Modeling and simulation of biomaterials

Annual Review of Materials Research

Volumn 34, Issue , 2004, Pages 279-314

  Redondo, Antonio ^a   LeSar, Richard ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Biology; Soft matter; Theory

Indexed keywords

BIOMEDICAL APPLICATIONS; BIOMOLECULES; SOFT MATTER; THEORIES;

ADHESION; BIOCHEMISTRY; BIOMEDICAL ENGINEERING; COMPUTER SIMULATION; DATA ACQUISITION; MATHEMATICAL MODELS; MUSCULOSKELETAL SYSTEM; PROBLEM SOLVING; SYNTHESIS (CHEMICAL);

BIOMATERIALS;

EID: 4344571165     PISSN: 15317331     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.matsci.34.070503.123908     Document Type: Review

References (301)

1. Adachi T, Tsubota K, Tomita Y, Hollister SJ. 2001. Trabecular surface remodeling simulation for cancellous bone using microstructural voxel finite element models. J. Biomech. Eng. 123:403-9
2. Alber MS, Kiskowski A. 2001. On aggregation in CA models in biology. J. Phys. A 34:10707-14
3. Alber MS, Kiskowski MA, Glazier JA, Jiang Y. 2003. On cellular automaton approaches to modeling biological cells. In Mathematical Systems Theory in Biology, Communication, Computation, and Finance, ed. J Rosenthal, DS Gilliam, pp. 1-39. New York: Springer
4. Alber MS, Kiskowski MA, Jiang Y. 2004. Two-stage aggregate formation via streams in Myxobacteria. Phys. Rev. Lett. Submitted
5. Alberts B. 1998. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92:291-94
6. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. 2002. Molecular Biology of the Cell. New York: Garland. 4th ed.
7. Albinet G, Pelce P. 1996. Computer simulation of neurite outgrowth. Europhys. Lett. 33:569-74
8. Alder BJ, Wainwright TE. 1959. Studies in molecular dynamics. I. General method. J. Chem. Phys. 31:459-66
9. Allen MP, Tildesley DJ. 1987. Computer Simulation of Liquids. Oxford, UK: Oxford Univ. Press
10. Allen TW, Bastug T, Kuyucak S, Chung SH. 2003. Gramicidin A channel as a test ground for molecular dynamics force fields. Biophys. J. 84:2159-68
11. Anderson MP, Srolovitz DJ, Grest GS, Sahni PS. 1984. Computer simulation of grain growth. I. Kinetics. Acta Metall. 32:783-91
12. Arakawa T, Timasheff SN. 1985. Theory of protein solubility. Meth. Enzymol. 114:49-77
13. Arbib MA, Érdi P, Szentágothai J. 1998. Neural Organization: Structure, Function and Dynamics. Cambridge, MA: MIT Press
14. Basmadjian D, Sefton MV, Baldwin SA. 1997. Coagulation on biomaterials in flowing blood: some theoretical considerations. Biomaterials 18:1511-22
15. Ben-Shaul A, Szleifer L, Gelbart WM. 1987. Molecular theory for amphiphile packing and elastic properties of monolayers and bilayers. See Ref. 179, pp. 2-8
16. + channel in a bilayer membrane. Biophys, J. 78:2900-17
17. Berry JL, Manoach E, Mekkaoui C, Rolland PH, Moore JE, Rachev A. 2002. Hemodynamics and wall mechanics of a compliance matching stent: in vitro and in vivo analysis. J. Vasc. Interv. Radiol. 13:97-105
18. Bicerano J, ed. 1992. Computational Modeling of Polymers. New York: Dekker
19. Biggin PC, Roosild T, Choe S. 2000. Potassium channel structure: domain by domain. Curr. Opin. Struct. Biol. 10: 456-61
20. Binder K, ed. 1995. Monte Carlo and Molecular Dynamics Simulations in Polymer Science. Oxford, UK: Oxford Univ. Press
21. Blaxter K. 1989. Energy Metabolism in Animals and Man. Cambridge, MA: Cambridge Univ. Press
22. Boal D. 2002. Mechanics of the Cell. Cambridge, MA: Cambridge Univ. Press
23. Bodig J, Jayne BA. 1982. Mechanics of Wood and Wood Composites. New York: Van Nostrand Reinhold
24. Bormann G, Brosens F, de Schutter E. 2001. Modeling biochemical networks: diffusion. See Ref. 293, pp. 189-224
25. Bragg WL, Williams EJ. 1934. The effect of thermal agitation on atomic arrangement in alloys. Proc. R. Soc. London Ser. A 145:699-730
26. Branden C, Tooze J. 1999. Introduction to Protein Structure. New York: Garland
27. Breuls RGM, Sengers BG, Oomens CWJ, Bouten CVC, Baaijens FPT. 2002. Predicting local cell deformations in engineered tissue constructs: a multilevel finite element approach. J. Biomech. Eng. 124:198-207
28. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217
29. Burykin A, Schutz CN, Villá A, Warshel A. 2002. Simulations of ion current in realistic models of ion channels: the KcsA potassium channel. Proteins 47:265-80
30. Bustamante C, Marko JF, Siggia ED, Smith S. 1994. Entropic elasticity of λ-phage DNA. Science 265:1599-600
31. Cahn RW. 2001. The Coming of Materials Science. Oxford, UK: Pergamon
32. Cantor CR, Schimmel PR. 1980. Biophysical Chemistry. Part III. The Behavior of Biological Macromolecules. New York: Freeman
33. Cardenas A, Coalson R, Kurnikova M. 2000. Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on Gramicidin A channel conductance. Biophys. J. 79:80-93
34. Cevc G, Marsh D. 1987. Phospholipid Bilayers: Physical Principles and Models. New York: Wiley & Sons
35. Chaikin PM, Lubensky TC. 1995. Principles of Condensed Matter Physics. Cambridge, MA: Cambridge Univ. Press
36. Chang I, Gilbert ES, Eliashberg N, Keasling JD. 2003. A three-dimensional, stochastic simulation of biofilm growth and transport-related factors that affect structure. Microbiology 149:2859-71
