

[279] Acar, B., Beaulieu, C.F., Sundaram, P., Paik, D., and Napel, S., Heat diffusion based detection of colonic polyps in CT colonography. IEEE Trans Med Imaging, 2003: p. submitted 10/03.

[280] Acar, B., Beaulieu, C.F., Napel, S., Jeffrey Jr., R.B., and Paik, D.S., Method for Comparing Medical Imaging Data. 2003: US.

[281] Acar, B., Beaulieu, C.F., Napel, S., Jeffrey Jr., R.B., Paik, D.S., Gokturk, S.B., and Tomasi, C., Method for Detecting and Identifying Shapes in Medical Images. 2003: US.

[282] Gokturk, S.B., Tomasi, C., Paik, D.S., Yee, J., Beaulieu, C.F., and Napel, S., Statistical approach for computer-aided detection (CAD) of colonic polyps. Radiology, 2001. 221(P): p. 331.

[283] Gokturk, S.B., Tomasi, C., Acar, B., Paik, D.S., Beaulieu, C.F., and Napel, S. A new 3-D volume processing method for polyp detection. in IEEE Engineering in Medicine and Biology Society, 23rd International Conference. 2001. Istanbul, Turkey.

[284] Gokturk, S.B., Tomasi, C., Acar, B., Beaulieu, C.F., and Napel, S. A learning method for automated polyp detection. in MICCAI (Medical Image Computing and Computer-aided Intervention). 2001. Utrecht, The Netherlands.

[285] Gokturk, S.B., Tomasi, C., Acar, B., Beaulieu, C.F., Paik, D.S., Jeffrey Jr., R.B., Yee, J., and Napel, S., A statistical 3-D pattern processing method for computer-aided detection of polyps in CT colonography. IEEE Trans Med Imaging, 2001. 20(12): p. 1251-60.

[286] Gokturk, S.B., Tomasi, C., Acar, B., Beaulieu, C.F., Napel, S., and Paik, D.S., Shape Recognition Method to Differentiate Normal and Abnormal Anatomical Shapes. 2003: US.

[287] Armato, S.G., 3rd, Giger, M.L., Moran, C.J., Blackburn, J.T., Doi, K., and MacMahon, H., Computerized detection of pulmonary nodules on CT scans. Radiographics, 1999. 19(5): p. 1303-11.

[288] Armato, S.G., 3rd, Giger, M.L., and MacMahon, H., Automated detection of lung nodules in CT scans: preliminary results. Med Phys, 2001. 28(8): p. 1552-61.

[289] Armato, S.G., 3rd, Li, F., Giger, M.L., MacMahon, H., Sone, S., and Doi, K., Lung cancer: performance of automated lung nodule detection applied to cancers missed in a CT screening program. Radiology, 2002. 225(3): p. 685-92.

[290] Brown, M.S., McNitt-Gray, M.F., Goldin, J.G., Suh, R.D., Sayre, J.W., and Aberle, D.R., Patient-specific models for lung nodule detection and surveillance in CT images. IEEE Trans Med Imaging, 2001. 20(12): p. 1242-50.

[291] Brown, M.S., Goldin, J.G., Suh, R.D., McNitt-Gray, M.F., Sayre, J.W., and Aberle, D.R., Lung micronodules: automated method for detection at thin-section CT--initial experience. Radiology, 2003. 226(1): p. 256-62.

[292] Giger, M.L., Bae, K.T., and MacMahon, H., Computerized detection of pulmonary nodules in computed tomography images. Invest Radiol, 1994. 29(4): p. 459-65.

[293] Gurcan, M.N., Sahiner, B., Petrick, N., Chan, H.P., Kazerooni, E.A., Cascade, P.N., and Hadjiiski, L., Lung nodule detection on thoracic computed tomography images: preliminary evaluation of a computer-aided diagnosis system. Med Phys, 2002. 29(11): p. 2552-8.

[294] Kanazawa, K., Kawata, Y., Niki, N., Satoh, H., Ohmatsu, H., Kakinuma, R., Kaneko, M., Moriyama, N., and Eguchi, K., Computer-aided diagnosis for pulmonary nodules based on helical CT images. Comput Med Imaging Graph, 1998. 22(2): p. 157-67.

[295] Ko, J.P. and Betke, M., Chest CT: automated nodule detection and assessment of change over time--preliminary experience. Radiology, 2001. 218(1): p. 267-73.

[296] Lee, Y., Hara, T., Fujita, H., Itoh, S., and Ishigaki, T., Automated detection of pulmonary nodules in helical CT images based on an improved template-matching technique. IEEE Trans Med Imaging, 2001. 20(7): p. 595-604.

[297] Wormanns, D., Fiebich, M., Saidi, M., Diederich, S., and Heindel, W., Automatic detection of pulmonary nodules at spiral CT: clinical application of a computer-aided diagnosis system. Eur Radiol, 2002. 12(5): p. 1052-7.

[298] Rubin, G.D., Lyo, J., Paik, D.S., Sherbondy, A., Chow, L., Leung, A.N., Mindelzun, R., Zinck, S.E., Naidich, D.P., and Napel, S., Pulmonary Nodules in MDCT Scans: Impact of Computer-aided Detection. Radiology, submitted, November 2003.

[299] Coulam, C.H., Paik, D.S., Napel, S., and Rubin, G.D. Evaluation of a Gold Standard for Computer Aided Detection of Lung Nodules. in Radiological Society of North America 87th Scientific Sessions. 2001. Chicago.

[300] Paik, D.S., Napel, S., Coulam, C.H., Naidich, D., and Rubin, G.D. Computer Aided Detection of Lung Nodules in CT: Preliminary Results. in Radiological Society of North America 87th Scientific Sessions. 2001. Chicago.

[301] Lyo, J., Paik, D.S., Zinck, F., Naidich, D., Napel, S., and Rubin, G.D. Computer-aided Detection (CAD) of Lung Nodules: Application to a Population Suspicious for Nodules on Chest X-Ray (CXR). in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[302] Lyo, J., Paik, D.S., Chow, L., Leung, A.N., Napel, S., and Rubin, G.D. Detection (CAD)–Reader Pairing for the Detection of Lung Nodules. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[303] Rubin, G.D., Naidich, D., Sherbondy, A., Lyo, J., and Napel, S. Inadequacy of lung nodule reference standard based upon standard methods of expert consensus review using cine-paging of transverse thin-section MDCT lung scans. in Radiological Society of North America 89th Scientific Sessions. 2003. Chicago.

[304] Rubin, G.D., Lyo, J., Sherbondy, A., Naidich, D., and Napel, S. Impact of Computer-Assisted Detection (CAD) Algorithm versus a Second Radiologist on Reader Sensitivity for Detecting Pulmonary Nodules in MDCT Scans. in Radiological Society of North America 89th Scientific Sessions. 2003. Chicago.

[305] Wei, L. and Altman, R.B., Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac Symp Biocomput, 1998: p. 497-508.

[306] Wei, L., Huang, E.S., and Altman, R.B., Are predicted structures good enough to preserve functional sites? Structure Fold Des, 1999. 7(6): p. 643-50.

[307] Waugh, A., Williams, G.A., Wei, L., and Altman, R.B., Using meta computing tools to facilitate large-scale analyses of biological databases. Pac Symp Biocomput, 2001: p. 360-71.

[308] Bagley, S.C. and Altman, R.B., Characterizing the microenvironment surrounding protein sites. Protein Sci, 1995. 4(4): p. 622-35.

[309] Bagley, S.C., Wei, L., Cheng, C., and Altman, R.B., Characterizing oriented protein structural sites using biochemical properties. Proc Int Conf Intell Syst Mol Biol, 1995. 3: p. 12-20.

[310] Tillich, M., Hill, B.B., Paik, D.S., Petz, K., Napel, S., Zarins, C.K., and Rubin, G.D., Prediction of aortoiliac stent-graft length: comparison of measurement methods. Radiology, 2001. 220(2): p. 475-83.

[311] Rubin, G.D., Paik, D.S., Johnston, P.C., and Napel, S., Measurement of the aorta and its branches with helical CT. Radiology, 1998. 206(3): p. 823-9.

[312] Raman, R., Napel, S., Paik, D.S., and Rubin, G.D. Quantification of Aortoiliac Irregularity in Patients with Abdominal Aortic Aneurysms: Method and Evaluation. in Radiological Society of North America 87th Scientific Sessions. 2001. Chicago.

