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@BOOK{Malvern:69,
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@BOOK{Pironneau:89,
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@BOOK{Simo:95,
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@BOOK{Thomas:61,
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AUTHOR = "C. A. Truesdell and R. A. Toupin",
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PUBLISHER = "Springer-Verlag, Berlin",
YEAR = {1960},
}

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@CONFERENCE{Willam:87,
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@CONFERENCE{Yu:91,
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     EDITOR  = {K. J. Willam},
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@CONFERENCE{Hvorslev:61,
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     EDITOR  = {},
     PUBLISHER  = {},
     PAGES   = {169--273} }

@CONFERENCE{Ingraffea:85,
     AUTHOR = "A. R. Ingraffea and V. Saouma",
     TITLE  = {Numerical {M}odeling of {D}iscrete {C}rack {P}ropagation in {R}einforced and {P}lain {C}oncrete},
     BOOKTITLE = {Fracture Mechanics of Concrete},
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@CONFERENCE{Larsson:95,
     AUTHOR = "R. Larsson and K. Runesson and M. Akesson",
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     BOOKTITLE = {Proceedings of Computational Plasticity IV},
     YEAR    = 1995,
     EDITOR  = {D. R. J. Owen and E. O\~nate and E. Hinton},
     PUBLISHER  = {CIMNE, Barcelona},
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@CONFERENCE{NeedlemanTver:84,
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     YEAR    = 1984,
     EDITOR  = {J. T. Oden and G. F. Carey},
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     PAGES   = {94--157} }


@CONFERENCE{Onate:87,
     AUTHOR = "E. O\~nate and S. Oller and J. Oliver and J. Lubliner",
     TITLE  = {A {C}onstitutive {M}odel for {C}racking of {C}oncrete based on the {I}ncremental {T}heory of {P}lasticity},
     BOOKTITLE = {Proceedings of the International Conference on Computational Plasticity, Models, Software and Applications},
     YEAR    = 1987,
     EDITOR  = {D. R. J. Owen and E. Hinton and E. O\~nate},
     PUBLISHER  = {Pineridge Press, Swansea},
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@CONFERENCE{Simo:98,
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     TITLE  = {Numerical {A}nalysis of {C}lassical {P}lasticity},
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     YEAR    = {},
     EDITOR  = {P. G. Ciarlet and J. L. Lions},
     PUBLISHER  = {},
     PAGES   =  {}}

@CONFERENCE{Taylor:38,
     AUTHOR = "G. I. Taylor",
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     EDITOR  = {J. M. Lessels},
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     PAGES   =  {}}

@MANUAL{FEAPmanual,
         AUTHOR= "R. L. Taylor",
         TITLE = {{F}{E}{A}{P} - {A} {F}inite {E}lement {A}nalysis {P}rogram},
         ORGANIZATION = {University of California at Berkeley},
         ADDRESS = {Berkeley, CA},
         MONTH = {September},
         YEAR  = {1999}
        }

% My additions go below

@BOOK{Alberts:02,
AUTHOR = "B. Alberts and A. Johnson and J. Lewis and M. Raff and K. Roberts and P. Walter",
TITLE = {Molecular {B}iology of the {C}ell},
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YEAR = 2002,}

@ARTICLE{Calve:04,
     AUTHOR = "S. Calve and R.G. Dennis and P.E. Kosnik and K. Baar and K. Grosh and E.M. Arruda",
     TITLE  = {{Engineering of functional tendon}},
     JOURNAL = "Tissue Engineering",
     VOLUME  = 10,
     PAGES   = "755--761",
     YEAR    = {2004}}

@ARTICLE{HarriganHamilton:93,
           AUTHOR = "T. P. Harrigan and J. J. Hamilton",
     TITLE  = {Finite element simulation of adaptive bone remodelling: A stability criterion and a time stepping method},
     JOURNAL= ijnme,
     YEAR   = 1993,
     VOLUME = 36,
     PAGES  = "837--854"}

@BOOK{sbromadill,
     AUTHOR = "S. Bromberg and K. A. Dill",
     TITLE  = {{Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology}},
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     YEAR    = 2002 }

@ARTICLE{Sengersetal:2004,
     AUTHOR = {B. G. Sengers and C. W. J. Oomens and F. P. T. Baaijens},
     TITLE  = {An integrated finite-element approach to mechanics, transport and biosynthesis in tissue engineering},
     JOURNAL = jbme,
     YEAR    = 2004,
     VOLUME  = 126,
     NUMBER  = {},
     PAGES   = {82--91} }