37. Chao SD, Kress JD, Redondo A. 2004. An alternative multipolar expansion for intermolecular potential functions. J. Chem. Phys. 120: In press
38. Chapman D. 1984. Biological Membranes, Vol. 5. London: Academic
39. Chiu SW, Subramaniam S, Jakobsson E. 1999. Simulation study of Gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. Biophys. J. 76:1929-38
40. Chopard B, Droz M. 1998. Cellular Automata Modeling of Physical Systems. Cambridge, UK: Cambridge Univ. Press
41. Chou SK, Chua KJ. 2003. Study of the drying behavior of a heat-sensitive biomaterial undergoing stepwise-varying temperature schemes. Ind. Eng. Chem. Res. 42:4939-52
42. Chua KJ, Mujumdar AS, Chou SK. 2003. A review on intermittent drying processes. Bioresour. Technol. 90:285-95
43. Chung SH, Allen TW, Kuyucak S. 2002. Modeling diverse range of potassium channels with Brownian dynamics. Biophys. J. 83:263-77
44. Chung SH, Kuyucak S. 2002. Ion channels: recent progress and prospects. Eur. Biophys. J. 31:283-93
45. Chung SH, Kuyucak S. 2002. Recent advances in ion channel research. Biochim. Biophys. Acta Biomembr. 1565:267-86
46. Cimrman R, Kroc J, Rohan E, Rosenberg J, Tona Z. 2003. On coupling cellular automata based activation and finite element muscle model applied to heart ventricle modelling. Adv. Comput. Bioeng. 7:25-34
47. Cordes JA, Chang AT, Charvet JL. 1998. Predicting fracture from the tensile properties of a composite biomaterial. Compos. Appl. Sci. Manuf. 29A: 1475-80
48. Corey DP, Hudspeth AJ. 1983. Analysis of the microphonic potential of the bullfrog's sacculus. J. Neurosci. 3:942-61
49. Corry B, Hoyles M, Allen T, Walker M, Kuyucak S, Chung SH. 2002. Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophys. J. 82:1975-84
50. Corry B, Kuyucak S, Chung SH. 2003. Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. Biophys. J. 84: 3594-606
51. Creighton TE. 1991. Stability of folded conformations. Curr. Opin. Struct. Biol. 1:5-16
52. Creighton TE. 1993. Proteins: Structures and Molecular Properties. New York: Freeman
53. Currey JD. 1984. The Mechanical Adaptations of Bones. Princeton, NJ: Princeton Univ. Press
54. Daoud M, Williams CE, eds. 1995. Soft Matter Physics. Berlin: Springer
55. Derjaguin BV. 1949. Theory of Stability of Colloids and Thin Films. New York: Consultants Bureau
56. Derjaguin BV, Landau LD. 1941. Theory of the stability of strongly charged lyophobic sols and the adhesion of strongly charged particles in solutions of electrolytes. Acta Physicochim. URSS 14:633-62
57. Destexhe A. 2001. Kinetic models of membrane excitability and synaptic interactions. See Ref. 293
58. Dinwoodie JM. 1981. Timber: Its Nature and Behavior. New York: Van Nostrand Reinhold
59. DeWitt N. 2003. Bone and cartilage. Nature 423:315
60. dos Reis AN, Mombach JCM, Walter M, de Ávila LF. 2003. The interplay between cell adhesion and environment rigidity in the morphology of tumors. Phys. A 322:546-54
61. Dossel O, Sachse FB, Seemann G, Werner CD. 2002. Computermodelle der elektrophysiologischen Eigenschaften des Herzens. Biomed. Tech. 47: 250-57
62. + conduction and selectivity. Science 280:69-77
63. Drexler KE. 1992. Nanosystems: Molecular Machines and Computation. New York: Wiley
64. Drozdov AD. 1998. Mechanics of Viscoelastic Solids. Chichester, UK: Wiley
65. Duysak A, Zhang JJ, Ilankovan V. 2003. An efficient modeling and simulation of soft tissue deformations using mass spring systems. Int. Congr. Ser. 1256:337-42
66. Edwards S, Cony B, Kuyucak S, Chung SH. 2002. Continuum electrostatics fails to describe ion permeation in the Gramicidin channel. Biophys. J. 83:348-60
67. Elbaum M, Fygenson DK, Libchaber A. 1995. Buckling microtubules in vesicles. Phys. Rev. Lett. 76:4078-81
68. Elliott GF, Worthington CR. 2000. Muscle contraction: viscous-like frictional forces and the impulsive model. Int. J. Biol. Macromol. 27:327-32
69. Eriksen EF. 1986. Normal and pathological remodeling of human trabecular bone: three dimensional reconstruction of the remodeling sequence in normals and in metabolic bone disease. Endocr. Rev. 7:379-408
70. Evans DF, Wennerström H. 1999. The Colloidal Domain. New York: Wiley-VCH
71. Eyring H, Eyring EM. 1963. Modern Chemical Kinetics. New York: Reinhold
72. Felgner H, Frank R, Schliwa M. 1996. Flexural rigidity of microtubules measured with the use of optical tweezers. J. Cell. Sci. 109:509-16
73. Fendler JH. 1987. Membrane Mimetic Chemistry. New York: Wiley
74. Ferreira CP, Fontanari JF, Zorzenon dos Santos RM. 2001. Phase-transitions in a model for the formation of herpes simplex ulcers. Phys. Rev. E 64:041903
75. Finkelstein AV. 1997. Protein structure: What is possible to predict now? Curr. Opin. Struct. Biol. 7:61-71
76. Fleer GJ, Cohen Stuart MA, Scheutjens JMHM, Cosgrove T, Vincent B. 1993. Polymers at Interfaces. London: Chapman and Hall
77. Flory PJ. 1969. Statistical Mechanics of Chain Molecule. New York: Interscience
78. Frenkel D, Smit B. 2002. Understanding Molecular Simulation: From Algorithms to Applications. San Diego: Academic. 2nd ed.
