Indiana University Department of Physics - James A. Glazier

Curriculum Vitae
JAMES ALEXANDER GLAZIER

Department of Physics
Swain Hall West 159
Indiana University
727 East Third Street
Bloomington, IN 47405-7105
U.S.A.
Phone: (812) 855-3735
FAX: (812) 855-5533
Birth date: June 27, 1962
Citizenship: U.S.A.


Fellowships and Grants:

  1. National Institutes of Health, National Institute of General Medical Sciences, 1R01 GM076692-01 “Multiscale Studies of Segmentation in Vertebrate Embryos,” (9/1/05-8/31/08, approx. $907,000).
  2. National Science Foundation, Molecular and Cell Biology, MCB-0513693, “Workshop: Biocomplexity VII - Unraveling the Function and Kinetics of Biochemical Networks: From Experiments to Systems Biology, at Indiana University-Bloomington May 9-12, 2005,” (5/1/05-4/30/06, $15,000) PI Santiago Schnell.
  3. National Institutes of Health, National Institute of General Medical Sciences, “Biocomplexity VII: Unraveling the Function and Kinetics of Biochemical Networks,” (5/9/05-5/8/04, $12,749) PI Santiago Schnell.
  4. Special State Research Funding, “Purchase of 2-Photon Multispectral Microscope,” (3/15/05-3/14/07, $750,000).
  5. Fellow of the Institute of Physics.
  6. National Institutes of Health, National Institute of General Medical Sciences, “Workshop: Biocomplexity VI, Complex Behavior in Unicellular Organisms: Bloomington, Indiana.” (5/12/04-5/16/04, $15,000)
  7. National Science Foundation, Molecular and Cell Biology, MCB 0352904, “Workshop: Biocomplexity VI, Complex Behavior in Unicellular Organisms: Bloomington, Indiana.” (5/12/04-5/16/04, $28,000).
  8. Pervasive Technologies Laboratories Fellowship (Indiana University Bloomington) (12/1/03-11/30/04, $64,000).
  9. IBM Innovation Institute Award (9/25/03-9/24/08, $55,000).
  10. Whitaker Foundation, “Biocomplexity V: Multiscale Modeling in Biology.” (8/1/03-10/31/03, $5,000).
  11. NASA Glenn Research Center, NAG 2-1619: “Comparative Study of Morphogenesis at 1g and Simulated Microgavity.” (4/1/03-3/31/06 $209,964).
  12. Whitaker Foundation, “Symposium: The Role of Tissue Mechanics in Biological Responses to Mechanical Loading.” (8/1/02-11/30/02, $10,000) PI Glen Niebur, co-PI Charles Turner.
  13. National Science Foundation, Biological and Environmental Sciences, BES-0228966 “Symposium: The Role of Tissue Mechanics in Biological Responses to Mechanical Loading, Notre Dame, Indiana.” (11/15/02-4/30/03, $10,000) PI Glen Niebur, co-PI Charles Turner.
  14. National Science Foundation, Division of Materials Research, DMR-0089162 “Effects of Local Interfacial Flow Dynamics on Foam Drainage and Coarsening.” (12/01/00-11/30/03, $359,958) co-PI Hsueh-Chia Chang.
  15. National Science Foundation, Division of Integrative Biology, IBN-0083653, “BIOCOMPLEXITY--Multiscale Simulation of Avian Limb Development.” (9/1/00-8/31/05, $2,999,320) co-PIs Jesus Izaguirre, Mark S. Alber.
  16. NASA Glenn Research Center, NAG3-2366, “Diffusive Coarsening of Liquid Foams in Microgravity.” (3/9/00-11/3/03, $290,000).
  17. Department of Energy, DE-FGO299ER45785, “Fingering Instabilities, Collapse, Avalanches and Self Organized Criticality in Liquid Foams.” (9/1/99-8/31/01, $163,386).
  18. National Science Foundation, C.N.Pq. International Award, INT98-02417, “US-Brazil Cooperative Research: Cellular Patterns.” (5/1/98-4/30/01, $15,750).
  19. National Science Foundation, Japan Society for the Promotion of Science International Award, INT96-03035, “Complex Pattern Formation.” (5/1/97-4/30/00, $49,575).
  20. National Science Foundation, Academic Research Infrastructure Award, CTS96-01691, “Acquisition of Wide Bore Magnetic Resonance Imager.” (11/1/96-12/31/00, $836,488).
  21. National Science Foundation Young Investigator Award (1992-1997, $322,500).
  22. American Chemical Society/Petroleum Research Fund, PRF #30773-AC9, “MRI Study of Three-Dimensional Liquid Foams.” (9/1/96-8/31/99, $50,000).
  23. American Chemical Society/Petroleum Research Fund (1994-1996, $20,000).
  24. Brazil C.N.Pq. Fellowship (1994-1995, $21,260).
  25. Ford Motor Company (1993-1995, $17,500).
  26. Exxon Educational Foundation (1993-1995, $20,000).
  27. NSF/JSPS Postdoctoral Research Fellowship (1991-1993, approx. $80,000).
  28. Grainger Fellowship (1988-1989, approx. $18,000).
  29. Phi Beta Kappa (1984).
  30. Hoopes Award for academic excellence (1984, $1500).