[313] Raman, B., Raman, R., Baek, D.N., Rubin, G.D., and Napel, S. Automated Measurement of Aortoaortic and Aortoiliac Angulation for CT Angiography (CTA) of Abdominal Aortic Aneurysms (AAAs) Prior to Endograft Repair. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[314] Raman, R., Raman, B., Sofilos, M., Zhuge, F., Rubin, G.D., and Napel, S. Automated Quantification of Arterial Calcification using CT Angiography (CTA): Method and Evaluation. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[315] Raman, R., Raman, B., Sofilos, M., Zhuge, F., Rubin, G.D., and Napel, S. Automated Measurement of Diameters and Volumes of Abdominal Aortic Aneurysm (AAA) using Multiscale 3D Texture Analysis. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[316] Raman, B., Raman, R., Liu, C., Frisoli, J., Napel, S., and Rubin, G.D. Automatic Identification of Major Arteries and their Ostea for Postprocessing of CT Angiographic (CTA) Studies of the Chest, Abdomen and Pelvis. in Radiological Society of North America 88th Scientific Sessions. 2002. Chicago.

[317] Raman, R., Napel, S., and Rubin, G.D., Quantification of Aortoiliac Endoluminal Irregularity. 2003: US.

[318] Raman, R., Raman, B., Rubin, G.D., and Napel, S., Method of Measuring, Identifying and Reporting Vessels and Vessel Parameters in Medical Images. 2003: US.

[319] Raman, R., Raman, B., Napel, S., and Rubin, G.D., Quantification Method of Arterial Calcification. 2003: US.

[320] Raman, B., Raman, R., Carnethon, M., Fortmann, S.P., Napel, S., and Rubin, G.D. Calcium Quantification In The Aortoiliac Arteries: Interscan Variability of Agatson Scoring vs. Automated Mass Quantification In Noncontrast and Contrast Enhanced Scans. in Radiological Society of North America 89th Scientific Sessions. 2003. Chicago.

[321] Raman, B., Raman, R., Liu, C., Frisoli, J., Napel, S., and Rubin, G.D. Automatic Identification of Major Arteries and their Ostea for Postprocessing of CT Angiographic (CTA) Studies of the Chest, Abdomen and Pelvis. in Radiological Society of North America 89th Scientific Sessions. 2003. Chicago.

[322] Napel, S., Xu, H., Paik, D.S., Ross, B.A., Sumanaweera, T.S., Hossack, J.A., and Jeffrey, R.B., Jr., Carotid disease: automated analysis with cardiac-gated three-dimensional US technique and preliminary results. Radiology, 2002. 222(2): p. 560-3.

[323] Brenowitz, M., Chance, M.R., Dhavan, G., and Takamoto, K., Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting". Curr Opin Struct Biol, 2002. 12(5): p. 648-53.

[324] Takamoto, K., He, Q., Morris, S., Chance, M.R., and Brenowitz, M., Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat Struct Biol, 2002. 9(12): p. 928-33.

[325] Uchida, T., Takamoto, K., He, Q., Chance, M.R., and Brenowitz, M., Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme. J Mol Biol, 2003. 328(2): p. 463-78.

[326] Doherty, E.A. and Doudna, J.A., Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct, 2001. 30: p. 457-75.

[327] Ferre-D'Amare, A.R. and Doudna, J.A., RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct, 1999. 28: p. 57-73.

[328] Gan, Z., Gor'kov, P., Cross, T.A., Samoson, A., and Massiot, D., Seeking higher resolution and sensitivity for NMR of quadrupolar nuclei at ultrahigh magnetic fields. J Am Chem Soc, 2002. 124(20): p. 5634-5.

[329] Glusker, J.P., X-ray crystallography of proteins. Methods Biochem Anal, 1994. 37: p. 1-72.

[330] Holbrook, S.R. and Kim, S.H., RNA crystallography. Biopolymers, 1997. 44(1): p. 3-21.

[331] Gronenborn, A.M. and Clore, G.M., Protein structure determination in solution using nuclear magnetic resonance spectroscopy. NIDA Res Monogr, 1991. 112: p. 78-105.

[332] Gorler, A., Ulyanov, N.B., and James, T.L., Determination of the populations and structures of multiple conformers in an ensemble from NMR data: multiple-copy refinement of nucleic acid structures using floating weights. J Biomol NMR, 2000. 16(2): p. 147-64.

[333] Prompers, J.J. and Bruschweiler, R., Dynamic and structural analysis of isotropically distributed molecular ensembles. Proteins, 2002. 46(2): p. 177-89.

[334] Doniach, S., Changes in biomolecular conformation seen by small angle X-ray scattering. Chem Rev, 2001. 101(6): p. 1763-78.

[335] Sorin, E.J., Engelhardt, M.A., Herschlag, D., and Pande, V.S., RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J Mol Biol, 2002. 317(4): p. 493-506.

[336] Chu, S., Biology and polymer physics at the single-molecule level. Philos Transact Ser A Math Phys Eng Sci, 2003. 361(1805): p. 689-98.

[337] Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D., and Chu, S., A single-molecule study of RNA catalysis and folding. Science, 2000. 288(5473): p. 2048-51.

[338] Fennen, J., Torda, A.E., and van Gunsteren, W.F., Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble. J Biomol NMR, 1995. 6(2): p. 163-70.

[339] Du, R., Pande, V., Grosberg, A.Y., Tanaka, T., and Shakhnovich, E., On the transition coordinate for protein folding. J. Chem. Phys., 1998. 108(1): p. 334-350.

[340] Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., and Shakhnovich, E.I., Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J., 2002. 83: p. 3525-3532.

[341] de Jong, D., Alonso, D.O.V., Riley, R., and Daggett, V., Probing the Energy Landscape of Protein Folding/Unfolding Transition States. J. Mol. Biol., 2002. 319: p. 229-242.

[342] Gsponer, J. and Caflisch, A., Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci., 2002. 99(10): p. 6719-6724.

[343] Golub, G. and C, v.L., Matrix Computations. 3 ed. 1996, London: The Johns Hopkins University Press.

[344] Friden, J. and Lieber, R.L., Spastic muscle cells are shorter and stiffer than normal cells. Muscle Nerve, 2003. 27(2): p. 157-64.

[345] Lieber, R.L., Runesson, E., Einarsson, F., and Friden, J., Inferior mechanical properties of spastic muscle bundles due to hypertrophic but compromised extracellular matrix material. Muscle Nerve, 2003. 28(4): p. 464-71.

[346] Lieber, R.L. and Friden, J., Mechanisms of muscle injury gleaned from animal models. Am J Phys Med Rehabil, 2002. 81(11 Suppl): p. S70-9.

[347] Freitag, L. and Ollivier-Gooch, C., Tetrahedral mesh improvement using swapping and smoothing. International Journal for Numerical Methods in Engineering, 1997. 40: p. 3979-4002.

[348] Joe, B., Construction of three-dimensional improved-quality triangulations using local transformations. SIAM Journal of Scientific Computing, 1995. 16(6): p. 1292-1307.

[349] de Cougny, H.L. and Shephard, M.S., Parallel refinement and coarsening of tetrahedral meshes. International Journal for Numerical Methods in Engineering, 1999. 46: p. 1101-1125.

[350] Staadt, O.G. and Gross, M.H., Progressive tetrahedralizations. Visualization, 1998: p. 397-402.

[351] Trotts, I.J., Hamann, B., and Joy, K.I., Simplification of tetrahedral meshes with error bounds. Visualization, 1999. 5(3): p. 224-237.

[352] Cignoni, P., Costanza, C., Montani, C., Rocchin, C., and Scopigno, R., Simplification of tetrahedral meshes with accurate error evaluation. Visualization, 2000.

[353] Hoppe, H., Progressive meshes. Computer Graphics (SIGGRAPH Proc.), 1996. 30: p. 98-108.

[354] Cutler, B., Dorsey, J., McMillan, L., M¨Uller, M., and Jagnow, R., A procedural approach to authoring solid models. ACM Trans. Gr. (SIGGRAPH Proc.), 2002. 21: p. 302-311.

[355] Levitt, M., A Simplified Representation of Protein Conformations for Rapid Simulation of Protein Folding. J Mol Biol 1976. 104(1): p. 59-107.

