Indiana University Department of Physics - James A. Glazier

Publications

Full Text: Dynamics of Cellular Patterns | PDF (9038 KB)
By Section:
Preface PDF (431 KB)
Chapter I PDF (191 KB)
Chapter II PDF (774 KB)
Chapter III PDF (220 KB)
Chapter IV PDF (1081 KB)
Chapter V PDF (1882 KB)
Chapter VI PDF (1125 KB)
Chapter VII PDF (448 KB)
Chapter VIII PDF (112 KB)
Chapter IX PDF (272 KB)
Chapter X PDF (1479 KB)
Chapter XI PDF (149 KB)
References PDF (891 KB)


Scientific:

  1. “Structure of Arnold Tongues and the f(α) Spectrum for Period Doubling: Experimental Results,” James A. Glazier, Mogens H. Jensen, Joel Stavans, and Albert Libchaber, Physical Review A 34, 1621 (1986).
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  2. “Dynamics of the Two-Dimensional Soap Froth,” James A. Glazier, S. P. Gross, and Joel Stavans, Physical Review A 36, 306 (1987).
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  3. “f(α) Curves: Experimental Results,” James A. Glazier, Gemunu H. Gunaratne, and Albert Libchaber, Physical Review A 37, 523 (1988).
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  4. “Quasiperiodicity and Dynamical Systems: An Experimentalists's View,” James A. Glazier and Albert Libchaber, IEEE Transactions on Circuits and Systems 35, 790 (1988). Reprinted in Hao Bai-Lin, Chaos II, (World Scientific, 1990), 299.
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  5. “Trajectory Scaling Functions at the Onset of Chaos: Experimental Results,” Andrew L. Belmonte, Michael J. Vinson, James A. Glazier, Gemunu H. Gunaratne, and Brian Kenny, Physical Review Letters 61, 539 (1988).
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  6. “Soap Froth Revisited: Dynamical Scaling in the Two-Dimensional Froth,” Joel Stavans and James A. Glazier, Physical Review Letters 62, 1318 (1989).
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  7. “Chaos and the Analysis of Experimental Data,” James A. Glazier, in Nonlinear Dynamics, proceedings of a conference in Bologna Italy, May 1988 (World Scientific, 1989), 250.
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  8. “Non-Ideal Effects in the Two-Dimensional Soap Froth,” James A. Glazier and Joel Stavans, Physical Review A 40, 7398 (1989).
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  9. “Coarsening in the Two-Dimensional Soap Froth and the Large-Q Potts Model: A Detailed Comparison,” James A. Glazier, Michael P. Anderson and Gary S. Grest, Philosophical Magazine B 62, 615 (1990).
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  10. “Ideal Two-Dimensional Grain Growth,” James A. Glazier, Gary S. Grest, and Michael P. Anderson, in Simulation and Theory of Evolving Microstructures, Michael P. Anderson and Anthony D. Rollett, editors, (The Minerals, Metals and Materials Society, Warrendale, PA, 1990) 41.
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  11. “Dispersive Chaos in One-Dimensional Traveling-Wave Convection,” Paul R. Kolodner, James A. Glazier, and Hugh L. Williams, Physical Review Letters 65, 1579 (1990).
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  12. “Interaction of Localized Pulses of Travelling-Wave Convection with Propagating Disturbances,” Paul R. Kolodner and James A. Glazier, Physical Review A 42, 7504 (1990).
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  13. “Dispersive Chaos,” James A. Glazier, Paul R. Kolodner, and Hugh L. Williams, Journal of Statistical Physics 64, 945 (1991).
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  14. “Interaction of Nonlinear Pulses in Convection in Binary Fluids,” James A. Glazier and Paul R. Kolodner, Physical Review A 43, 4269 (1991).
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  15. “Effects of Lattice Anisotropy and Temperature on Domain Growth in the Two-Dimensional Potts Model,” Elizabeth A. Holm, James A. Glazier, David J. Srolovitz, and Gary S. Grest, Physical Review A 43, 2662 (1991).
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  16. “Investigation of an Elementary Model for Magnetic Froth,” Denis Weaire, F. Bolton, Pierre Molho, and James A. Glazier, Journal of Physics: Condensed Matter 3, 2101 (1991).
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  17. “Modelling Grain Growth and Soap Froth Coarsening: Past, Present and Future,” Denis Weaire and James A. Glazier, Materials Science Forum 94-96, 27 (1992).
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  18. “Comparison of Soap Froth and Simulation of Large-Q Potts Model,” S. Ling, Michael P. Anderson, Gary S. Grest and James A. Glazier, Materials Science Forum 94-96, 39 (1992).
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  19. “The Kinetics of Cellular Patterns,” James A. Glazier and Denis Weaire, Journal of Physics: Condensed Matter 4, 1867 (1992).
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  20. “Global Fractal Dimension of Human DNA Sequences Treated as Pseudorandom Walks,” C. Berthelsen, James A. Glazier, and Mark H. Skolnick, Physical Review A 45, 8902-8913 (1992).