Education:

  • Physics and Mathematics (B.A.) magna cum laude, Harvard College, Cambridge, MA (1984).
  • Student, Les Houches NATO Summer School, Les Houches, France (summer 1986). “Chance and Matter.”
  • Physics (M.A.) University of Chicago, Chicago, IL (1987).
  • Physics (Ph.D.) University of Chicago, Chicago, IL (1989).
    Thesis advisor: Prof. Albert Libchaber. Thesis subject: Dynamics of Cellular Patterns.
  • Student, Marine Biology Laboratory, Woods Hole, MA (summer 1991).
    “Neural Systems and Behavior.”


Employment:

2006 March-June:
Feb. 2006 - Present Founding CEO, Spherosense Technologies, Inc.
Mar. 2006 - Present Vice Chair, Division of Biological Physics, American Physical Society.
Mar. - Jun. 2006 Core Participant, Institute of Pure and Applied Mathematics, University of California, Los Angeles, California.
Nov. 2003 - Present Adjunct Professor, School of Informatics, Indiana University, Bloomington, IN.
Aug. 2002 - Present Professor, Department of Physics, Adjunct Professor, Department of Biology, Director, Biocomplexity Institute, Indiana University, Bloomington, IN.
Sept. 2001 - Aug. 2002 Director, Interdisciplinary Center for the Study of Biocomplexity, University of Notre Dame, Notre Dame, IN.
Sept. - Dec. 2000 Visiting Scientist, Laboratory of Physical Spectrometry, University of Grenoble, Grenoble, France.
May - Nov. 1999 Visiting Full Professor, Research Institute of Electrical Communication, Tohoku University, Sendai, Japan.
Fall 1997 - Sum. 2002 Associate Professor, Department of Physics, University of Notre Dame, Notre Dame, IN.
Fall 1992 - Fall 1997 Assistant Professor, Department of Physics, University of Notre Dame, Notre Dame, IN.
Fall 1991 - 1993 JSPS/NSF Fellowship, Research Institute of Electrical Communication, Tohoku University, Sendai, Japan.
Spring 1991 Visitor, Department of Physics, Trinity College, Dublin, Ireland.
1989 - 1994 Consultant, Department of Genetic Epidemiology, University of Utah, Salt Lake City, UT.
1989 - 1991 Postdoctoral Researcher, AT&T Bell Laboratories, Murray Hill, NJ.
Summer 1989 Visiting Fellow, University of Western Australia, Perth, Australia.
1985 - 1989 Research Assistant (Grainger Fellowship, 1988-1989), University of Chicago, Chicago, IL.


Teaching:

Graduate Classical Mechanics (University of Notre Dame, Physics 505), Graduate Nonlinear Dynamics (University of Notre Dame, Physics 525), Graduate Mathematical Biology (Indiana University, Physics 548), Graduate Computational Biology (Indiana University, Physics 700), Undergraduate Modern Physics Laboratory (University of Notre Dame, Physics 442), Undergraduate Physics I (University of Notre Dame, Physics 221), Graduate Experimental Physics Laboratory (University of Notre Dame, Physics 510).



Departmental Service:

Graduate Admissions Committee (University of Notre Dame, Indiana University), Graduate Recruiting Committee (Indiana University), Faculty Search Committee (University of Notre Dame, Indiana University), Biophysics Curriculum Development Committee (Indiana University), Library Committee (Indiana University).