[356] Anderson, W.F., Fletterick, R.J., and Steitz, T.A., Structure of yeast hexokinase. 3. Low resolution structure of a second crystal form showing a different quaternary structure, heterologous interaction of subunits and substrate binding. J Mol Biol, 1974 Jun 25. 86(2): p. 261-9.

[357] Levitt, M., Conformation Analysis of Proteins. Ph. D. Thesis, Cambridge University, 1972.

[358] Schwab, C., P- and hp-finite element methods: Theory and applications in solid and fluid mechanics. 1998, Oxford: Oxford University Press.

[359] Hawkins, G., Cramer, CJ and Truhlar, DG., Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem., 1995. 100: p. 19824-19839.

[360] Chiang, D.Y., Brown, P.O., and Eisen, M.B., Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics, 2001. 17: p. S49-55.

[361] Hamelryck, T. and Manderick, B., PDB file parser and structure class implemented in Python. Bioinformatics, 2003. 19(17): p. 2308-10.

[362] Mangalam, H., The Bio* toolkits--a brief overview. Brief Bioinform, 2002. 3(3): p. 296-302.

[363] Dellago, C., Bolhuis, P., and D., C., Efficient Transition Path Sampling: Application to Lennard-Jones Cluster Rearrangments. J. Chem. Phys., 1998. 108(22): p. 9236-9245.

[364] Metropolis, N., Rosenbluth, A., Rosenbluth, N., Teller, M., and Teller, E., Equation of State Calculations by Fast Computing Machines. J. Chem. Phys., 1953. 21: p. 1087-1092.

[365] Allen, M. and Tildesley, D., Computer Simulation of Liquids. 1987, Oxford: Clarendon Press.

[366] Delp, S.L., Loan, J.P., Hoy, M.G., Zajac, F.E., Topp, E.L., and Rosen, J.M., An interactive graphics-based model of the lower extremity to study orthopaedic surgical procedures. IEEE Transactions on Biomedical Engineering, 1990. 37(8): p. 757-767.

[367] Lewis, F., Abdallah, C., and Dawson, D., Control of Robot Manipulators. 1993, New York, NY: Macmillan Publishing Company.

[368] Thelen, D.G., Anderson, F.C., and Delp, S.L., Generating dynamic simulations of movement using computed muscle control. J Biomech, 2003. 36(3): p. 321-8.

[369] Hupp, S.a., The "Worm" Programs -- Early Experience with Distributed Computation. Communications of the ACM, 1982. 25(3).

[370] Sullivan, W., Werthimer, S., Bowyer, S., Cobb, J., Gedye, D., and Anderson, D., {A new major SETI project based on Project Serendip data and 100,000 personal computers}, in Astronomical and Biochemical Origins and the Search for Life in the Universe, Proc. of the Fifth Intl. Conf. on Bioastronomy. 1997. p. 1997.

[371] Entropia, The Great Internet Mersene Prime Search (GIMPS). 1997: http://www.mersenne.org/.

[372] Shirts, M.R. and Pande, V.S., Screen Savers of the World, Unite! Science, 2000. 290: p. 1903-1904.

[373] Entropia, Fight Aids At Home. 2000: http://www.fightaidsathome.org/.

[374] Parabon, Compute Against Cancer. 2000: http://www.computeagainstcancer.org/.

[375] Oram, A., Peer-To-Peer: Harnessing the Power of Disruptive Technologies. 2001, Sebastopol, CA, USA: O'Reilly.

[376] Foster, I. and Kesselman, C., The Grid: Blueprint for a New Computing Infrastructure. 2 ed. 2004, San Francisco: Elsevier/Morgan Kaufmann.

[377] Steele, B.N., Ku, J.P., Draney, M.T., and Taylor, C.A., Internet-Based System for Simulation-Based Medical Planning. IEEE Transactions on Information Technology in Biomedicine, 2003. 7(2): p. 123-129.

[378] Nilsen, T.W., The spliceosome: the most complex macromolecular machine in the cell? Bioessays, 2003. 25(12): p. 1147-9.

[379] DeRose, V.J., Two decades of RNA catalysis. Chem Biol, 2002. 9(9): p. 961-9.

[380] Grubmuller, H., Predicting slow structural transitions in macromolecular systems: Conformational flooding. Physical Review. E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 1995. 52(3): p. 2893-2906.

[381] Rymer, W.Z. and Katz, R.T., Mechanisms of spastic hypertonia. Physical Medicine and Rehabilitation, 1994. 8: p. 441-454.

[382] Arnold, A.S., Salinas, S., Asakawa, D.J., and Delp, S.L., Accuracy of muscle moment arms estimated from MRI-based musculoskeletal models of the lower extremity. Comput Aided Surg, 2000. 5(2): p. 108-19.

[383] Taylor, C.A., Hughes, T.J.R., and Zarins, C.K., Finite Element Modeling of Blood Flow in Arteries. Computer Methods in Applied Mechanics and Engineering, 1998. 158: p. 155-196.

[384] Taylor, C.A., Hughes, T.J.R., and Zarins, C.K., Computational Investigations in Vascular Disease. Computers in Physics, 1996. 10(3): p. 224-232.

[385] Taylor, C.A., Draney, M.T., Ku, J.P., Parker, D., Steele, B.N., Wang, K., and Zarins, C.K., Predictive Medicine: Computational Techniques in Therapeutic Decision-Making. Computer Aided Surgery, 1999. 4(5): p. 231-247.

[386] Batey, R.T. and Doudna, J.A., The parallel universe of RNA folding. Nat. Struct. Biol., 1998. 5(5): p. 337-40.

[387] Misra, V.K. and Draper, D.E., On the role of magnesium ions in RNA stability. Biopolymers, 1998. 48(2-3): p. 113-35.

[388] Silverman, S.K., Deras, M.L., Woodson, S.A., Scaringe, S.A., and Cech, T.R., Multiple folding pathways for the P4-P6 RNA domain. Biochemistry, 2000. 39(40): p. 12465-75.

[389] Ralston, C.Y., He, Q., Brenowitz, M., and Chance, M.R., Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation. Nat. Struct. Biol., 2000. 7(5): p. 371-4.

[390] Tullius, T.D. and Dombroski, B.A., Hydroxyl radical footprinting: high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc. Natl. Acad. Sci. U.S.A., 1986. 83(15): p. 5469-73.

[391] Svergun, D.I. and Koch, M.H., Advances in structure analysis using small-angle scattering in solution. Curr Opin Struct Biol, 2002. 12(5): p. 654-60.

[392] dos Remedios, C.G. and Moens, P.D., Fluorescence resonance energy transfer spectroscopy is a reliable "ruler" for measuring structural changes in proteins. Dispelling the problem of the unknown orientation factor. J Struct Biol, 1995. 115(2): p. 175-85.

[393] Collins, C.A. and Guthrie, C., The question remains: is the spliceosome a ribozyme? Nat. Struct. Biol., 2000. 7(10): p. 850-4.

[394] Deras, M.L., Brenowitz, M., Ralston, C.Y., Chance, M.R., and Woodson, S.A., Folding mechanism of the Tetrahymena ribozyme P4-P6 domain. Biochemistry, 2000. 39: p. 10975-85.

[395] Russell, R., Millett, I.S., Tate, M.W., Kwok, L.W., Nakatani, B., Gruner, S.M., Mochrie, S.G., Pande, V., Doniach, S., Herschlag, D., and Pollack, L., Rapid compaction during RNA folding. Proc. Natl. Acad. Sci. U.S.A., 2002. 99(7): p. 4266-71.

[396] Russell, R., Millett, I.S., Doniach, S., and Herschlag, D., Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol., 2000. 7(5): p. 367-370.

[397] Russell, R. and Herschlag, D., New pathways in folding of the Tetrahymena group I RNA enzyme. J. Mol. Biol., 1999. 291(5): p. 1155-67.

[398] Treiber, D.K. and Williamson, J.R., Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction. J. Mol. Biol., 2001. 305(1): p. 11-21.

[399] Dinner, A.R., Sali, A., Smith, L.J., Dobson, C.M., and Karplus, M., Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem. Sci., 2000. 25(7): p. 331-9.

[400] Wolynes, P.G., Onuchic, J.N., and Thirumalai, D., Navigating the folding routes. Science, 1995. 267(5204): p. 1619-20.