79. Franks F. 1995. Protein destabilization at low temperatures. Adv. Protein Chem. 46:105-39
80. Fredrickson GH, Ganesan V, Drolet F. 2002. Field-theoretic computer simulation methods for polymers and complex fluids. Macromolecules 35:16-39
81. Frisch U, Hasslacher B, Pomeau Y. 1986. Lattice-gas automata for the Navier-Stokes equation. Phys. Rev. Lett. 56:1505-8
82. Frost HM. 1985. The pathomechanics of osteoporosis. Clin. Orthoped. Relat. Res. 200:198-225
83. Galam S, Radomski JP. 2001. Cancerous tumor: the high frequency of a rare event. Phys. Rev. E 63:051907
84. Gan CK, Sewell TD, Challacombe M. 2004. All-electron density functional studies of hydrostatic compression of pentaerythritol tetranitrate (PETN). Phys. Rev. B. In press
85. García de la Torre JG, Bloomfield VA. 1981. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q. Rev. Biophys. 14:81-139
86. Geeves MA, Holmes KC. 1999. Structural mechanism of muscle contraction. Annu. Rev. Biochem. 68:687-728
87. Geissler PS. 1981. Configurational entropy of tethered polymers and the swelling properties of connective tissue. ACS Symp. Ser. 150:265-74
88. Gerstein M, Lesk MA, Chothia C. 1994. Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-49
89. Gibson LJ, Ashby MF. 1997. Cellular Solids: Structure and Properties. Cambridge, UK: Cambridge Univ. Press. 2nd ed.
90. Gibson LJ, Ashby MF, Schajer GS, Robertson CI. 1982. The mechanics of two dimensional cellular solids. Proc. R. Soc. London Ser. A 382:25-42
91. Gilbert EN. 1962. Random subdivisions of space into crystals. Ann. Math. Stat. 33:958-72
92. Gittes F, Meyhofer E, Baek S, Howard J. 1996. Directional loading of the kinesin motor molecule as it buckles a microtubule. Biophys. J. 70:418-29
93. Gittes F, Mickey B, Nettleton J, Howard J. 1996. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J. Cell Biol. 120:923-34
94. Goetz R, Lipowsky R. 1998. Computer simulations of bilayer membranes: self-assembly and interfacial tension. J. Chem. Phys. 108:7397-407
95. Goetz R, Gompper G, Lipowsky R. 1999. Mobility and elasticity of self-assembled membranes. Phys. Rev. Lett. 82:221-24
96. Gompper G, Kroll DM. 1995. Phase diagram and scaling behavior of fluid vesicles. Phys. Rev. E 51:514-25
97. Gompper G, Kroll DM. 1997. Freezing flexible vesicles. Phys. Rev. Lett. 78: 2859-62
98. Greenspan D. 1997. Particle Modeling. Boston: Birkhauser
99. de Groot BL, Tieleman DP, Pohl P, Grubmuller H. 2002. Water permeation through Gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys. J. 82:2943-42
100. Guldbrand L, Jönsson B, Wennerström H, Linse P. 1984. Electrical double layer forces: a Monte Carlo study. J. Chem. Phys. 80:2221-28
101. Haile JM. 1992. Molecular Dynamics Simulations. New York: Wiley & Sons
102. Hamaker HC. 1937. The London-van der Waals attraction between spherical particles. Physica 4:1058-72
103. Hansson T, Oostenbrink C, van Gunsteren WF. 2002. Molecular dynamics simulations. Curr. Opin. Struct. Biol. 12: 190-96
104. Haynie DT. 2001. Biological Thermodynamics. Cambridge, UK: Cambridge Univ. Press
105. Hazelwood SJ, Martin RB, Rashid MM, Rodrigo JJ. 2001. A mechanistic model for internal bone remodeling exhibits different dynamic responses in disuse and overload. J. Biomech. 34:299-308
106. Helfrich W. 1978. Steric interaction of fluid membranes in multilayer systems. Z. Naturforsch. 33a:305-15
107. Hermans J, Berendsen HJC, van Gunsteren WF, Postma JPM. 1984. A consistent empirical potential for water-protein interactions. Biopolymers 23:1513-18
108. Hill AV. 1922. The maximum work and mechanical efficiency of human muscles, and their most economical speed. J. Physiol. 56:19-41
109. Hill TL. 1963. Thermodynamics of Small Systems. New York: Benjamin
110. Hockney RW, Eastwood JW. 1988. Computer Simulation Using Particles. Bristol, UK: Hilger
111. Holm EA, Glazier JA, Srolovitz DJ, Grest G. 1991. Effect of lattice anisotropy and temperature on domain growth in the two-dimensional Potts model. Phys. Rev. A 43:2262-68
112. Horgan CO, Saccomandi G. 2003. A description of arterial wall mechanics using limiting chain extensibility constitutive models. Biomech. Model Mechanobiol. 1:251-66
113. Howard J. 2001. Mechanics of Motor Proteins and the Cytoskeleton. Sunderland, MA: Sinauer
114. Howard J, Roberts WM, Hudspeth AJ. 1988. Mechanoelectrical transduction by hair cells. Annu. Rev. Biophys. Biophys. Chem. 17:99-124
115. Hunt AJ, Gittes F, Howard J. 1994. The force exerted by a single kinesin molecule against a viscous load. Biophys. J. 67:766-81
116. Huxley A. 1957. Muscle structure and theories of contraction. Prog. Biophys. Biophys. Chem. 7:255-317
117. Im W, Seefeld S, Roux B. 2000. A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79:788-801
118. Irons B, Shrive N. 1983. Finite Element Primer. New York. Halsted
119. Israelachvili J. 1992. Intermolecular and Surface Forces. San Diego: Academic
120. Jacobs CR, Levenston ME, Beaupré GS, Simo JC, Carter DR. 1995. Numerical instabilities in bone remodeling simulations: the advantages of a node-based finite element approach. J. Biomech. 28: 449-59