University Service:

Founder and Director, Biocomplexity Institute (Indiana University), Founder and Director Interdisciplinary Center for the Study of Biocomplexity (University of Notre Dame), Informatics Faculty Search Committee (Indiana University), University Scientific Ph.D. Development Committee (Indiana University), Founding Director, Magnetic Resonance Imaging Facility (University of Notre Dame).



Professional Society Membership:

American Physical Society, Materials Research Society, Society for Industrial and Applied Mathematics, Biophysical Society, Society for Mathematical Biology, European Society for Mathematical Biology, Biomedical Engineering Society, Institute of Physics (Fellow).



Refereeing:

Referee for Journals:

American Journal of Physics, Applied Optics, ASME Applied Mechanics Reviews, Developmental Dynamics, Europhysics Letters, IEEE Transactions on Circuits and Systems, International Journal of Solids and Structures, Journal of Cell Science, Journal of Physics Condensed Matter, Journal of Theoretical Biology, Philosophical Magazine Letters, Physics of Fluids, Physical Review E, Physical Review Letters, Nature.

Referee for Funding Agencies:

Enterprise Ireland, Genoma Espana, National Science Foundation, American Chemical Society, Wellcome Trust, Israel Science Foundation, NASA, DOE, USCRDF, Danish National Research Foundation.



Other Service:

Member, Board of Editors, Nonlinearity. Associate Editor, Mathematical Biosciences and Engineering. Board of Directors, Boston Early Music Festival. Member, Advisory Committee on Biophysics, SUNY Albany. Member, Scientific Advisory Board, Reify Corporation, Cambridge, MA. Member, Advisory Board, Center for Bioinformatics and Computational Biology, Indiana University School of Medicine.



Professional Society Membership:

American Physical Society, Materials Research Society, Society for Industrial and Applied Mathematics, Biophysical Society



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).
    More Information - PDF (799.2 KB) - PS (2.264 MB)
     
  2. “Dynamics of the Two-Dimensional Soap Froth,” James A. Glazier, S. P. Gross, and Joel Stavans, Physical Review A 36, 306 (1987).
    More Information - PDF (1.059 MB) - PS (3.507 MB)
     
  3. “f(α) Curves: Experimental Results,” James A. Glazier, Gemunu H. Gunaratne, and Albert Libchaber, Physical Review A 37, 523 (1988).
    More Information - PDF (1.541 MB) - PS (4.361 MB)
     
  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.
    More Information - PDF (1.922 MB) - PS (4.911 MB)
     
  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).
    More Information - PDF (611.9 KB) - PS (2.090 MB)
     
  6. “Soap Froth Revisited: Dynamical Scaling in the Two-Dimensional Froth,” Joel Stavans and James A. Glazier, Physical Review Letters 62, 1318 (1989).
    More Information - PDF (624.4 KB) - PS (2.039 MB)
     
  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.
    More Information - PDF (429.0 KB) - PS (1178 KB)
     
  8. “Non-Ideal Effects in the Two-Dimensional Soap Froth,” James A. Glazier and Joel Stavans, Physical Review A 40, 7398 (1989).
    More Information - PDF (635.0 KB) - PS (2.086 MB)
     
  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).
    More Information - PDF (1.356 MB) - PS (3.537 MB)
     
  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.
    More Information - PDF (565.4 KB) - PS (1.541 MB)
     
  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).
    More Information - PDF (389.5 KB) - PS (7.623 MB)
     
  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).
    More Information - PDF (1.101 MB) - PS (3.104 MB)
     
  13. “Dispersive Chaos,” James A. Glazier, Paul R. Kolodner, and Hugh L. Williams, Journal of Statistical Physics 64, 945 (1991).
    More Information - PDF (622.2 KB) - PS (1.430 MB)
     
  14. “Interaction of Nonlinear Pulses in Convection in Binary Fluids,” James A. Glazier and Paul R. Kolodner, Physical Review A 43, 4269 (1991).
    More Information - PDF (1.245 MB) - PS (2.813 MB)
     
  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).
    More Information - PDF (605.1 KB) - PS (1.504 MB)
     
  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).
    More Information - PDF (596.7 KB) - PS (1.571 MB)
     
  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).
    More Information - PDF (506.5 KB) - PS (1.369 MB)
     
  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).
    More Information - PDF (433.8 KB) - PS (1.153 MB)
     