@ARTICLE{Provenzanoetal:2003,
     AUTHOR = "P. P. Provenzano and D. A. Martinez and R. E. Grindeland and K. W. Dwyver and J. Turner and A. C. Vailas and R. Vanderby",
     TITLE  = {{Hindlimb unloading alters ligament healing}},
     JOURNAL = "Journal of Applied Physiology",
     YEAR    = 2003,
     VOLUME  = 94,
     PAGES   = "314--324" }




@ARTICLE{tezduyarsupg,
           AUTHOR = "T. Tezduyar and S. Sathe",
     TITLE  = {Stabilization Parameters in {SUPG} and {PSPG} Formulations}, 
     JOURNAL= "Journal of {C}omputational and {A}pplied {M}echanics", 
     YEAR   = 2003,
     VOLUME = 4,
     PAGES  = "71-88"}

@BOOK{cavitationchris,
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     TITLE  = {{Cavitation and Bubble Dynamics}},
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@Article{kuhlremod05 ,
language = {English},
copyright = {Copyright 2005, IEE},
title = {Remodeling of biological tissue: Mechanically induced reorientation of a transversely isotropic chain network},
journal = {Journal of the Mechanics and Physics of Solids},
author = {Kuhl, E. and Garikipati, K. and Arruda, E.M. and Grosh, K.},
volume = { 53},
number = { 7},
year = {2005},
pages = {1552 - 73},
issn = {0022-5096},
abstract = {A new class of micromechanically motivated chain network models for soft biological tissues is presented. On the microlevel, it is based on the statistics of long chain molecules. A wormlike chain model is applied to capture the behavior of the collagen microfibrils. On the macrolevel, the network of collagen chains is represented by a transversely isotropic eight chain unit cell introducing one characteristic material axis. Biomechanically induced remodeling is captured by allowing for a continuous reorientation of the predominant unit cell axis driven by a biomechanical stimulus. To this end, we adopt the gradual alignment of the unit cell axis with the direction of maximum principal strain. The evolution of the unit cell axis' orientation is governed by a first-order rate equation. For the temporal discretization of the remodeling rate equation, we suggest an exponential update scheme of Euler-Rodrigues type. For the spatial discretization, a finite element strategy is applied which introduces the current individual cell orientation as an internal variable on the integration point level. Selected model problems are analyzed to illustrate the basic features of the new model. Finally, the presented approach is applied to the biomechanically relevant boundary value problem of an in vitro engineered functional tendon construct. [All rights reserved Elsevier]},
keywords = {biological tissues;biomechanics;finite element analysis;micromechanics;molecular biophysics;physiological models;proteins;},
} 

@Article{mauck:03 ,

language = {English},

copyright = {Copyright 2003, IEE},

title = {Modeling of neutral solute transport in a dynamically loaded porous permeable gel: implications for articular cartilage biosynthesis and tissue engineering},

journal = {Transactions of the ASME. Journal of Biomechanical Engineering},

journal = {Trans. ASME, J. Biomech. Eng. (USA)},

author = {Mauck, R.L. and Hung, C.T. and Ateshian, G.A.},

volume = { 125},

number = { 5},

year = {2003},

pages = {602 - 14},

issn = {0148-0731},

} 

@ARTICLE{simotarnow:1992a,
           AUTHOR = "J. C. Simo and N. Tarnow",
     TITLE  = {Exact energy-momentum conserving algorithms and symplectic schemes for nonlinear dynamics},
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     VOLUME = 100,
     PAGES  = "63--116"}

@article{simotarnow:1992b,
title = {The discrete energy-momentum method. Conserving algorithms for nonlinear elastodynamics},
journal = {Zeitschrift fur Angewandte Mathematik und Physik},
author = "J. C. Simo and N. Tarnow",
volume = { 43},
number = { 5},
year = {1992},
pages = {757 - 92},} 

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@ARTICLE{Klischetal:2001,
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     TITLE  = {{A theory of volumetric growth for compressible elastic biological materials}},
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     YEAR    = 2001,
     VOLUME  = 6,
     PAGES   = "551--575" }

@UNPUBLISHED{remodelpaper,
     AUTHOR = "K. Garikipati and E. M. Arruda
      and K. Grosh and S. Calve",
     TITLE  = {{A continuum treatment of remodelling in biological tissue: Self assembly and evolving reference configurations}},
     NOTE   = "Submitted to {\sl J. Mech. Phys. Sol.}",
     MONTH   = {},
     YEAR    = {2003}}

@UNPUBLISHED{Gonzalez:94,
           AUTHOR = "O. Gonzalez",
     TITLE  = {Computational {P}lasticity in {P}rincipal {S}tretches: {C}losed-{F}orm {E}xpressions for {E}lastoplastic {M}oduli},
     NOTE   = "Private communication",
     MONTH   = {},
     YEAR    = 1994}