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  21. “Simulation of Biological Cell Sorting Using a Two-Dimensional Extended Potts Model,” François Graner and James A. Glazier, Physical Review Letters 69, 2013-2016 (1992).
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  22. “Coarsening in Two-Dimensional Soap Froths and the Large-Q Potts Model,” G. S. Grest, James A. Glazier, Michael P. Anderson, Elizabeth A. Holm, and David J. Srolovitz, Materials Research Society Symposium 237, 101 (1992).
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  23. “Cellular Patterns,” James A. Glazier, Bussei Kenkyu 58, 608-612 (1993).
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  24. “Simulation of the Differential Adhesion Driven Rearrangement of Biological Cells,” James A. Glazier and François Graner, Physical Review E 47, 2128-2154 (1993).
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  25. “Grain Growth in Three Dimensions Depends on Grain Topology,” James A. Glazier, Physical Review Letters 70, 2170-2173 (1993).
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  26. “Relation between Volume, Number of Faces and Three-Dimensional Growth Laws in Coarsening Cellular Patterns,” Denis Weaire and James A. Glazier, Philosophical Magazine Letters 68, 363-365 (1993).
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  27. “Effective Multifractal Spectrum of a Random Walk,” Cheryl L. Berthelsen, James A. Glazier, and Sridhar Raghavachari, Physical Review E 49(3), 1860-1864 (1994).
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  28. “Magnetic Resonance Images of Coarsening inside a Foam,” Constantinos P. Gonatas, Arjun G. Yodh, John S. Leigh, James A. Glazier and Burkhard Prause, Physical Review Letters 75, 573-576 (1995).
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  29. “The Energetics of Cell Sorting in Three Dimensions,” James A. Glazier, Richard C. Raphael, François Graner, and Yasuji Sawada, in Interplay of Genetic and Physical Processes in the Development of Biological Form, D. Beysens, G. Forgacs, F. Gaill, editors (World Scientific Publishing Company, Singapore, 1995) 54-61.
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  30. “Construction of Candidate Minimal-Area Space-Filling Partitions,” James A. Glazier and Denis Weaire, Philosophical Magazine Letters 70, 351-356 (1994).
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  31. “Reconstructing Phylogeny from the Multifractal Spectrum of Mitochondrial DNA Sequences,” James A. Glazier, Sridhar Raghavachari, Cheryl L. Berthelsen, and Mark H. Skolnick, Physical Review E 51, 2665-2668 (1995).
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  32. “Spatially Coherent States in Fractally Coupled Map Lattices,” Sridhar Raghavachari and James A. Glazier, Physical Review Letters 74, 3297-3300 (1995).
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  33. “Quantitative Comparison between Differential Adhesion Models and Cell Sorting in the Presence and Absence of Fluctuations,” Jose Carlos M. Mombach, James A. Glazier, Richard C. Raphael, and Mark Zajac, Physical Review Letters 75, 2244-2247 (1995).
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  34. “Magnetic Resonance Imaging of a Three-Dimensional Foam,” Burkhard Prause, James A. Glazier, Samuel Gravina and Carlo Montemagno, Journal of Physics: Condensed Matter 7, L511-L516 (1995).
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  35. “Grain Growth from Homogeneous Initial Conditions: Anomalous Grain Growth and Special Scaling States,” Yi Jiang, Jose Carlos M. Mombach, James A. Glazier, Physical Review E 52, 3333-3336 (1995).
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  36. “Thermal Turbulence in Mercury,” Tohru Takeshita, Takehiko Segawa, James A. Glazier and Masaki Sano, Physical Review Letters 76, 1465-1468 (1996).
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  37. “Thermodynamics of Cell Sorting,” James A. Glazier, Bussei Kenkyu 65, 691-700 (1996).
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  38. “Single Cell Motion in Aggregates of Embryonic Cells,” Jose Carlos M. Mombach and James A. Glazier, Physical Review Letters 76, 3032-3035 (1996).
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  39. “Extended Large-Q Potts Model Simulation of Foam Drainage,” Yi Jiang and James A. Glazier, Philosophical Magazine Letters 74, 119-128 (1996).
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  40. “High Rayleigh Number Turbulence in a Low Prandtl Number Fluid,” T. Segawa, Masaki Sano, Antoine Naert, and James A. Glazier, in Flow at Ultra-High Reynolds and Rayleigh Numbers, A Status Report, R. J. Donnelly and K. R. Sreenivasan editors (Springer Verlag, New York, NY, 1998), 247-257.
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  41. “Foam Drainage: Extended Large-Q Potts Model Simulation,” Yi Jiang and James A. Glazier, Materials Research Society Symposium Proceedings 463, 307-312 (1997).