121. Jacobs CR. 2000. The mechanobiology of cancellous bone structural adaptation. J. Rehab. Res. Dev. 37:209-16
122. Jacobson K, Sheets ED, Simson R. 1995. Revisiting the fluid mosaic model of membranes. Science 268:1441-42
123. Janeway CA, Travers P, Walport M, Schlomchik M. 2001. Immunobiology. New York: Garland. 5th ed.
124. Jeronimidis G. 2000. Structure-property relationships in biological materials. In Structural Biological Materials, ed. M Elices. Oxford, UK: Pergamon
125. Jiang Y, Levine H, Glazier JA. 1998. Possible cooperation of differential adhesion and chemotaxis in mound formation of Dictyostelium. Biophys. J. 75:2615-25
126. Johansson T, Meier P, Blickhan R. 2000. A finite-element model for the mechanical analysis of skeletal muscles. J. Theor. Biol. 206:131-49
127. Kansal AR, Torquato S, Harsh OR IV, Chiocca EA, Deisboeck TS. 2000. Simulated brain tumor growth dynamics using a three-dimensional cellular automaton. J. Theor. Biol. 203:367-82
128. Kansal AR, Torquato S, Harsh GR IV, Chiocca EA, Deisboeck TS. 2000. Cellular automaton of idealized brain tumor growth dynamics. Biosystems 55:119-27
129. Katti DR, Katti KS, Sopp JM, Sarikaya M. 2001. 3D finite element modeling of mechanical response in nacre-based hybrid nanocomposites. J. Theor. Comp. Polym. Sci. 11:397-404
130. Kellermeyer MS, Smith S, Granzier HL, Bustamante C. 1997. Folding-unfolding transitions in single titin molecules characterized by force-measuring laser tweezers. Science 276:1112-16
131. Ketchem RR, Hu W, Cross TA. 1993. High-resolution conformation of Gramicidin A in a lipid bilayer by solid-state NMR. Science 261:1457-60
132. Koeppe RE, Killian JA, Greathouse DV. 1994. Orientations of the tryptophan 9 and 11 side chains of the Gramicidin channel based on deuterium nuclear magnetic resonance spectroscopy. Biophys. J. 66:14-24
133. Kong Y-Y, Penninger JM. 2000. Molecular control of bone remodeling and osteoporosis. Exp. Gerontol. 35:947-56
134. Koontz JT, Charras GT, Guldberg RE. 2001. A microstructural finite element simulation of mechanically induced bone formation. J. Biomech. Eng. 123:607-12
135. Kowalczyk P. 2003. Elastic properties of cancellous bone derived from finite element models of parametrized microstructure cells. J. Biomech. 36:961-72
136. Kramers HA. 1940. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7:284-304
137. Kratky O, Porod G. 1949. Röntgenuntersuchung gelöster Fadenmoleküle. Rec. Trav. Chim. Pays-Bas. 68:1106-22
138. Kraynik AM, Reinelt DA, Princen HM. 1991. The nonlinear elastic behavior of polydisperse hexagonal foams and concentrated emulsions. J. Rheol. 35:1235-53
139. Kreis T, Vale R. 1999. Guidebook to the Cytoskeleton and Motor Proteins. Oxford, UK: Oxford Univ. Press
140. Kubik T, Pasowicz M, Tabor Z, Rokita E. 2002. Optimizing the assessment of age-related changes in trabecular bone. Phys. Med. Biol. 47:1543-53
141. Kurnikova M, Coalson R, Graf P, Nitzan A. 1999. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the Gramicidin A channel. Biophys. J. 76:642-56
142. Kurz JC, Williams RC Jr. 1995. Microtubule-associated proteins and the flexibility of microtubules. Biochemistry 34:13374-80
143. Kuyacak S, Andersen OS, Chung SH. 2001. Models of permeation in ion channels. Rep. Prog. Phys. 64:1427-72
144. Kyriacou SK, Mohamed A, Miller K, Neff S. 2002. Brain mechanics for neurosurgery: modeling issues. Biomech. Model. Mechanobiol. 1:151-64