  19. “The Kinetics of Cellular Patterns,” James A. Glazier and Denis Weaire, Journal of Physics: Condensed Matter 4, 1867 (1992).
    More Information - PDF (1.460 MB) - PS (3.452 MB)
     
  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).
    More Information - PDF (2.010 MB) - PS (6.496 MB)
     
  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).
    More Information - PDF (374.4 KB) - PS (0.968 MB)
     
  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).
    More Information - PDF (462.4 KB) - PS (1.224 MB)
     
  23. “Cellular Patterns,” James A. Glazier, Bussei Kenkyu 58, 608-612 (1993).
    More Information - PDF (240.6 KB) - PS (30.0 KB)
     
  24. “Simulation of the Differential Adhesion Driven Rearrangement of Biological Cells,” James A. Glazier and François Graner, Physical Review E 47, 2128-2154 (1993).
    More Information - PDF (2.357 MB) - PS (5.722 MB)
     
  25. “Grain Growth in Three Dimensions Depends on Grain Topology,” James A. Glazier, Physical Review Letters 70, 2170-2173 (1993).
    More Information - PDF (368.8 KB) - PS (7.500 MB)
     
  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).
    More Information - PDF (130.7 KB) - PS (387.3 KB)
     
  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).
    More Information - PDF (409.1 KB) - PS (1.044 MB)
     
  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).
    More Information - PDF (75.3 KB) - PS (1.522 MB)
     
  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.
    More Information - PDF (593.4 KB) - PS (49.1 KB)
     
  30. “Construction of Candidate Minimal-Area Space-Filling Partitions,” James A. Glazier and Denis Weaire, Philosophical Magazine Letters 70, 351-356 (1994).
    More Information - PDF (258.7 KB) - PS (704.8 KB)
     
  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).
    More Information - PDF (311.0 KB) - PS (830.1 KB)
     
  32. “Spatially Coherent States in Fractally Coupled Map Lattices,” Sridhar Raghavachari and James A. Glazier, Physical Review Letters 74, 3297-3300 (1995).
    More Information - PDF (83.9 KB) - PS (1.461 MB)
     
  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).
    More Information - PDF (141.6 KB) - PS (1.960 MB)
     
  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).
    More Information - PDF (465.4 KB) - PS (2.533 MB)
     
  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).
    More Information - PDF (693.3 KB) - PS (2.089 MB)
     
  36. “Thermal Turbulence in Mercury,” Tohru Takeshita, Takehiko Segawa, James A. Glazier and Masaki Sano, Physical Review Letters 76, 1465-1468 (1996).
    More Information - PDF (57.5 KB) - PS (1.683 MB)
     
  37. “Thermodynamics of Cell Sorting,” James A. Glazier, Bussei Kenkyu 65, 691-700 (1996).
    More Information
     
  38. “Single Cell Motion in Aggregates of Embryonic Cells,” Jose Carlos M. Mombach and James A. Glazier, Physical Review Letters 76, 3032-3035 (1996).
    More Information - PDF (55.7 KB) - PS (1.092 MB)
     
  39. “Extended Large-Q Potts Model Simulation of Foam Drainage,” Yi Jiang and James A. Glazier, Philosophical Magazine Letters 74, 119-128 (1996).
    More Information - PDF (355.8 KB) - PS (2.165 MB)
     
  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.
    More Information - PDF (382.9 KB) - PS (1.089 MB)
     
  41. “Foam Drainage: Extended Large-Q Potts Model Simulation,” Yi Jiang and James A. Glazier, Materials Research Society Symposium Proceedings 463, 307-312 (1997).
    More Information - PDF (522.6 KB) - PS (864.3 KB)
     
  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.
    More Information - PDF (161.7 KB) - PS (491.0 KB)
     
  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.
    More Information
     
  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).
    More Information - PDF (183.1 KB) - PS (8.208 MB)
     
  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).
    More Information - PDF (2.171 MB) - PS (5.391 MB)
     
  46. “Waves in Diffusively Coupled Bursting Cells,” Sridhar Raghavachari and James A. Glazier, Physical Review Letters 82, 2991-2994 (1999).
    More Information - PDF (352.0 KB) - PS (2.009 MB)
     
  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.
    More Information - PDF (207.9 KB) - PS (1.958 MB)
     
  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).
    More Information
     
  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).
    More Information - PDF (104.8 KB) - PS (2.761 MB)
     