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  42. “First Steps Towards a Comprehensive Model of Tissues, or: A Physicist Looks at Development,” James A. Glazier and Arpita Uphadyaya, in Dynamical Networks in Physics and Biology: At the Frontier of Physics and Biology, D. Beysens and G. Forgacs editors (EDP Sciences/Springer Verlag, Berlin, Germany, 1998), 149-160.
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  43. “Networks of Droplets Induce by Coalescence: Application to Cell Sorting,” Daniel A. Beysens, Gabor Forgacs and James A. Glazier, in Dynamical Networks in Physics and Biology: At the Frontier of Physics and Biology, D. Beysens and G. Forgacs editors (EDP Sciences/Springer Verlag, Berlin, Germany, 1998), 161-169.
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  44. “Possible Cooperation of Differential Adhesion and Chemotaxis in Mound Formation of Dictyostelium,” Yi Jiang, Herbert Levine and James A. Glazier, Biophysical Journal 75, 2615-2625 (1998).
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  45. “Hysteresis and Avalanches in Two-Dimensional Foam Rheology Simulations,” Yi Jiang, Pieter J. Swart, Avadh Saxena, M. Asipauskas and James A. Glazier, Physical Review E 59, 5819-5832 (1999).
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  46. “Waves in Diffusively Coupled Bursting Cells,” Sridhar Raghavachari and James A. Glazier, Physical Review Letters 82, 2991-2994 (1999).
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  47. “Magnetic Resonance Imaging of Structure and Coarsening in Three-Dimensional Foams,” Burkhard Prause and James A. Glazier, in Proceedings of the 5th Experimental Chaos Conference Orlando, Florida 28 June - 1 July 1999, M. Ding, W. L. Ditto, L. M. Pecora and M. L. Spano editors (World Scientific, Singapore, 2001) 427-436.
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  48. “Stochastic Simulation of Benign Avascular Tumor Growth Using the Potts Model,” Emma Stott, N. F. Britton, James A. Glazier and Mark Zajac, Mathematical and Computer Modelling 30, 183-198 (1999).
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  49. “Evidence against ‘Ultrahard’ Thermal Turbulence at Very High Rayleigh Numbers,” James A. Glazier, Takehiko Segawa, Antoine Naert and Masaki Sano, Nature 398, 307-310 (1999).
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  50. “Foams Out of Stable Equilibrium: Cell Elongation and Side Swapping,” Florence Elias, Cyrille Flament, James A. Glazier, François Graner and Yi Jiang, Philosophical Magazine B 79, 729-751 (1999).
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  51. “Bursting in Neurons with Fast and Slow Inhibition,” Sridhar Raghavachari and James A. Glazier, preprint (1999).
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  52. “Diffusion and Deformations of Single Hydra Cells in Cellular Aggregates,” Jean Paul Rieu, Arpita Upadhyaya, James A. Glazier, Noryuki Bob Ouchi and Yasuji Sawada, Biophysical Journal 79, 1903-1914 (2000).
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  53. “Bursts and Cavity Formation in Hydra Cell Aggregates: Experiments and Simulations,” Jose C. M. Mombach, Rita M. C. de Almeida, Gilberto L. Thomas, Arpita Upadhyaya and James A. Glazier, Physica A 297, 495-508 (2001).
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  54. “ Anomalous Diffusion in Two-Dimensional Hydra Cell Aggregates ,” Arpita Upadhyaya, Jean Paul Rieu, James A. Glazier, and Yasuji Sawada, Physica A 293 , 549-558 (2001).
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  55. “Thermal Hard Turbulence in Mercury,” Takehiko Segawa, Antoine Naert, James A. Glazier and Masaki Sano, preprint (2000).
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  56. “Current Status of Three-Dimensional Growth Laws,” James A. Glazier and Burkhard Prause, in Foams, Emulsions and their Applications, P. Zitha, J. Banhart and G. Verbist editors (Verlag MIT Publishing, Bremen, Germany, 2000), 120-127.
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  57. “Energy Landscape of 2D Fluid Foams,” Yi Jiang, Eric Jainaud, Cyril Flament, James A. Glazier and Francois Graner, in Foams, Emulsions and their Applications, P. Zitha, J. Banhart and G. Verbist editors (Verlag MIT Publishing, Bremen, Germany, 2000), 321-327.
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  58. “Embryonic Tissues Are Viscoelastic Materials,” Daniel Beysens, Gabor Forgacs and James A. Glazier, Canadian Journal of Physics 78, 243-251 (2000).
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  59. “Cell Sorting is Analogous to Phase Ordering in Fluids,” Daniel A. Beysens, Gabor Forgacs and James A. Glazier, Proceedings of the National Academy of Sciences (USA) 97, 9467-9471 (2000).
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  60. “Model of Convergent Extension in Animal Morphogenesis,” Mark Zajac, Gerald L. Jones, and James A. Glazier, Physical Review Letters 85, 2022-2025 (2000).
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  61. Ab Initio Derivation of Stress and Strain in Fluid Foams,” Yi Jiang, Marius Asipauskas, James A. Glazier, M. Aubouy and Francois Graner, in Foams, Emulsions and their Applications, P. Zitha, J. Banhart and G. Verbist editors (Verlag MIT Publishing, Bremen, Germany, 2000), 297-304.