145. Landau LD. 1965. Collected Papers of L.D. Landau, ed. D ter Haar. New York: Pergamon
146. Landau LD, Lifshitz EM. 1986. Theory of Elasticity. Oxford, UK: Butterworth-Heinemann. 3rd ed.
147. Langton CM, Haire TJ, Ganney PS, Dobson CA, Pagan MJ. 1998. A dynamic stochastic simulation of the mechanical properties of cancellous bone associated with osteoporosis. Bone 22:375-80
148. Latour RA Jr. 1999. Molecular modeling of biomaterial surfaces. Curr. Opin. Solid State Mater. Sci. 4:413-17
149. Latour RA Jr, Hench LL. 2002. A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces. Biomaterials 23:4633-48
150. Lakes RS. 1991. Deformation mechanisms of negative Poisson's ratio materials: structural aspects. J. Mater. Sci. 26:2287-92
151. Leibler S. 1989. Equilibrium statistical mechanics of fluctuating films and membranes. In Statistical Mechanics of Membranes and Surfaces, ed. D Nelson, T Piran, S Weinberg, pp. 45-103 Singapore: World Scientific
152. Leibler S, Huse DA. 1993. Porters versus rowers: a unified stochastic model for motor proteins. J. Cell Biol. 121:1357-68
153. Leitner DM, Brown FLH, Wilson KR. 2000. Regulation of protein mobility in cell membranes: a dynamic corral model. Biophys. J. 78:125-35
154. Lerner AL, Kuhn JL, Hollister SJ. 1998. Are regional variations in bone growth related to mechanical stress and strain parameters? J. Biomech. 31:327-35
155. LeSar R, Redondo A. 2004. An analytical model of bone remodeling. Bone. Submitted
156. Levine H. 1998. The dynamics of Dictyostelium development. Phys. A 249: 53-63
157. Lifshitz EM. 1956. Theory of molecular attractive forces. Sov. Phys. JETP 2:73-83
158. Lipowsky R, Sackmann E. 1995. The Structure and Dynamics of Membranes. Amsterdam: Elsevier
159. Luebeck EG, de Gunst MCM. 2001. A stereological method for the analysis of cell counts in tissue sections using 3-dimensional cellular automata. Math. Comp. Model. 33:1387-400
160. Luzzati V. 1968. X-ray diffraction studies of lipid-water systems. Biol. Membr. 1:71-123
161. Mackerle J. 1998. A finite element bibliography for biomechanics. Appl. Mech. Rev. 51:587-634
162. Mackerle J. 2000. Gradient-based refinement indicators in adaptive finite element analysis with special reference to sheet metal forming. Eng. Comput. 17:813-56
163. Maggelakis AA, Savakis AE. 2003. Modeling techniques in epidermal wound healing. See Ref. 294, pp. 89-118
164. Mamonov A, Coalson R, Nitzan A, Kurnikova M. 2003. The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single channel currents. Biophys. J. 84:1-15
165. Mansury Y, Kimura M, Lobo J, Deisboeck TS. 2002. Emerging pattern in tumor systems: simulating the complex dynamics of multicellular cluster structures by using a novel agent-based spatiotemporal agglomeration model. J. Theor. Biol. 219:343-70
166. Marée AFM, Hogeweg P. 2002. Modelling Dictyostelium discoideum morphogenesis: the culmination. Bull. Math. Biol. 64:327-53
167. Marsh D. 1990. CRC Handbook of Lipid Bilayers. Boca Raton, FL: CRC Press
168. Martin RB. 2000. Toward a unifying theory of bone remodeling. Bone 26:1-6
169. Martin RB. 2002. Is all cortical bone remodeling initiated by microdamage? Bone 30:8-13
170. Martin RB. 2003. Fatigue damage, remodeling, and the minimization of skeletal weight. J. Theor. Biol. 220:271-76
171. McCammon JA, Gelin BR, Karplus M, Wolynes PG. 1976. The hinge-bending mode in lysozyme. Nature 262:325-26
172. McCammon JA, Harvey SC. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge, UK: Cambridge Univ. Press
173. Meaney DF. 2003. Relationship between structural modeling and hyperelastic material behavior: application to CNS white matter. Biomech. Model. Mechanobiol. 1:279-93
174. Meinhardt H. 1982. Models of Biological Pattern Formation. London: Academic
175. Meinhardt H, Klinger M. 1987. A model for pattern formation on the shells of molluscs. J. Theor. Biol. 126:63-89
176. Mendelson RA, Morales MF, Botts J. 1973. Segmental flexibility of SI moiety of myosin. Biochemistry 12:2250-55
177. Merz BR, Müller R, Lengsfeld M. 2003. Automated three dimensional finite element modeling techniques of bone and bone implant systems. See Ref. 294, pp. 1-37
178. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AN, Teuer E. 1953. Equation of state calculations by fast computer machines. J. Chem. Phys. 21: 1087-92
179. Meunier J, Langevin D, Boccara N, ed. 1987. Physics of Amphiphilic Layers. Berlin: Springer-Verlag
180. Milik M, Skolnick J. 1993. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins 15:10-25
181. Mohanty J, Ninham BW. 1976. Dispersion Forces. London: Academic
182. Muller-Borer BJ, Erdman DJ, Buchanan JW. 1994. Electrical coupling and impulse propagation in anatomically modeled ventricular tissue. IEEE Trans. Biomed. Eng. 41:445-54
183. Murray JD. 1993. Mathematical Biology. Berlin: Springer. 2nd ed.
184. Nabhani F, Wake M. 2002. Computer modelling and stress analysis of the lumbar spine. J. Mater. Proc. Tech. 127:40-47
185. Nagle JF, Goldstein M. 1985. Decomposition of entropy and enthalpy for the melting transition of polyethylene. Macromolecules 18:2643-52
186. Nelson DR. 2002. Defects and Geometry in Condensed Matter Physics. Cambridge, UK: Cambridge Univ. Press
187. Ni H, Datta AK, Torrance KE. 1999. Moisture transport in intensive microwave heating of biomaterials: a multiphase porous media model. Int. J. Heat Mass Transfer 42:1501-12
188. Osborn M, Webster R, Weber K. 1978. Individual microtubules viewed by immunofluorescence and electron microscopy in the same PtK2 cell. J. Cell Biol. 77:R27-34
189. Ott SM. 2002. Theoretical and methodological approach. In Principles of Bone Biology, ed. JP Bilezikian, LG Raisz, GA Rodan, pp. 303-19. New York: Academic. 2nd ed.