[401] Shakhnovich, E.I., Modeling protein folding: the beauty and power of simplicity. Fold Des, 1996. 1(3): p. R50-4.

[402] Pande, V.S., Grosberg, A., Tanaka, T., and Rokhsar, D.S., Pathways for protein folding: is a new view needed? Curr Opin Struct Biol, 1998. 8(1): p. 68-79.

[403] Brooks, C.L., 3rd, Gruebele, M., Onuchic, J.N., and Wolynes, P.G., Chemical physics of protein folding. Proc Natl Acad Sci U S A, 1998. 95(19): p. 11037-8.

[404] Russell, R., Zhuang, X., Babcock, H.P., Millett, I.S., Doniach, S., Chu, S., and Herschlag, D., Exploring the folding landscape of a structured RNA. Proc. Natl. Acad. Sci. U.S.A., 2002. 99: p. 155-60.

[405] Rosen, C.A., Regulation of HIV gene expression by RNA-protein interactions. Trends Genet., 1991. 7(1): p. 9-14.

[406] Gale, E.F., Cundliffe, E., Reynolds, P.E., Richmond, M.H., and Waring, M.J., The molecular basis of anti-biotic action, ed. J.W. sons. 1981.

[407] Philips, A.V. and Cooper, T.A., RNA processing and human disease. Cell. Mol. Life Sci., 2000. 57(2): p. 235-49.

[408] Cech, T.R., Ribozymes and their medical implications. Jama, 1988. 260(20): p. 3030-4.

[409] Bertrand, E. and Rossi, J., Anti-HIV therapeutic hammerhead ribozymes: Targeting strategies and optimization of intracellular function., in Nucleic Acids and Molecular Biology, F. Eckstein and D.M. Lilley, Editors. 1996, Springer-Verlag: Berlin.

[410] Herschlag, D., Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc. Natl. Acad. Sci. USA, 1991. 88(16): p. 6921-5.

[411] Tsuchihashi, Z., Khosla, M., and Herschlag, D., Protein enhancement of hammerhead ribozyme catalysis. Science, 1993. 262(5130): p. 99-102.

[412] Hertel, K.J., Herschlag, D., and Uhlenbeck, O.C., Specificity of hammerhead ribozyme cleavage. EMBO J., 1996. 15(14): p. 3751-7.

[413] Woese, C.R., Translation: in retrospect and prospect. Rna, 2001. 7(8): p. 1055-67.

[414] Joyce, G.F., The rise and fall of the RNA world. New Biol, 1991. 3(4): p. 399-407.

[415] Staley, J.P. and Guthrie, C., Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell, 1998. 92(3): p. 315-26.

[416] Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S., The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 1983. 35(3 Pt 2): p. 849-57.

[417] Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E., and Cech, T.R., Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 1982. 31(1): p. 147-57.

[418] Hermann, T. and Patel, D.J., Adaptive recognition by nucleic acid aptamers. Science, 2000. 287(5454): p. 820-5.

[419] Blackburn, E.H., The end of the (DNA) line. Nat. Struct. Biol., 2000. 7(10): p. 847-50.

[420] Puglisi, J.D., Blanchard, S.C., and Green, R., Approaching translation at atomic resolution. Nat. Struct. Biol., 2000. 7(10): p. 855-61.

[421] Keenan, R.J., Freymann, D.M., Stroud, R.M., and Walter, P., The signal recognition particle. Annu. Rev. Biochem., 2001. 70: p. 755-75.

[422] Black, D.L., Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell, 2000. 103(3): p. 367-70.

[423] Graveley, B.R., Alternative splicing: increasing diversity in the proteomic world. Trends Genet, 2001. 17(2): p. 100-7.

[424] Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A., The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 2000. 289(5481): p. 905-20.

[425] Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A., The structural basis of ribosome activity in peptide bond synthesis. Science, 2000. 289(5481): p. 920-30.

[426] Wimberly, B.T., Brodersen, D.E., Clemons, W.M., Jr., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V., Structure of the 30S ribosomal subunit. Nature, 2000. 407(6802): p. 327-39.

[427] Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F., Crystal structure of the ribosome at 5.5 A resolution. Science, 2001. 292(5518): p. 883-96.

[428] Peluso, P., Herschlag, D., Nock, S., Freymann, D.M., Johnson, A.E., and Walter, P., Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor. Science, 2000. 288(5471): p. 1640-3.

[429] Yanofsky, C., Attenuation in the control of expression of bacterial operons. Nature, 1981. 289(5800): p. 751-8.

[430] Hentze, M.W., Translational control by iron-responsive elements. Adv Exp Med Biol, 1994. 356: p. 119-26.

[431] Muckenthaler, M. and Hentze, M.W., Mechanisms for posttranscriptional regulation by iron-responsive elements and iron regulatory proteins. Prog Mol Subcell Biol, 1997. 18: p. 93-115.

[432] Leulliot, N. and Varani, G., Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry, 2001. 40(27): p. 7947-56.

[433] Repsilber, D., Wiese, S., Rachen, M., Schroder, A.W., Riesner, D., and Steger, G., Formation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis. Rna, 1999. 5(4): p. 574-84.

[434] Raghunathan, P.L. and Guthrie, C., RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol., 1998. 8(15): p. 847-55.

[435] Staley, J.P. and Guthrie, C., An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell, 1999. 3(1): p. 55-64.

[436] Linder, P., Lasko, P.F., Ashburner, M., Leroy, P., Nielsen, P.J., Nishi, K., Schnier, J., and Slonimski, P.P., Birth of the D-E-A-D box. Nature, 1989. 337(6203): p. 121-2.

[437] Herschlag, D., RNA chaperones and the RNA folding problem. J. Biol. Chem., 1995. 270(36): p. 20871-4.

[438] Uhlenbeck, O.C., Keeping RNA happy. Rna, 1995. 1(1): p. 4-6.

[439] Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., and Turner, D.H., Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA, 1986. 83(24): p. 9373-7.

[440] Weeks, K.M., Protein-facilitated RNA folding. Curr. Opin. Struct. Biol., 1997. 7(3): p. 336-42.

[441] Karpel, R.L., Miller, N.S., and Fresco, J.R., Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein. Biochemistry, 1982. 21(9): p. 2102-8.

[442] Clodi, E., Semrad, K., and Schroeder, R., Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J., 1999. 18(13): p. 3776-82.

[443] Pannone, B.K., Xue, D., and Wolin, S.L., A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J., 1998. 17(24): p. 7442-53.

[444] Portman, D.S. and Dreyfuss, G., RNA annealing activities in HeLa nuclei. EMBO J., 1994. 13(1): p. 213-21.

[445] Herschlag, D., Khosla, M., Tsuchihashi, Z., and Karpel, R.L., An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J., 1994. 13(12): p. 2913-24.

[446] Pan, T. and Sosnick, T.R., Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nat. Struct. Biol., 1997. 4(11): p. 931-8.

[447] Treiber, D.K. and Williamson, J.R., Exposing the kinetic traps in RNA folding. Curr. Opin. Struct. Biol., 1999. 9(3): p. 339-45.

[448] Gartland, W.J. and Sueoka, N., Two interconvertible forms of tryptophanyl tRNA in E. coli. Proc. Natl. Acad. Sci. U.S.A., 1966. 55(4): p. 948-56.

[449] Adams, A., Lindahl, T., and Fresco, J.R., Conformational differences between the biologically active and inactive forms of a transfer ribonucleic acid. Proc. Natl. Acad. Sci. U.S.A., 1967. 57(6): p. 1684-91.

[450] Lindahl, T., Adams, A., and Fresco, J.R., Renaturation of transfer ribonucleic acids through site binding of magnesium. Proc. Natl. Acad. Sci. U.S.A., 1966. 55(4): p. 941-8.

[451] Cole, P.E. and Crothers, D.M., Conformational changes of transfer ribonucleic acid. Relaxation kinetics of the early melting transition of methionine transfer ribonucleic acid (Escherichia coli). Biochemistry, 1972. 11(23): p. 4368-74.

[452] Sigler, P.B., An analysis of the structure of tRNA. Annu. Rev. Biophys. Bioeng., 1975. 4(00): p. 477-527.

[453] Fang, X., Pan, T., and Sosnick, T.R., A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme. Biochemistry, 1999. 38(51): p. 16840-6.

[454] Fang, X.W., Pan, T., and Sosnick, T.R., Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat. Struct. Biol., 1999. 6(12): p. 1091-5.