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  62. “The Fractal Structure of the Mitochondrial Genomes,” Nestor Oiwa and James A. Glazier, Physica A 311, 221-230 (2002).
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  63. “On Cellular Automaton Approaches to Modeling Biological Cells,” Mark S. Alber, Maria A. Kiskowski, James A. Glazier and Yi Jiang, in Mathematical Systems Theory in Biology, Communication, and Finance, J. Rosenthal, and D. S. Gilliam, editors (IMA 142, Springer-Verlag, New York, 2002), 1-40.
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  64. “Multi-model Simulations of Chicken Limb Morphogenesis,” Rajiv Chaturvedi, Jesus A. Izaguirre, ChengBang Huang, Trevor Cickovski, Patrick Virtue, Gilberto Thomas, Gabor Forgacs, Mark Alber, George Hentschel, Stuart A. Newman, and James A. Glazier, in Computational Science – ICCS 2003: International Conference Melbourne, Australia and St. Petersburg, Russia, June 2-4, 2003. Proceedings, Part III, P. M. A. Sloot, D. Abramson, A. V. Bogdanov, J. J. Dongarra, A. Y. Zomaya and Y. E. Gorbachev editors (LNCS 2659, Springer-Verlag, New York, 2003), 39-49.
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  65. “A Texture Tensor to Qualify Deformations,” Miguel Aubouy, Yi Jiang, James A. Glazier, and François Granner, Granular Matter 5, 67-70 (2003).
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  66. “A Texture Tensor to Qualify Deformations: The Example of Two-Dimensional Flowing Foams,” Marius Asipauskas, Miguel Aubouy, James A. Glazier, François Granner and Yi Jiang, Granular Matter 5, 71-74 (2003).
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  67. “A Novel Mechanism for Mesenchymal Condensation during Limb Chondrogenesis in Vitro,” Wei Zeng, Gilberto L. Thomas, Stuart A. Newman and James A. Glazier, in Mathematical Modelling and Computing in Biology and Medicine, 5th ESMTB Conference 2002, V. Capasso editor (Società Editrice Esculapio, Bologna, 2003), 80-86.
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  68. “Improving the Realism of the Cellular Potts Model in Simulations of Biological Cells,” Noriyuki Bob Ouchi, James A. Glazier, Jean-Paul Rieu, Arpita Upadhyaya and Yasuji Sawada, Physica A 329, 451–458 (2003).
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  69. “Dynamics and Topological Aspects of a Reconstructed Two-Dimensional Foam Time Series Using Potts Model on a Pinned Lattice,” Igor F. Vasconcelos, Isabelle Cantat, James A. Glazier, Journal of Computational Physics 192, 1-20 (2003).
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  70. “CompuCell, a Multi-model Framework for Simulation of Morphogenesis,” J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman and J. A. Glazier, Bioinformatics 20, 1129-1137 (2004).
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  71. “Interplay between Activator–Inhibitor Coupling and Cell-Matrix Adhesion in a Cellular Automaton Model for Chondrogenic Patterning,” M.A. Kiskowski et al. Developmental Biology 271 (2004) 372–387.
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  72. “Dynamical Mechanisms for Skeletal Pattern Formation in the Vertebrate Limb,” H. George. E. Hentschel, Tilmann Glimm, James A. Glazier and Stuart A. Newman, Proceedings of the Royal Society London B 271, 1713-1722 (2004).
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  73. “Self-Similar Mitochondrial DNA,” Nestor N. Oiwa and James A. Glazier, Cell Biochemistry and Biophysics 41, 41-62 (2004).
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  74. “Non-Turing Stripes and Spots: A Novel Mechanism for Biological Cell Clustering,” Wei Zeng, Gilberto L. Thomas and James A. Glazier, Physica A 341, 482-494.
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  75. “Cell-Oriented Modeling of in Vitro Capillary Development,” Roeland M.H. Merks, Stuart A. Newman and James A. Glazier, in Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry, ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004. Proceedings, P. M. A. Sloot, B. Chopard and A. G. Hoekstra editors (Lecture Notes in Computer Science 3305, Springer-Verlag Heidelberg, 2004), 425-434.
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  76. “A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb,” R. Chaturvedi, et al., ed. P.M.A. Sloot, B. Chopard, and A.G. Hoekstra: ACRI 2004, LNCS 3305, 543-552 (2004).
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  77. “The Rheology of Two-Dimensional Foams,” Simon Cox, Denis Weaire and James A. Glazier, Rheol. Acta 43, 442-448 (2004).
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  78. “Simulating Convergent Extension by Way of Anisotropic Differential Adhesion,” Zajac M, Jones GL, and Glazier JA, Journal of Theoretical Biology 222 (2), 247-259 (May 21 2003).
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  79. “Introduction to Special Issue on Multiscale Modeling in Biology,” Mark Alber, Thomas Hou, James A. Glazier, Yi Jiang, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal 3, xii-xiii (2005).
     