190. Ouchi NB, Glazier JA, Rieu J-P, Upadhyaya A, Sawada Y. 2003. Improving the realism of the cellular Potts model in simulations of biological cells. Phys. A 329:451-58
191. Papka SD, Kyriakides S. 1994. Inplane compressive response and crushing of honeycomb. J. Mech. Phys. Solids 41:571-92
192. Partenskii MB, Jordan PC. 1992. Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches. Q. Rev. Biophys. 24:477-510
193. Pastor RW. 1994. Molecular dynamics and Monte Carlo simulations of lipid bilayers. Curr. Opin. Struct. Biol. 4:486-92
194. Peleg M. 1994. A model of mechanical changes in biomaterials at and around their glass transition. Biotechnol. Prog. 10:385-88
195. Peskin CS, Odell GM, Oster GF. 1993. Cellular motions and thermal fluctuations: the Brownian ratchet. Biophys. J. 65:316-24
196. Peterson MA, Strey H, Sackmann E. 1992. Theoretical and phase contrast microscope eigenmode analysis of erythrocyte flicker: amplitudes. J. Phys. France 2:1273-85
197. Petrache HI, Feller SE, Nagle JE 1997. Determination of component volumes of lipid bilayers from simulations. Biophys. J. 70:2237-42
198. Plum GE, Breslauer KJ. 1995. The thermodynamics of DNA structures that contain lesions or guanine tetrads. Curr. Opin. Struct. Biol. 5:682-90
199. Pohorile A, Wilson MA. 2001. Unassisted and assisted ion transport across membranes: insights from computer simulations. Cell. Biol. Mol. Lett. 6:369-74
200. Poshusta AK, Bowman CN, Anseth KS. 2002. Application of a kinetic gelation simulation to the characterization of in situ crosslinking biomaterials. J. Biomater. Sci. Polym. Ed. 13:797-815
201. Pratt LR, Hummer G, eds. 1999. Simulation and Theory of Electrostatic Interactions in Solution. AIP Conference Proceedings 492. New York: Am. Inst. Phys.
202. Pullman A. 1987. Energy profiles in the Gramicidin-A channel. Q. Rev. Biophys. 20:173-200
203. Quinn PJ, Cherry RJ, eds. 1992. Structural and Dynamics Properties of Lipids and Membranes. London: Portland
204. Rand RP, Parsegian VA. 1989. Hydration forces between phospholipid bilayers. Biochym. Biophys. Acta 988:351-76
205. a. LeSar R, Rickman JM, Clarke, DR, Rühle M, Bravman JC, eds. 2002. Annual Review of Materials Research. Vol. 32. Palo Alto, CA: Annual Reviews. 498 pp.
206. Raabe D. 2002. Cellular automata in materials science with particular reference to recrystallization simulation. See Ref. 204a, pp. 53-76
207. Rappaport DC. 1995. The Art of Molecular Dynamics Simulations. Cambridge, UK: Cambridge Univ. Press
208. Ramtani S, Zidi M. 1999. Damagedbone remodeling theory: thermodynamical approach. Mech. Res. Commun. 26: 701-8
209. Ramtani S, Zidi M. 2001. A theoretical model of the effect of continuum damage on a bone adaptation model. J. Biomech. 34:471-79
210. Reeve JA. 1986. A stochastic analysis of iliac trabecular bone dynamics, Clin. Orthop. 213:264-68
211. Rief M, Mehta AD, Rock RS, Spudich JA, Mooseker MS, Cheney RE. 2000. Myosin-V stepping kinetics: a molecular model for processivity. Proc. Natl. Acad. Sci. USA 97:9482-86
212. Rivier N. 1982. Recent results on the ideal structure of glasses. J. Phys. 43:C9-91
213. Roux B. 2002. Computational studies of the Gramicidin channel. Acc. Chem. Res. 35:366-75
214. Roux B, Bernèche S. 2002. On the potential functions used in molecular dynamics simulations of ion channels. Biophys. J. 82:1677-84
215. Roux B, Karplus M. 1994. Molecular dynamics simulations of the Gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 23:731-61
216. Ruan XG, Hu RC. 2002. Proc. 4th World Congress in Intelligent Control and Automation. 1-4:2266-69. New York. IEEE
217. Saffman PG. 1976. Brownian motion in thin sheets of viscous fluid. J. Fluid Mech. 73:593-602
218. Saffman PG, Delbrück M. 1975. Brownian motion in biological membranes. Proc. Natl. Acad. Sci. USA 72:3111-13
219. Safran SA. 1994. Statistical Thermodynamics of Surfaces, Interfaces and Membranes. Reading, MA: Addison-Wesley
220. Salzberg SL, Searls DB, Kasif S, eds. 1998. Computational Methods in Molecular Biology. Amsterdam: Elsevier
221. Sander EA, Shimko DA, Dee KC, Nauman EA. 2003. Microscale and macroscale examination of human vertebral cancellous bone using combined cellular solid models. Biomech. Model Mechanobiol. 2:97-107
222. Sander LM. 2000. Diffusion-limited aggregation: a kinetic critical phenomenon? Contemp. Phys. 41:203-18
223. Sansom MSP. 1998. Models and simulations of ion channels and related membrane proteins. Curr. Opin. Struct. Biol. 8:237-44
224. Saville N, Hogeweg P. 1997. The modelling of slug morphogenesis. J. Theor. Biol. 22:437-67
225. Saxton M, Jacobson K. 1997. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 26:373-99
226. Schliwa M. 1986. The Cytoskeleton: An Introductory Survey. New York: Springer-Verlag
227. Schoenberg M. 1985. Equilibrium muscle cross-bridge behavior: theoretical considerations. Biophys. J. 48:467-75
228. Schmauder S. 2002. Computational mechanics. See Ref. 204a, pp. 437-65