[455] Pan, T., Fang, X., and Sosnick, T., Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J. Mol. Biol., 1999. 286(3): p. 721-31.

[456] Pan, J., Thirumalai, D., and Woodson, S.A., Folding of RNA involves parallel pathways. J. Mol. Biol., 1997. 273(1): p. 7-13.

[457] Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A., Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 1996. 273(5282): p. 1678-85.

[458] Golden, B.L. and Cech, T.R., Conformational switches involved in orchestrating the successive steps of group I RNA splicing. Biochemistry, 1996. 35(12): p. 3754-63.

[459] Lehnert, V., Jaeger, L., Michel, F., and Westhof, E., New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol., 1996. 3(12): p. 993-1009.

[460] Murphy, F.L. and Cech, T.R., An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry, 1993. 32(20): p. 5291-300.

[461] Michel, F. and Westhof, E., Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 1990. 216(3): p. 585-610.

[462] Cech, T.R. and Bass, B.L., Biological catalysis by RNA. Annu. Rev. Biochem., 1986. 55: p. 599-629.

[463] Cech, T.R., Self-splicing of group I introns. Annu. Rev. Biochem., 1990. 59: p. 543-68.

[464] Cech, T.R., RNA chemistry. Ribozyme self-replication? Nature, 1989. 339(6225): p. 507-8.

[465] Herschlag, D. and Cech, T.R., Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry, 1990. 29(44): p. 10159-71.

[466] Herschlag, D., Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme. Biochemistry, 1992. 31(5): p. 1386-99.

[467] Narlikar, G.J. and Herschlag, D., Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem., 1997. 66: p. 19-59.

[468] Narlikar, G.J., Khosla, M., Usman, N., and Herschlag, D., Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme. Biochemistry, 1997. 36(9): p. 2465-77.

[469] Golden, B.L., Gooding, A.R., Podell, E.R., and Cech, T.R., A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science, 1998. 282(5387): p. 259-64.

[470] Latham, J.A. and Cech, T.R., Defining the inside and outside of a catalytic RNA molecule. Science, 1989. 245(4915): p. 276-82.

[471] Celander, D.W. and Cech, T.R., Visualizing the higher order folding of a catalytic RNA molecule. Science, 1991. 251(4992): p. 401-7.

[472] Michel, F., Hanna, M., Green, R., Bartel, D.P., and Szostak, J.W., The guanosine binding site of the Tetrahymena ribozyme. Nature, 1989. 342(6248): p. 391-5.

[473] Pyle, A.M. and Cech, T.R., Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups. Nature, 1991. 350(6319): p. 628-31.

[474] Strobel, S.A. and Cech, T.R., Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry, 1993. 32(49): p. 13593-604.

[475] Ortoleva-Donnelly, L., Kronman, M., and Strobel, S.A., Identifying RNA minor groove tertiary contacts by nucleotide analogue interference mapping with N2-methylguanosine. Biochemistry, 1998. 37(37): p. 12933-42.

[476] Joyce, G.F., van der Horst, G., and Inoue, T., Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res., 1989. 17(19): p. 7879-89.

[477] Doherty, E.A. and Doudna, J.A., The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry, 1997. 36(11): p. 3159-69.

[478] Doherty, E.A., Herschlag, D., and Doudna, J.A., Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry, 1999. 38(10): p. 2982-2990.

[479] Engelhardt, M.A., Doherty, E.A., Knitt, D.S., Doudna, J.A., and Herschlag, D., The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry, 2000. 39(10): p. 2639-51.

[480] Bevilacqua, P.C., Sugimoto, N., and Turner, D.H., A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme. Biochemistry, 1996. 35(2): p. 648-58.

[481] Zarrinkar, P.P. and Williamson, J.R., Kinetic intermediates in RNA folding. Science, 1994. 265(5174): p. 918-24.

[482] Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M., and Woodson, S.A., RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 1998. 279(5358): p. 1940-3.

[483] Treiber, D.K., Rook, M.S., Zarrinkar, P.P., and Williamson, J.R., Kinetic intermediates trapped by native interactions in RNA folding. Science, 1998. 279(5358): p. 1943-6.

[484] Russell, R. and Herschlag, D., Probing the folding landscape of the Tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway. J. Mol. Biol., 2001. 308(5): p. 839-51.

[485] De La Cruz, E.M., Wells, A.L., Rosenfeld, S.S., Ostap, E.M., and Sweeney, H.L., The kinetic mechanism of myosin V. Proc Natl Acad Sci U S A, 1999. 96(24): p. 13726-31.

[486] Rief, M., Rock, R.S., Mehta, A.D., Mooseker, M.S., Cheney, R.E., and Spudich, J.A., Myosin-V stepping kinetics: a molecular model for processivity. Proc Natl Acad Sci U S A, 2000. 97(17): p. 9482-6.

[487] Mehta, A.D., Rock, R.S., Rief, M., Spudich, J.A., Mooseker, M.S., and Cheney, R.E., Myosin-V is a processive actin-based motor. Nature, 1999. 400(6744): p. 590-3.

[488] Kron, S.J. and Spudich, J.A., Fluorescent actin filaments move on myosin fixed to a glass surface. Proc Natl Acad Sci U S A, 1986. 83(17): p. 6272-6.

[489] Finer, J.T., Simmons, R.M., and Spudich, J.A., Single myosin molecule mechanics: piconewton forces and nanometre steps. Nature, 1994. 368(6467): p. 113-9.

[490] Veigel, C., Wang, F., Bartoo, M.L., Sellers, J.R., and Molloy, J.E., The gated gait of the processive molecular motor, myosin V. Nat Cell Biol, 2002. 4(1): p. 59-65.

[491] Rice, S., Purcell, T., and Spudich, J.A., Building and using optical traps to study properties of molecular motors. Methods in Enzymology, 2002. 361: p. 112-133.

[492] Tokunaga, M., Kitamura, K., Saito, K., Iwane, A.H., and Yanagida, T., Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy. Biochem Biophys Res Commun, 1997. 235(1): p. 47-53.

[493] Mercer, J.A., Seperack, P.K., Strobel, M.C., Copeland, N.G., and Jenkins, N.A., Novel myosin heavy chain encoded by murine dilute coat colour locus. Nature, 1991. 349(6311): p. 709-13.

[494] Howard, J., Molecular motors: structural adaptations to cellular functions. Nature, 1997. 389(6651): p. 561-7.

[495] Hackney, D.D., The kinetic cycles of myosin, kinesin, and dynein. Annu Rev Physiol, 1996. 58: p. 731-50.

[496] Trybus, K.M., Krementsova, E., and Freyzon, Y., Kinetic characterization of a monomeric unconventional myosin V construct. J Biol Chem, 1999. 274(39): p. 27448-56.

[497] Purcell, T.J., Morris, C., Spudich, J.A., and Sweeney, H.L., Role of the lever arm in the processive stepping of myosin V. Proc Natl Acad Sci U S A, 2002. 99(22): p. 14159-64.

[498] Tanaka, H., Homma, K., Iwane, A.H., Katayama, E., Ikebe, R., Saito, J., Yanagida, T., and Ikebe, M., The motor domain determines the large step of myosin-V. Nature, 2002. 415(6868): p. 192-5.

[499] De La Cruz, E.M., Ostap, E.M., and Sweeney, H.L., Kinetic mechanism and regulation of myosin VI. J Biol Chem, 2001. 276(34): p. 32373-81.

[500] Molyneaux, B.J., Mulcahey, M.K., Stafford, P., and Langford, G.M., Sequence and phylogenetic analysis of squid myosin-V: a vesicle motor in nerve cells. Cell Motil Cytoskeleton, 2000. 46(2): p. 108-15.

[501] Mehta, A., Myosin learns to walk. J Cell Sci, 2001. 114(Pt 11): p. 1981-98.

[502] Walker, M.L., Burgess, S.A., Sellers, J.R., Wang, F., Hammer, J.A., 3rd, Trinick, J., and Knight, P.J., Two-headed binding of a processive myosin to F-actin. Nature, 2000. 405(6788): p. 804-7.

[503] Yanagida, T. and Iwane, A.H., A large step for myosin. Proc Natl Acad Sci U S A, 2000. 97(17): p. 9357-9.