  80. “A Cell-centered Approach to Developmental Biology,” Roeland H. M. Merks and James A. Glazier, Physica A 352, 113-130 (2005).
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  81. “On Multiscale Approaches to Three-dimensional Modeling of Morphogenesis,” Rajiv Chaturvedi, ChengBang Huang, Bogdan Kazmierczak, Terry Schneider, Jesus A. Izaguirre, Tilmann Glimm, H. George E. Hentschel, James A. Glazier, Stuart A. Newman, Mark S. Alber, Journal of the Royal Society Interface 2, 237-253 (2005).
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  82. “Extraction of Relevant Physical Parameters from 3D Images of Foams Obtained by X-ray Tomography,” Jérôme Lambert, Isabelle Cantat, Renaud Delannay, Anne Renault, François Graner, James A. Glazier, Igor Veretennikov, Peter Cloetens, Colloids and Surfaces A: Physicochem. Eng. Aspects 263, 295-302 (2005).
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  83. “A Framework for Three-Dimensional Simulation of Morphogenesis,” Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, and Jesús A. Izaguirre, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2, 1-16 (2005).
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  84. “Solving the Advection-diffusion Equations in Biological Contexts Using the Cellular Potts Model,” Debasis Dan, Christopher Mueller, Kun Chen, and James A. Glazier, Physical Review E 72, 041909 (2005).
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  85. “Dynamic Mechanisms of Blood Vessel Growth,” Roeland MH Merks and James A. Glazier, Nonlinearity 19, C1-C10 (2006).
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  86. “Cell Elongation Is Key to in silico Replication of in vitro Vasculogenesis and Subsequent Remodeling,” Roeland M.H. Merks, Sergey V. Brodsky, Michael S. Goligorksy, Stuart A. Newman and James A. Glazier, Developmental Biology 289, 44-54 (2006).
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  87. “A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis,” Nan Chen, James A. Glazier, and Mark S. Alber, in Cellular Automata: 7th International Conference on Cellular Automata, for Research and Industry, ACRI 2006, Perpignan, France, September 20-23, 2006 Proceedings, S. El Yacoubi, B. Chopard and S. Bandini, eds. (Lecture Notes in Computer Science) 4173, Springer-Verlag, Heidelberg, 2006), 58-67.
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  88. “Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb,” Nikodem J. Poplawski, Maciej Swat, J. Scott Gens and James A. Glazier, Physica A 373C, 521-532 (2007).
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  89. “Cell movement during chick primitive streak formation,” Manli Chuai, Wei Zeng, Xuesong Yang, Veromka Boychenko, James A. Glazier, Cornelis J. Weijer, Developmental Biology 296: 137-149 (2006).
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  90. “Analysis of tissue flow patterns during primitive streak formation in the chick embryo,” Cheng Cui, Xuesong Yang, ManLi Chuai, James A. Glazier, Corneljis J. Weijer, Developmental Biology 284, 37-47 (2005).
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  91. “Viscous Instabilities in Flowing Foams: a Cellular Potts Model Approach,” Soma Sanyal and James A Glazier, J. Stat. Mech. P10008 (2006).
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  92. “A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis,” Nan Chen, James A. Glazier, Jesús A. Izaguirre and Mark S. Alber, Computer Physics Communications 176: 670-681 (2007).
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  93. “Experimental Growth Law for Bubbles in a Moderately "Wet" 3D Liquid Foam,”Jerome Lambert, Isabelle Cantat, Renaud Delannay, Rajmund Mokso, Peter Cloetens, James A. Glazier, and Francois Graner, Physical Review Letters 99: 058304 (2007) .
    More Information - PDF (740 KB) - PS (2.6 MB)
     