229. Secrest D. 1996. Osmotic pressure and the effects of gravity on solutions. J. Chem. Ed. 73:998-1000
230. Sedivy R, Thurner S, Budinsky AC, Kostler WJ, Zielinski CC. 2002. Shortterm rhythmic proliferation of human breast cancer cell lines: surface effects and fractal growth patterns. J. Pathol. 197:163-69
231. Shi J, Le Maguer M, 2003. Mass transfer in cellular material at solid-liquid contacting interface. Lebensm. Wissen. Technol. 36:3-11
232. Singer SJ, Nicolson GL. 1972. The fluid mosaic model of the structure of cell membranes. Science 175:720-31
233. Servuss RM, Helfrich W. 1989. Mutual adhesion of lecithin membranes at ultralow tensions. J. Phys. France 50:809-27
234. Skalak R, Farrow DA, Roger A. 1997. Kinematics of surface growth. J. Math. Biol. 35:869-907
235. Smith SB, Finzi L, Bustamante C. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258: 1122-26
236. Spector AA, Ameen M, Schmiedt RA. 2002. Modeling three-dimensional deformation of outer hair cells in the cochlea. Biomech. Model Mechanobiol. 1:123-35
237. Srolovitz DJ, Anderson MP, Grest GS, Sahni PS. 1983. Grain growth in two dimensions. Scr. Metall. 17:241-46
238. Srolovitz DJ, Yang WH, Najafabadi R, Wang HY, LeSar R. 1992. Microstructural and segregation effects in the fracture of polycrystals. In Atomic-Level Properties of Interface Materials, ed. D Wolf, S Yip, pp. 691-702. London: Chapman and Hall
239. Stamenovic S, Ingber DE. 2002. Models of cytoskeletal mechanics of adherent cells. Biomech. Model Mechanobiol. 1:95-108
240. Stanley HE. 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford, UK: Oxford Univ. Press
241. Steigenberger J. 2003. Contribution to the mechanics of worm-like motion systems and artificial muscle. Biomech. Model Mechanobiol. 2:37-57
242. Stein WD. 1990. Channels, Carriers and Pumps: An Introduction to Membrane Transport. San Diego, CA: Academic
243. Stevens A. 2000. A stochastic cellular automaton modeling gliding and aggregation of Myxobacteria. SIAM J. Appl. Math. 61:172-82
244. Stevens M. 2003. Modeling selfassembly in a variety of molecular systems. cint.lanl.gov/docs/posters/Mark%20StevensMain.pdf/01/10/04
245. Stokke BT, Mikkelsen A, Elgsaeter A. 1985. Human erythrocyte spectrin dimer intrinsic viscosity: temperature dependence and implications for the molecular basis of the erythrocyte membrane free energy. Biochim. Biophys. Acta 816: 102-10
246. Stölken JS, Kinney JH. 2003. On the importance of geometric nonlinearity in finite-element simulations of trabecular bone failure. Bone 33:494-504
247. Summers AP, Koob TJ. 2002. The evolution of tendon-morphology and material properties. Comp. Biochem. Physiol. A 133:1159-70
248. Tabor Z, Rokita E. 2002. Stochastic simulations of remodeling applied to a two-dimensional trabecular bone structure. Bone 31:413-17
249. Tanford C. 1983. Mechanism of free energy coupling in active transport. Annu. Rev. Biochem. 52:379-409
250. Tawada K, Sekimoto K. 1991. Protein friction exerted by motor enzymes through a weak-binding interaction. J. Theor. Biol. 150:193-200
251. Tayyar S, Weinhold PS, Butler RA, Woodard JC, Zardiackas LD, et al. 1999. Computer simulation of trabecular remodeling using a simplified structural model. Bone 25:733-39
252. Tieleman DP, Berensden HJC, Sansom MSP. 1999. An alamethicin channel in a bilayer: molecular dynamics simulations. Biophys. J. 76:1757-69
253. Tieleman DP, Biggin PC, Smith GR, Sansom MS. 2001. Simulation approaches to ion channel structurefunction relationships. Q. Rev. Biophys. 34:473-561
254. Tolédano P, Neto AMF. 1998. Phase Transitions in Complex Fluids. Singapore: World Scientific
255. Thomsen JS, Mosekilde L, Boyce RW, Mosekilde E. 1994. Stochastic simulation of vertebral trabecular bone remodeling. Bone 15:655-66
256. Thomsen JS, Mosekilde L, Mosekilde E. 1996. Quantification of remodeling parameter sensitivity: assessed by a computer simulation model. Bone 19:505-11
257. Tschoegl NW. 1989. The Phenomenalogical Theory of Linear Viscoelastic Behavior: An Introduction. Berlin: Springer-Verlag
258. Tsili MC. 2000. Theoretical solutions for internal bone remodeling of diaphyseal shafts using adaptive elasticity theory. J. Biomech. 33:235-39
259. Tskhovrebova L, Trinick J, Sleep JA, Simmons RM. 1997. Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature 387:308-12
260. Tsubota K, Adachi T. 2003. Comparison of mechanical quantities at single trabecular level as candidates for bone remodeling stimuli. In Computational Fluid and Solid Mechanics, ed. KJ Nathe, pp. 1833-35. Amsterdam: Elsevier
261. Turner S, Sherratt JA. 2002. Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model. J. Theor. Biol. 216:85-100
262. Turing AM. 1952. The chemical basis of morphogenesis. Philos. Trans. R. Soc. London Ser. B 237:37-72
263. Urry DW. 1971. The Gramicidin A transmembrane channel: a proposed pi(L,D) helix. Proc. Natl. Acad. Sci. USA 68:672-76
264. Vaidehi N, Goddard WA III. 2001. Atomic-level simulation and modeling of biomacromolecules. See Ref. 293, pp. 161-88.