[504] Nishikawa, S., Homma, K., Komori, Y., Iwaki, M., Wazawa, T., Hikikoshi Iwane, A., Saito, J., Ikebe, R., Katayama, E., Yanagida, T., and Ikebe, M., Class VI myosin moves processively along actin filaments backward with large steps. Biochem Biophys Res Commun, 2002. 290(1): p. 311-7.

[505] Ishii, Y. and Yanagida, T., Single Molecule Measurements and Molecular Motors, in Molecular Motors, M. Schliwa, Editor. 2002, Wiley: Hoboken, N.J. p. 305-326.

[506] Rost, B. and Sander, C., Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol, 1993. 232(2): p. 584-99.

[507] Silverman, J.A. and Harbury, P.B., Rapid mapping of protein structure, interactions, and ligand binding by misincorporation proton-alkyl exchange. J Biol Chem, 2002. 277(34): p. 30968-75.

[508] Perry, J., Antonelli, D., and Ford, W., Analysis of knee-joint forces during flexed-knee stance. Journal of Bone and Joint Surgery, 1975. 57A: p. 961-967.

[509] Campbell, J. and Ball, J., Energetics: application to the study and management of locomotor disabilities. Energetics of walking in cerebral palsy. Orthopedic Clinics of North America, 1978. 9: p. 374-377.

[510] Rose, J., Gamble, J., Medeiros, J., Burgos, A., and Haskell, W., Energy expenditure index of walking for normal children and for children with cerebral palsy. Developmental Medicine and Child Neurology, 1990. 32(333-340).

[511] Sutherland, D.H. and Cooper, L., The pathomechanics of progressive crouch gait in spastic diplegia. Orthopedic Clinics of North America, 1978. 9(1): p. 143-154.

[512] Bleck, E.E., Orthopaedic Management in Cerebral Palsy. 2 ed. 1987, London: Mac Keith Press.

[513] Lloyd-Roberts, G.C., Jackson, A.M., and Albert, J.S., Avulsion of the distal pole of the patella in cerebral palsy. Journal of Bone and Joint Surgery, 1985. 67B: p. 252-254.

[514] Rosenthal, R.K. and Levine, D.B., Fragmentation of the distal pole of the patella in spastic cerebral palsy. Journal of Bone and Joint Surgery, 1977. 59A: p. 934-939.

[515] Sutherland, D.H. and Davids, J.R., Common gait abnormalities of the knee in cerebral palsy. Clinical Orthopaedics and Related Research, 1993. 288: p. 139-147.

[516] DeLuca, P.A., Davis, R.B., Ounpuu, S., Rose, S., and Sirkin, R., Alterations in surgical decision making in patients with cerebral palsy based on three-dimensional gait analysis. Journal of Pediatric Orthopaedics, 1997. 17: p. 608-614.

[517] Gage, J.R., Gait Analysis in Cerebral Palsy. 1991, London: Mac Keith Press.

[518] Nashner, L.M., Shumway-Cook, A., and Marin, O., Stance posture control in select groups of children with cerebral palsy: deficits in sensory organization and muscular coordination. Experimental Brain Research, 1983. 49: p. 393-409.

[519] Neilson, P.D., O'Dwyer, N.J., and Nash, J., Control of isometric muscle activity in cerebral palsy. Developmental Medicine and Child Neurology, 1990. 32: p. 778-788.

[520] Lespargot, A., Renaudin, E., Khouri, N., and Robert, M., Extensibility of hip adductors in children with cerebral palsy. Developmental Medicine and Child Neurology, 1994. 36: p. 980-988.

[521] Rose, J., Haskell, W.L., Gamble, J.G., Hamilton, R.L., Brown, D.A., and Rinsky, L., Muscle pathology and clinical measures of disability in children with cerebral palsy. Journal of Orthopaedic Research, 1994. 12: p. 758-768.

[522] Tardieu, G. and Tardieu, C., Cerebral palsy: mechanical evaluation and conservative correction of limb joint contractures. Clinical Orthopaedics and Related Research, 1986. 219: p. 63-69.

[523] Cornell, M.S., The hip in cerebral palsy. Developmental Medicine and Child Neurology, 1995. 37: p. 3-18.

[524] Laplaza, F.J., Root, L., Tassanawipas, A., and Glasser, D.B., Femoral torsion and neck-shaft angles in cerebral palsy. Journal of Pediatric Orthopaedics, 1993. 13: p. 192-199.

[525] Lundy, D.W., Ganey, T.M., Ogden, J.A., and Guidera, K.J., Pathologic morphology of the dislocated proximal femur in children with cerebral palsy. Journal of Pediatric Orthopaedics, 1998. 18: p. 528-534.

[526] Sussman, M.D., ed. The Diplegic Child. 1991, American Academy of Orthopaedic Surgeons: Rosemont, IL.

[527] Zajac, F.E. and Gordon, M.E., Determining muscle's force and action in multi-articular movement. Exercise and Sport Sciences Reviews, 1989. 17(6): p. 187-230.

[528] DeLuca, P.A., Ounpuu, S., Davis, R.B., and Walsh, J.H., Effect of hamstring and psoas lengthening on pelvic tilt in patients with spastic diplegic cerebral palsy. Journal of Pediatric Orthopaedics, 1998. 18: p. 712-718.

[529] Gage, J.R., Surgical treatment of knee dysfunction in cerebral palsy. Clinical Orthopaedics and Related Research, 1990. 253: p. 45-54.

[530] Perry, J. and Newsam, C., Function of the hamstrings in cerebral palsy, in The Diplegic Child: Evaluation and Management, M.D. Sussman, Editor. 1992, American Academy of Orthopaedic Surgeons: Rosemont, IL. p. 299-307.

[531] Baumann, H.U., Reutsch, H., and Schurmann, K., Distal hamstring lengthening in cerebral palsy. International Orthopaedics, 1980. 3: p. 305-309.

[532] Dhawlikar, S.H., Root, L., and Mann, R.L., Distal lengthening of the hamstrings in patients who have cerebral palsy. Journal of Bone and Joint Surgery, 1992. 74-A(9): p. 1385-1391.

[533] Gage, J., Fabian, D., Hicks, R., and Tashman, S., Pre- and postoperative gait analysis in patients with spastic diplegia: a preliminary report. Journal of Pediatric Orthopaedics, 1984. 4(6): p. 715-725.

[534] Thometz, J., Simon, S., and Rosenthal, R., The effect on gait of lengthening of the medial hamstrings in cerebral palsy. Journal of Bone and Joint Surgery, 1989. 71-A(3): p. 345-353.

[535] Nene, A.V., Evans, G.A., and Patrick, J.H., Simultaneous multiple operations for spastic diplegia. Journal of Bone and Joint Surgery, 1993. 75-B(3): p. 488-94.

[536] Rab, G., Consensus on crouched gait, in The Diplegic Child: Evaluation and Management, M.D. Sussman, Editor. 1992, American Academy of Orthopaedic Surgeons: Rosemont, IL. p. 337-339.

[537] Renshaw, T.S., Green, N.E., Griffin, P.P., and Root, L., Cerebral palsy: orthopaedic management. Journal of Bone and Joint Surgery, 1995. 77-A(10): p. 1590-1606.

[538] Delp, S.L., Arnold, A.S., Speers, R.A., and Moore, C.A., Hamstrings and psoas lengths during normal and crouch gait: implications for muscle-tendon surgery. Journal of Orthopaedic Research, 1996. 14(1): p. 144-151.

[539] Schutte, L.M., Hayden, S.W., and Gage, J.R., Lengths of hamstrings and psoas muscles during crouch gait: effects of femoral anteversion. Journal of Orthopaedic Research, 1997. 15: p. 615-621.

[540] Hoffinger, S.A., Rab, G.T., and Abou-Ghaida, H., Hamstrings in cerebral palsy crouch gait. Journal of Pediatric Orthopaedics, 1993. 13: p. 722-726.

[541] Thompson, N.S., Baker, R.J., Cosgrove, A.P., Corry, I.S., and Graham, H.K., Musculoskeletal modelling in determining the effect of botulinum toxin on the hamstrings of patients with crouch gait. Developmental Medicine and Child Neurology, 1998. 40: p. 622-625.

[542] Waters, R.L., Perry, J., McDaniels, J.M., and House, K., The relative strength of the hamstrings during hip extension. Journal of Bone and Joint Surgery, 1974. 56-A(8): p. 1592-1597.