  94. “Magnetization to Morphogenesis: A Brief History of the Glazier-Graner-Hogeweg Model,”James A. Glazier, Ariel Balter, Nikodem J. Poplawski, Single-Cell-Based Models in Biology and Medicine A. R. A. Anderson, M. A. J. Chaplain and K. A. Rejniak, editors (Birkhäuser, Basel, Boston and Berlin, 2007), 79-106.
    PDF (1.4 MB)
     
  95. “The Glazier-Graner-Hogeweg Model: Extensions, Future Directions and Opportunities for Further Study,” Ariel Balter, Roeland M. H. Merks, Nikodem J. Poplawski, Maciej Swat and James A. Glazier,Single-Cell-Based Models in Biology and Medicine A. R. A. Anderson, M. A. J. Chaplain and K. A. Rejniak, editors (Birkhäuser, Basel, Boston and Berlin, 2007), 151-168.
    PDF (892 KB)
     
  96. “Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick,” James A. Glazier, Ying Zhang, Maciej Swat, Benjamin Zaitlen, and Santiago Schnell, Current Topics in Developmental Biology 81: 205-247 (2008).
    More Information - PDF (1.5 MB) - PS (2.3 MB)
     
  97. “Compact Microfluidic Structures for Generating Spatial and Temporal Gradients,” Dragos Amarie, James A. Glazier, and Stephen C. Jacobson, Analytical Chemistry 79: 471 -9477 (2007).
    More Information - PDF (275 KB) - PS (866 KB)
     
  98. “Simulation of Single-species Bacterial-Biofilm Growth using the Glazier-Graner-Hogeweg Model and the CompuCell3D Modeling Environment,” Nikodem J. Poplawski, Abbas Shirinifard, Maciej Swat and James A. Glazier, Mathematical Biosciences and Engineering , 5: 355-388 (2008).
    More Information - PDF (2.3 MB) - PS (55 MB)
     
  99. “From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development,” Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman and Jesus A. Izaguirre,, Computing in Science and Engineering, 9: 50-60 (2007).
    More Information - PDF (448 KB) - PS (997 KB)
     
  100. “Contact-Inhibited Chemotaxis in De Novo and Sprouting Blood-Vessel Growth,” Roeland M. H. Merks, Erica D. Perryn, Abbas Shirinifard, James A. Glazier, PLoS Computational Biology, 4: e1000163 (2008)
    PDF (1.75 MB)
     
  101. “ Bulk Elastic Properties of Chicken Embryos during Somitogenesis,” Ubirajara Agero, James A Glazier and Michael Hosek, /BioMedical Engineering OnLine/ *9*,19 (2010)
    PDF (4.00 MB)
     
  102. “Workflows for Parameter Studies of Multi-Cell Modeling,” Randy Heiland, Maciek Swat, Benjamin Zaitlen, James A. Glazier, and Andrew Lumsdaine, in Proceedings of the HPC 2010 Symposium of the Spring Simulation Multiconference 2010, Orlando, Florida, 12 April - 14 April 2010, ISBN: 1-56555-342-X, 140-145.
    More Information - PDF (1.1 MB)
     
  103. “Modeling Gastrulation in the Chick Embryo: Formation of the Primitive Streak,” Bakhtier Vasiev, Ariel Balter, Mark Chaplain, James A. Glazier, Cornelis J. Weijer, /PLoS ONE/ *5*, e10571 (2010).
    More Information - PDF (1.1 MB)
     
  104. “Microfluidic Devices Integrating Microcavity Surface-Plasmon-Resonance Sensors: Glucose Oxidase Binding-Activity Detection,” Dragos Amarie, Abdelkrim Alileche, Bogdan Dragnea, and James A. Glazier, Analytical Chemistry, 82, 343-352; doi:10.1021/ac902038d (2010).
    Link (ACM Anal.Chem.)   -   PDF (1.2 MB)
     
  105. “A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation."”Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA, PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002155
    More Information - Link

  106. Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study,” Abbas Shirinifard, James Alexander Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus,
    PLoS Comput Biol 7(10): e1002155. doi:10.1371/journal.pcbi.1002440
    Link (PLoS Comput Biol)   -   PDF (1.1 MB)   -   (IU press release)   -   (GSU press release)
     