265. van der Linden JC, Verhaar JAN, Weinans H. 2001. A three-dimensional simulation of age related remodeling in trabecular bone. J. Bone Min. Res. 16:688-96
266. Vanderzande C. 1998. Lattice Models of Polymers. Cambridge, UK: Cambridge Univ. Press
267. Venable RM, Zhang Y, Hardy BJ, Pastor RW. 1993. Molecular dynamics simulation of lipid bilayer and hexadecane: an investigation into the fluidity of membranes. Science 262:223-28
268. Venier P, Maggs AC, Carlier MF, Pantaloni D. 1994. Analysis of microtubule rigidity using hydrodynamic flow and thermal fluctuations. J. Biol. Chem. 269:13353-60
269. Verwey EJW, Overbeek JTG. 1948. Theory of Stability of Lyophobic Colloids. Amsterdam: Elsevier
270. Vincent JFV. 1990. Structural Biomechanics, 2nd edition. Princeton, NJ: Princeton Univ. Press
271. Voter AF, Montalenti F, Germann TC. 2002. Extending the time scale in atomistic simulation of materials. See Ref. 204a, pp. 321-46
272. Deleted in proof
273. Waddington CH, Cowe J. 1969. Computer simulation of a molluscan pigmentation pattern. J. Theor. Biol. 25:219-25
274. Wang W, Donini O, Reyes CM, Kollman PA. 2001. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis and protein-ligand, protein-protein and protein-nucleic acid non-covalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30:211-43
275. Wang X, Dumas GA. 2002. Simulation of bone adaptive remodeling using a stochastic process as loading history. J. Biomech. 35:375-80
276. Ward JP, King JR, Koerber AJ, Croft JM, Stockett RE, Williams P. 2003. Early development and quorum sensing in bacterial biofilms. J. Math. Biol. 47:23-55
277. Warren WE, Kraynik AM. 1987. Foam mechanics: the linear elastic response of two-dimensional spatially periodic cellular materials. Mech. Mater. 6:27-37
278. Warren WE, Kraynik AM. 1988. The linear elastic properties of open-cell foams. J. Appl. Mech. 55:341-46
279. Weaire D, Rivier N. 1984. Soaps, cells and statistics: random patterns in two dimensions. Contemp. Phys. 25:59-99
280. Weiner S, Wagner HD. 1998. The material bone: structure-mechanical function relations. Annu. Rev. Mater. Sci. 28:271-98
281. Weerts AH, Lian G, Martin D. 2003. Modeling rehydration of porous biomaterials: anisotropy effects. J. Food Sci. 68:937-42
282. Westmoreland PR, Kollman PA, Chaka AM, Cummings PT, Morokuma K, et al. 2002. Applying Molecular and Materials Modeling. Dordrecht: Kluwer
283. Wolfram S. 1984. Cellular automata as models of complexity. Nature 311:419-24
284. Yamakawa H. 1971. Modern Theory of Polymer Solutions. New York: Harper & Row
285. Yamakawa H. 1997. Helical Wormlike Chains in Polymer Solutions. New York: Springer-Verlag
286. Yguerabide J, Epstein HF, Stryer L. 1970. Segmental flexibility in an antibody molecule. J. Mol. Biol. 51:573-90
287. Young TH, Hsu JP, Nien TW. 2003. Kinetic modelling of blood glucose variation in a bioartificial pancreas, biomaterials. Biomaterials 24:2251-56
288. Zannoni C, Mantovani R, Viceconti M. 1999. Material properties assignment to finite element models of bone structures: new methods. Med. Eng. Phys. 20:735-40
289. Zhdanov VP, Kasemo B. 2003. Simulation of morphogenesis: from a pluripotent stem cell to an ensemble of differentiated cells. Phys. Chem. Chem. Phys. 5:1433-39
290. Zidi M, Ramtani S. 1999. Bone remodeling theory applied to the study of n unit elements model. J. Biomech. 32:743-47
291. Zienkiewicz OC, Taylor RL. 1991. The Finite Element Method. 4th Edition. Vol. 2. New York: Mcgraw-Hill
292. Zienkiewicz OC, Taylor RL. 1994. The Finite Element Method. 4th Edition. Vol. 1. New York: Mcgraw-Hill
293. -1 regime by microinterferometry combined with fast image processing. Phys. Rev. A. 46:7998-8001
294. Bower, JM, Bolouri H, eds. 2001. Computational Modeling of Genetic and Biochemical Networks. Cambridge, MA: MIT Press
295. Leondes CT, ed. 2003. Computational Methods in Biophysics, Biomaterials, Biotechnology, and Medical Systems, Vol. 2. Boston: Kluwer
296. Karsenty G. 2003. Complexities of skeletal biology. Nature 423:316-18
297. Helms JA, Schneider RA. 2003. Cranial skeletal biology. Nature 423:326-31
298. Boyle WJ, Simonet WS, Lacey DL. 2003. Osteoclast differentiation and activation. Nature 423:337-42
299. Harada SI, Rodan GA. 2003. Control of osteoblast function and regulation of bone mass. Nature 423:349-55
300. Bell GI. 1978. Models for the specific adhesion of cells to cells. Science 200:618-27
301. Ermentrout GB, Campbell J, Oster G. 1986. A model for shell patterns based on neural activity. Veliger 28:369-88