@ARTICLE{HumphreyRajagopal:02,
     AUTHOR = "J. D. Humphrey and Rajagopal",
     TITLE  = {{A constrained mixture model for growth and remodeling of soft tissues}},
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     YEAR    = 2002,
     VOLUME  = 12,
     NUMBER  = 3,
     PAGES   = "407--430" }


@ARTICLE{KlischHoger:2003,
     AUTHOR = "S. M. Klisch and A. Hoger",
     TITLE  = {{Volumetric growth of thermoelastic materials and mixtures}},
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@ARTICLE{Brewardetal:2003,
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     TITLE  = {{A multiphase model describing vascular tumour growth}},
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     VOLUME  = 65,
     PAGES   = "609--640" }

@ARTICLE{PreziosiFarina:2002,
     AUTHOR = "L. Preziosi and A. Farina",
     TITLE  = {{On Darcy's Law for growing porous media}},
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     PAGES   = "485--491" }


@BOOK{Fung:1993,
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     TITLE  = {{Biomechanics: Mechanical properties of living tissues}},
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     EDITION = {2}}

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     PUBLISHER = "McGraw-Hill, New York",
     YEAR= 2003,
     EDITION = {9}}

Vander, Sherman, Luciano's Human Physiology: The Mechanisms of Body Function

@BOOK{Terzaghi:1943,
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@BOOK{DeGrootMazur:1984,
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     TITLE  = {{Non-equilibrium thermodynamics.}},
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@BOOK{deBoer:2000,
     AUTHOR = "R. de {B}oer",
     TITLE  = {{Theory of {P}orous {M}edia: {H}ighlights in {H}istorical {D}evelopment and {C}urrent {S}tate}},
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     YEAR    = 2000,}

@ARTICLE{Lee:1969,
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     VOLUME  = 36,
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@PHDTHESIS{Gonzalezphd:1996,
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     TITLE  = {Design and analysis of conserving integrators for nonlinear Hamiltonian systems with
symmetry},
     SCHOOL = {Stanford University},
     YEAR   = 1996}

@Article{namyetal:04,
  author = {P. Namy and J. Ohayon and P. Tracqui},
  title = {{Critical conditions for pattern formation and in vitro tubulogenesis driven by cellular traction fields}},
  journal = {Journal of Theoretical Biology},
  volume = {227},
  pages = {103--120},
  year = {2004}
}

@Article{calveetal:07,
  author = {Calve, S. and Lytle, I. F. and Ma, J. and Grosh, K. and Brown, D. L. and Arruda, E. M.},
  title = {{In vivo conditioning increases tensile strength and collagen content of self-assembled tendon constructs}},
  journal = {{\em In preparation}},
  volume = {},
  pages = {},
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@article{3763321 ,

language = {English},

copyright = {Copyright 1990, IEE},

title = {Effects of friction on the unconfined compressive response of articular cartilage: a finite element analysis},

journal = {Transactions of the ASME. Journal of Biomechanical Engineering},

journal = {Trans. ASME, J. Biomech. Eng. (USA)},

author = {Spilker, R.L. and Jun-Kyo Suh and Mow, V.C.},

volume = { 112},

number = { 2},

year = {1990/05/},

pages = {138 - 46},

issn = {0148-0731},

abstract = {A finite element analysis is used to study a previously unresolved issue of the effects of platen-specimen friction on the response of the unconfined compression test; effects of platen permeability are also determined. The finite element formulation is based on the linear KLM biphasic model for articular cartilage and other hydrated soft tissues. A Galerkin weighted residual method is applied to both the solid phase and the fluid phase, and the continuity equation for the intrinsically incompressible binary mixture is introduced via a penalty method. The solid phase displacements and fluid phase velocities are interpolated for each element in terms of unknown nodal values, producing a system of first order differential equations which are solved using a standard numerical finite difference technique. An axisymmetric element of quadrilateral cross-section is developed and applied to the mechanical test problem of a cylindrical specimen of soft tissue in unconfined compression. These studies show that interfacial friction plays a major role in the unconfined compression response of articular cartilage specimens with small thickness to diameter ratios},

keywords = {biomechanics;finite element analysis;friction;},

note = {friction effects;unconfined compressive response;articular cartilage;finite element analysis;platen-specimen friction;platen permeability;linear KLM biphasic model;hydrated soft tissues;Galerkin weighted residual method;solid phase;fluid phase;continuity equation;first order differential equations;quadrilateral cross-section;cylindrical specimen;},

} 





@inproceedings{spilkersuh1990 ,
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