[543] Reimers, J., Static and dynamic problems in spastic cerebral palsy. Journal of Bone and Joint Surgery, 1973. 55-B(4): p. 822-827.

[544] Roosth, H.P., Flexion deformity of the hip and knee in spastic cerebral palsy: treatment by early release of spastic hip-flexor muscles. Journal of Bone and Joint Surgery, 1971. 53-A(8): p. 1489-1510.

[545] Wiley, M.E. and Damiano, D.L., Lower-extremity strength profiles in spastic cerebral palsy. Developmental Medicine and Child Neurology, 1998. 40: p. 100-107.

[546] Gage, J.R., DeLuca, P.A., and Renshaw, T.S., Gait analysis: principles and applications. Journal of Bone and Joint Surgery, 1995. 77-A(10): p. 1607-1623.

[547] Cerebral palsy among children. 2001, Prevalence rates determined by the Metropolitan Atlanta Developmental Disabilities Surveillance Program, 1991-1994, as reported by the Developmental Disabilities Branch of the Division of Birth Defects, Child Development, and Disability and Health, http://www.cdc.gov/nceh/cddh/dd/ddcp.htm.

[548] Arnold, A.S., Salinas, S., Asakawa, D.J., and Delp, S.L., Accuracy of muscle moment arms estimated from MRI-based musculoskeletal models of the lower extremity. Computer Aided Surgery, 2000. 5: p. 108-119.

[549] Arnold, A.S., Asakawa, D.J., and Delp, S.L., Do the hamstrings and adductors contribute to excessive internal rotation of the hip in persons with cerebral palsy? Gait and Posture, 2000. 11(3): p. 181-190.

[550] Murray, W.M., Arnold, A.S., Salinas, S., Durbhakula, M., Buchanan, T.S., and Delp, S.L. Building biomechanical models based on medical image data: an assessment of model accuracy. in Proceedings from the First Annual Conference on Medical Image Computing and Computer-Assisted Interventions. 1998. Cambridge, MA: Springer-Verlag.

[551] van der Helm, F.C.T., Veeger, H.E.J., Pronk, G.M., van der Woude, L.H.V., and Rozendal, R.H., Geometry parameters for musculoskeletal modelling of the shoulder system. Journal of Biomechanics, 1992. 25(2): p. 129-144.

[552] Davis, R.B., Ounpuu, S., Tyburski, D., and Gage, J.R., A gait analysis data collection and reduction technique. Human Movement Science, 1991. 10: p. 575-587.

[553] Kadaba, M.P., Ramakrishnan, H.K., and Wootten, M.E., Measurement of lower extremity kinematics during level walking. Journal of Orthopaedic Research, 1990. 8: p. 383-392.

[554] Delp, S.L. and Zajac, F.E., Force- and moment-generating capacity of lower-extremity muscles before and after tendon lengthening. Clinical Orthopaedics and Related Research, 1992. 284: p. 247-259.

[555] Delp, S.L., Statler, K., and Carroll, N.C., Preserving plantar flexion strength after surgical treatment for contracture of the triceps surae: a computer simulation study. Journal of Orthopaedic Research, 1995. 13(1): p. 96-104.

[556] Delp, S.L., Ringwelski, D.A., and Carroll, N.C., Transfer of the rectus femoris: effects of transfer site on moment arms about the knee and hip. Journal of Biomechanics, 1994. 27(10): p. 1201-1211.

[557] Delp, S.L., Bleck, E.E., Zajac, F.E., and Bollini, G., Biomechanical analysis of the Chiari pelvic osteotomy: preserving hip abductor strength. Clinical Orthopaedics and Related Research, 1990. 254: p. 189-198.

[558] Free, S.A. and Delp, S.L., Trochanteric transfer in total hip replacement: effects on the moment arms and force-generating capacities of the hip abductors. Journal of Orthopaedic Research, 1996. 14(2): p. 245-250.

[559] Schmidt, D.J., Arnold, A.S., Carroll, N.C., and Delp, S.L., Length changes of the hamstrings and adductors resulting from derotational osteotomies of the femur. Journal of Orthopaedic Research, 1999. 17(2): p. 279-285.

[560] Delp, S.L. and Maloney, W., Effects of hip center location on the moment-generating capacity of the muscles. Journal of Biomechanics, 1993. 26(4/5): p. 485-499.

[561] Delp, S.L., Komattu, A.V., and Wixson, R.L., Superior displacement of the hip in total joint replacement: effects of prosthetic neck length, neck-stem angle, and anteversion angle on the moment-generating capacity of the muscles. Journal of Orthopaedic Research, 1994. 12(6): p. 860-870.

[562] Delp, S.L., Kocmond, J.H., and Stern, S.H., Trade-offs between motion and stability in posterior substituting knee arthroplasty design. Journal of Biomechanics, 1995. 28(10): p. 1155-1166.

[563] Delp, S.L., Wixson, R.L., Komattu, A.V., and Kocmond, J.H., How superior placement of the joint center in hip arthroplasty affects the abductor muscles. Clinical Orthopaedics and Related Research, 1996. 328: p. 137-146.

[564] Arnold, A.S., Quantitative Descriptions of Musculoskeletal Geometry in Persons with Cerebral Palsy: Guidelines for the Evaluation and Treatment of Crouch Gait, in Department of Biomedical Engineering. 1999, Northwestern University: Evanston, IL.

[565] Witka, J., Khawly, R., Arnold, A., and Delp, S. Dependence of estimated peak psoas and hamstring lengths on walking speed. in Proceedings from the 4th Annual Meeting of the Gait and Clinical Movement Analysis Society. 1999. Dallas, TX: Gait and Posture.

[566] Anderson, F.C. and Pandy, M.G., A dynamic optimization solution for vertical jumping in three dimensions. Computer Methods in Biomechanics and Biomedical Engineering, 1999. 2: p. 201-231.

[567] Yamaguchi, G.T. and Zajac, F.E., A planar model of the knee joint to characterize the knee extensor mechanism. J. Biomech., 1989. 22(1): p. 1-10.

[568] Zajac, F.E., Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. Critical Reviews in Biomedical Engineering, 1989. 17: p. 359-411.

[569] McConville, J.T., Clauser, C.E., Churchill, T.D., Cuzzi, J., and Kaleps, I., Anthropometric relationships of body and body segment moments of inertia, in Technical Report AFAMRL-TR-80-119. 1980, Air Force Aerospace Medical Research Laboratory, Wright-Patterson Air Force Base, OH.

[570] Schwartz, M.H. and Lakin, G. The effect of tibial torsion on soleus function. in Proceedings from the 24th Annual Meeting of the American Society of Biomechanics. 2000. Chicago, IL.

[571] Tardieu, C., Huet de la Tour, E., Bret, M.D., and Tardieu, G., Muscle hypoextensibility in children with cerebral palsy: I. clinical and experimental observations. Archives of Physical Medicine and Rehabilitation, 1982. 63: p. 97-102.

[572] Jenson, R.K., Changes in segment inertia proportions between 4 and 20 years. Journal of Biomechanics, 1989. 22(6/7): p. 529-536.

[573] Schutte, L.M., Narayanan, U., Stout, J.L., Selber, P., Gage, J., and Schwartz, M.H., An index for quantifying deviations from normal gait. Gait and Posture, 2000. 11: p. 25-31.

[574] Schwartz, M.H., Novacheck, T.F., and Trost, J., A tool for quantifying hip flexor function during gait. Gait and Posture, 2000. 12: p. 122-127.

[575] Sheskin, D.J., Handbook of Parametric and Nonparametric Statistical Procedures. 2nd Edition ed. 2000, Boca Raton, FL: Chapman and Hall/CRC Press.

[576] Markl, M., Chan, F.P., Alley, M.T., Wedding, K.L., Draney, M.T., Elkins, C.J., Parker, D.W., Wicker, R., Taylor, C.A., Herfkens, R.J., and Pelc, N.J., Time-resolved three-dimensional phase-contrast MRI. J Magn Reson Imaging, 2003. 17(4): p. 499-506.

[577] Perktold, K. and Rappitsch, G., Computer Simulation of Local Blood Flow and Vessel Mechanics in a Compliant Carotid Artery Bifurcation Model. Journal of Biomechanics, 1995. 28(7): p. 845-856.