  107. Visualizing Cells and their Connectivity Graphs for CompuCell3D,” Randy Heiland, Maciek Swat, James Sluka, Benjamin Zaitlen, Abbas Shirinifard, Gilberto Thomas, Andrew Lumsdaine, James Glazier,
    2nd IEEE Symposium on Biological Data Visualization
    Link (BioVis)   -   PDF (3.7 MB)
     
  108. Label-Free Microcavity Biosensors: Steps towards Personalized Medicine.,” Dragos Amarie and James A. Glazier, Sensors, 12, 17262-17294; doi:10.3390/s121217262 (2012).
    Link (Sensors)   -   PDF (1 MB)
     


Ph.D. Theses Supervised:

  1. “Fractal Analysis of DNA Sequence Data (Chaos Theory),” Cheryl L. Berthelsen, Ph.D. University of Utah, Department of Medical Informatics, March 1993 (supervised with Prof. Mark H. Skolnick).
    More Information - PDF (5.16 MB) - PS (6.58 MB)
     
  2. “Cellular Pattern Formation,” Yi Jiang, Ph.D. University of Notre Dame, Department of Physics, November, 1998.
    More Information - PDF (6.33 MB) - PS (84.91 MB)
     
  3. “Synchrony and Chaos in Coupled Oscillators and Neural Networks,” Sridhar Raghavachari, Ph.D. University of Notre Dame, Department of Physics, April, 1999.
    More Information - PDF (2.74 MB) - PS (18.00 MB)
     
  4. “Magnetic Resonance Imaging of Structure and Coarsening in Three-Dimensional Foams,” Burkhard A. Prause, Ph.D. University of Notre Dame, Department of Physics, March, 2000.
    More Information - PDF (1.27 MB) - PS (11.79 MB)
     
  5. “Thermodynamic and Fluid Properties of Cells, Tissues, and Membranes,” Upadaya, Arpita, Ph.D. University of Notre Dame, Department of Physics, April, 2000.
    More Information - PDF (7.01 MB) - PS (60.51 MB)
     
  6. “Modeling Convergent Extension by Way of Anisotropic Differential Adhesion,” Mark Zajac, Ph.D. University of Notre Dame, Department of Physics, May, 2002 (supervised with Prof. Gerald L. Jones).
     
  7. “Living Matter: Generic Mechanisms in Embryonic Tissue Morphogenesis,” Wei, Zeng, Ph.D. Indiana University, Department of Physics, December, 2004.
    PDF (7.20 MB)
     
  8. “A Cursory Study of the Thermodynamic and Mechanical Properties of Monte-Carlo Simulations of the Ising Model,” Seng Kai Wong, Ph.D. University of Notre Dame, Department of Physics, April, 2005 (supervised with Prof. Kathie E. Newman).Wong, Seng Kai.
    PDF (2.88 MB) - Source Code (300 KB)
     
  9. “Dynamics of Cell Movement and Tissue Motion in Gastrulation and Micromass Cell Culture,” Cheng Cui, Ph.D. Indiana University, Department of Physics, July 2005.
    PDF (9.89 MB)
     
  10. “Dynamic Spatio-Temporal Interaction of Morphogens, Forces and Growth in Embryonic Morphogenesis,” Ying, Zhang, Ph.D. Indiana University, Department of Physics, August, 2007.
    More Information - PDF (8.8 MB) - PS (16 MB)
     
  11. “An Object-Oriented Modeling Framework for the Arterial Wall,” Manuel Ignacio Balaguera Jiménez, Ph.D. University of Los Andes, Department of Mechanical Engineering (supervised with Juan Carlos Briceño), September, 2007.
    PDF (2.7 MB) - PS (35 MB)
     
  12. Vascular Patterning and Its Application in Cancer and Choroidal Neovascularization,” Abbas Shirinifard, Ph.D. Indiana University, Department of Physics, March, 2012.
    PDF (7.3MB)
     
  13. Multi-Scale Cell-Based Computational Models of Vertabrate Segmentation and Somitogenesis Illuminate Coordination of Developmental Mechanisms Across Scales,” Susan D. Hester, Ph.D. Indiana University, Department of Physics, April, 2012.
    PDF (12MB)
     

Undergraduate Theses Supervised:


  1. “Cell Based Modeling of Arteriosclerosis,” Megan Knapp Undergraduate Thesis, University of Rochester, (supervised with Roeland merks and Stepen Teitel).
    PDF (621 KB) - PS (788 KB)
     


Popular Write Ups:

  1. “Soap Bubbles Make Serious Physics,” J. Maddox, Nature 338 , 293 (1989).
  2. “Frothy Physics,” F. Flam, Science News 136 , 72 (1989).
  3. “Humble Froth Offers Clues to New Materials,” M. W. Browne, New York Times C1 (March 20, 1990).
  4. Book Review of Chaos: the Making of a New Science, by J. Gleick, James A. Glazier and Gemunu H. Gunaratne, Physics Today 41, 79 (February 1988).
  5. “Probing the Interior of a Coarsening Foam,” I. Peterson, Science News 148, 68 (1995).
  6. “Whipping up an Image of a Foam's Interior,” I. Peterson, Science News 148, 231 (1995).
  7. “Physicists Advance Into Biology,” J. Glanz, Science 272, 646-648 (1996).
  8. “At the End of Pfalsgraf there is Chaos: An Assessment of Proximate Cause in the Light of Chaos Theory,” Edward S. Adams, Gordon B. Brumwell and James A. Glazier, University of Pittsburgh Law Review 59 (Spring), 507-555 (1998).
  9. “The elusive ‘ultimate state’ of thermal convection,” Joël Sommeria, Nature 398 , 294-295 (1999).
  10. “Transitions Still to be Made,” Philip Ball, Nature supplement to 402, C73-C76 (1999).
  11. “Biophysics: Science in Motion,” Philip Ball, Nature 406, 244-245 (2000).
  12. “Ramping up to Multiscale: Taking Biomedical Modeling to a New Level,” Dana Mackenzie, Biomedical Computation Review 19-26 (Spring 2006). [PDF]


Edited Volumes:

  1. Special Issue on Multiscale Modeling in Biology, Mark Alber, Thomas Hou, James A. Glazier, Yi Jiang, Guest Editors, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal 3 (2), 245-475 (2005).
  2. Proceedings of the Workshop “Biocomplexity VI: Complex Behavior in Unicellular Organisms”, James A. Glazier, Clay Fuqua, Yves Brun and Mark S. Alber, Biofilms 1 (4), 227-391 (2004).


Meetings Organized

  • Biophysics Workshop, “Biocomplexity I: Modeling Limb Development,” University of Notre Dame, 2/24/01-2/25/01 (with Mark Alber).
  • Biophysics Workshop, “Biocomplexity II: Structure and Function of the Cytoskeleton,” University of Notre Dame, 11/9/01-11/12/01 (with Mark Alber).
  • Minisymposium, “Towards a Comprehensive Modelling of Organogenesis,” ECMTB 2002, Milan, Italy, 7/2/02-7/6/02 (with George Hentschel).
  • Biophysics Workshop, “Biocomplexity III, Biomechanics,” University of Notre Dame, 11/7/02-11/10/02 (with Glen Niebur and Charles Turner).
  • Biophysics Workshop, “Biocomplexity IV, Regenerative Medicine and Biology,” Indiana University, 5/14/03-5/18/03 (with David Stocum, Anton Neff, Anthony Mescher, and Mark Alber).
  • Biophysics Workshop, “Biocomplexity V, Multiscale Modeling in Biology,” University of Notre Dame, 8/13/03-8/17/03 (with Mark Alber and Yi Jiang).
  • Biophysics Workshop, “Biocomplexity VI, Complex Behavior in Unicellular Organisms,” Indiana University, Bloomington, 5/12/04-5/16/04 (with Clay Fuqua, Yves Brun, and Mark Alber).
  • Biophysics Workshop, “Biocomplexity VII, “Unraveling the Function and Kinetics of Biochemical Networks,” Indiana University, Bloomington, 5/9/05-5/12/05 (with Santiago Schnell).
  • Minisymposium, “Cell-Oriented Models of Biological Development,” SIAM Conference on Applications of Dynamical Systems, Snowbird, UT, 5/22/05-5/27/05 (with Roeland Merks).
  • Minisymposium, “Cell-Oriented Models of Biological Development,” ECMTB 2005, 7/18/05-7/22/05, Dresden, Germany (with Roeland Merks).
  • Biophysics Workshop, “Biocomplexity VIII, Applications of Methods of Stochastic Systems and Statistical Physics in Biology,” University of Notre Dame, 10/28/05-10/30/05 (with Mark Alber, Yi Jiang and Laszlo Barabasi).
  • Biophysics Workshop, “Biocomplexity IX, Multiscale Modeling of Multicellular Systems,” Indiana University, 5/8/06-5/10/06 (with Santiago Schnell, Timothy Newman and Philip Maini).
  • Institute of Pure and Applied Mathematics Workshop, “Workshop IV: Systems Biology and Molecular Modeling,” 5/22/06-5/26/06, University of California Los Angeles (with Dan Kamei).
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