[578] Zarins, C.K., Xu, C., and Glagov, S., Atherosclerotic enlargement of the human abdominal aorta. Atherosclerosis, 2001. 155(1): p. 157-64.

[579] Xu, C., Zarins, C.K., and Glagov, S., Aneurysmal and occlusive atherosclerosis of the human abdominal aorta. Journal of Vascular Surgery, 2001. 33(1): p. 91-6.

[580] Xu, C., Zarins, C.K., Bassiouny, H.S., Briggs, W.H., Reardon, C., and Glagov, S., Differential transmural distribution of gene expression for collagen types I and III proximal to aortic coarctation in the rabbit. Journal of Vascular Research, 2000. 37(3): p. 170-82.

[581] Xu, C., Zarins, C.K., Pannaraj, P.S., Bassiouny, H.S., and Glagov, S., Hypercholesterolemia superimposed by experimental hypertension induces differential distribution of collagen and elastin. Arteriosclerosis, Thrombosis & Vascular Biology, 2000. 20(12): p. 2566-72.

[582] Xu, C., Bassiouny, H.S., Zarins, C.k., and Glagov, S., Tropoelastin Gene Expression During Artery Wall Remodeling in Response to Acute Blood Pressure Elevation. Circulation, 1995. 92(1): p. 425.

[583] Xu, C., Zarins, C.K., and Glagov, S., Biphasic response of tropoelastin at the poststenotic dilation segment of the rabbit aorta. Journal of Vascular Surgery, 2002. 36(3): p. 605-12.

[584] Xu, C., Lee, S., Singh, T.M., Sho, E., Li, X., Sho, M., Masuda, H., and Zarins, C.K., Molecular mechanisms of aortic wall remodeling in response to hypertension. Journal of Vascular Surgery, 2001. 33(3): p. 570-8.

[585] Masuda, H., Zhuang, Y.J., Singh, T.M., Kawamura, K., Murakami, M., Zarins, C.K., and Glagov, S., Adaptive remodeling of internal elastic lamina and endothelial lining during flow-induced arterial enlargement. Arteriosclerosis Thrombosis & Vascular Biology, 1999. 19(10): p. 2298-307.

[586] Sho, M., Sho, E., Singh, T.M., Komatsu, M., Sugita, A., Xu, C., Nanjo, H., Zarins, C.K., and Masuda, H., Subnormal shear stress-induced intimal thickening requires medial smooth muscle cell proliferation and migration. Experimental & Molecular Pathology, 2002. 72(2): p. 150-60.

[587] Sho, E., Sho, M., Singh, T.M., Xu, C., Zarins, C.K., and Masuda, H., Blood flow decrease induces apoptosis of endothelial cells in previously dilated arteries resulting from chronic high blood flow. Arteriosclerosis, Thrombosis & Vascular Biology, 2001. 21(7): p. 1139-45.

[588] Zhuang, Y.J., Singh, T.M., Zarins, C.K., and Masuda, H., Sequential Increases and Decreases in Blood Flow Stimulates Progressive Intimal Thickening. European Journal of Vascular and Endovascular Surgery, 1998. 16(4): p. 301-310.

[589] Singh, T.M., Zhuang, Y.J., Masuda, H., and Zarins, C.K., Intimal Hyperplasia in Response to Reduction of Wall Shear Stress. Surgical Forum, 1997. 48: p. 445-446.

[590] Asari, Y., Sugita, A., Murakami, M., Sho, E., Kobayashi, M., Kawamura, K., Sugiyama, T., Nanjo, H., Xu, C., Singh, T.M., Zarins, C.K., and Masuda, H., High-flow augments myo-endothelial couplings in rabbit common carotid artery before internal elastic lamina remodeling. Submitted, 2002.

[591] Sho, E., Sho, M., Singh, T.M., Nanjo, H., Komatsu, M., Xu, C., Masuda, H., and Zarins, C.K., Arterial enlargement in response to high flow requires early expression of matrix metalloproteinases to degrade extracellular matrix. Experimental & Molecular Pathology, 2002. 73(2): p. 142-53.

[592] Tropea, B.I., Schwarzacher, S.P., Chang, A., Asvar, C., Huie, P., Sibley, R.K., and Zarins, C.K., Reduction of aortic wall motion inhibits hypertension-mediated experimental atherosclerosis. Arteriosclerosis, Thrombosis & Vascular Biology, 2000. 20(9): p. 2127-33.

[593] Wolinsky, H. and Glagov, S., A lamellar unit of aortic medial structure and function in mammals. Circulation Research, 1967. 20(1): p. 99-111.

[594] Draney, M.T., Herfkens, R.J., Hughes, T.J., Pelc, N.J., Wedding, K.L., Zarins, C.K., and Taylor, C.A., Quantification of vessel wall cyclic strain using cine phase contrast magnetic resonance imaging. Ann Biomed Eng, 2002. 30(8): p. 1033-45.

[595] Draney, M.T., Arko, F.R., Alley, M.T., Markl, M., Herfkens, R.J., Pelc, N.J., Zarins, C.K., and C.A., T., In Vivo Quantification of Porcine Aortic Wall Motion and Cyclic Strain Using Cine Phase Contrast MRI. Submitted to Magnetic Resonance in Medicine, 2003.

[596] Pelc, N.J., Drangova, M., Pelc, L.R., Zhu, Y., Noll, D.C., Bowman, B.S., and Herfkens, R.J., Tracking of Cyclical Motion Using Phase Contrast Cine MRI Velocity Data. Journal of Magnetic Resonance Imaging, 1995. 5: p. 339-345.

[597] Marsden, J.E. and Hughes, T.J.R., Mathematical Foundations of Elasticity. 1993, New York: Dover Publications, Inc.

[598] Wedding, K.L., Draney, M.T., Herfkens, R.J., Zarins, C.K., Taylor, C.A., and Pelc, N.J., Measurement of vessel wall strain using cine phase contrast MRI. Journal of Magnetic Resonance Imaging, 2002. 15(4): p. 418-28.

[599] Draney, M.T., Xu, C., Arko, F.R., Herfkens, R.J., Pelc, N.J., C.A., T., and Zarins, C.K. In Vivo Quantitation of Aortic Wall Motion: Relationship to Asymmetric Wall Thickness. in American College of Surgeons. 2002. San Francisco, CA.

[600] Taylor, C.A., Hughes, T.J.R., and Zarins, C.K., Finite Element Modeling of Three-Dimensional Pulsatile Flow in the Abdominal Aorta: Relevance to Atherosclerosis. Annals of Biomedical Engineering, 1998. 26(6): p. 1-14.

[601] Taylor, C.A., Hughes, T.J.R., and Zarins, C.K., Effect of Exercise on Hemodynamic Conditions in the Abdominal Aorta. Journal of Vascular Surgery, 1999. 29(6): p. 1077-1089.

[602] Wang, K., Taylor, C.A., Hsiau, Z., Parker, D., and Dutton, R.W. Level Set Methods and MR Image Segmentation for Geometric Modeling in Computational Hemodynamics. in IEEE Biomedical Engineering in Medicine and Biology Society. 1998. Hong Kong, China.

[603] Wan, J., Steele, B.N., Spicer, S.A., Strohband, S., Feijoo, G.R., Hughes, T.J., and Taylor, C.A., A one-dimensional finite element method for simulation-based medical planning for cardiovascular disease. Computer methods in Biomechanics and Biomedical Engineering, 2001.

[604] Steele, B.N., Wan, J., Ku, J.P., Hughes, T.J.R., and Taylor, C.A., In Vivo Validation of a One-Dimensional Finite Element Method for Simulation-Based Medical Planning for Cardiovascular Bypass Surgery. Accepted for Publication in IEEE Transactions on Biomedical Engineering, 2003.

[605] Taylor, C.A. and Hughes, T.J.R., A Multiscale Finite Element Method for Blood Flow in Deformable Vessels, in Podium Presentation at the 1998 World Congress of Biomechanics,. 1998: Sapporo, Japan.

[606] Vignon, I. and Taylor, C.A. A Multidomain Finite Element Method to Solve the Nonlinear One-dimensional Equations of Blood Flow in Deformable Vessels. in Submitted to 2003 ASME Summer Bioengineering Meeting. 2003. Key Biscayne, FL.

[607] Altman, R.B., A curriculum for bioinformatics: the time is ripe. Bioinformatics, 1998. 14(7): p. 549-50.