  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).
    More Information - PDF (415.6 KB) - PS (1.702 MB)
     
  51. “Bursting in Neurons with Fast and Slow Inhibition,” Sridhar Raghavachari and James A. Glazier, preprint (1999).
    More Information - PDF (248.4 KB) - PS (398.4 KB)
     
  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).
    More Information - PDF (1.062 MB) - PS (2.528 MB)
     
  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).
    More Information - PDF (280.6 KB) - PS (1.230 MB)
     
  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).
    More Information - PDF (97.2 KB) - PS (345.6 KB)
     
  55. “Thermal Hard Turbulence in Mercury,” Takehiko Segawa, Antoine Naert, James A. Glazier and Masaki Sano, preprint (2000).
    More Information - PDF (225.3 KB) - PS (429.4 KB)
     
  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.
    More Information - PDF (132.2 KB) - PS (666.2 KB)
     
  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.
    More Information - PDF (216.3 KB) - PS (4.892 MB)
     
  58. “Embryonic Tissues Are Viscoelastic Materials,” Daniel Beysens, Gabor Forgacs and James A. Glazier, Canadian Journal of Physics 78, 243-251 (2000).
    More Information - PDF (538.0 KB) - PS (1.241 MB)
     
  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).
    More Information - PDF (239.4 KB) - PS (1.045 MB)
     
  60. “Model of Convergent Extension in Animal Morphogenesis,” Mark Zajac, Gerald L. Jones, and James A. Glazier, Physical Review Letters 85, 2022-2025 (2000).
    More Information - PDF (90.4 KB) - PS (505.6 KB)
     
  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.
    More Information - PDF (679.2 KB) - PS (1.168 MB)
     
  62. “The Fractal Structure of the Mitochondrial Genomes,” Nestor Oiwa and James A. Glazier, Physica A 311, 221-230 (2002).
    More Information - PDF (174.1 KB) - PS (1.124 MB)
     
  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.
    More Information - PDF (1.256 MB) - PS (3.133 MB)
     
  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.
    More Information - PDF (653.0 KB) - PS (1.642 MB)
     
  65. “A Texture Tensor to Qualify Deformations,” Miguel Aubouy, Yi Jiang, James A. Glazier, and François Granner, Granular Matter 5, 67-70 (2003).
    More Information - PDF (152.5 KB) - PS (535.4 KB)
     
  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).
    More Information - PDF (316 KB) - PS (2080 KB)
     
  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.
    More Information - PDF (473 KB) - PS (653 KB)
     
  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).
    More Information - PDF (165 KB) - PS (524 KB)
     
  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).
    More Information - PDF (790 KB) - PS (5 MB)
     
  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).
    More Information - PDF (243 KB) - PS (725 KB)
     
  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.
    More Information - PDF (737 KB) - PS (2.62 MB)
     
  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).
    More Information - PDF (511 KB) - PS (3.87 MB)
     
  73. “Self-Similar Mitochondrial DNA,” Nestor N. Oiwa and James A. Glazier, Cell Biochemistry and Biophysics 41, 41-62 (2004).
    More Information - PDF (1.12 MB) - PS (2.17 MB)
     
  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.
    More Information - PDF (807 KB) - PS (2.91 MB)
     
  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.
    More Information - PDF (807 KB) - PS (2.91 MB)
     
  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).
    More Information - PDF (155 KB) - PS (1.15 MB)
     
  77. “The Rheology of Two-Dimensional Foams,” Simon Cox, Denis Weaire and James A. Glazier, Rheol. Acta 43, 442-448 (2004).
    More Information - PDF (503 KB) - PS (1.53 MB)
     
  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).
    More Information - PDF (1.01 MB) - PS (3.14 MB)
     
  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).
    More Information - PDF (517 KB) - PS (3.56 MB)
     
  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).
    More Information - PDF (1.37 MB) - PS (4.17 MB)
     
  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).
    More Information - PDF (599 KB) - PS (1.10 MB)
     
  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).
    More Information - PDF (2.81 MB) - PS (6.14 MB)
     
  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).
    More Information - PDF (917 KB) - PS (2.22 MB)
     
  85. “Dynamic Mechanisms of Blood Vessel Growth,” Roeland MH Merks and James A. Glazier, Nonlinearity 19, C1-C10 (2006).
    More Information - PDF (794 KB) - PS (1.63 MB)
     
  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).
    More Information - PDF (1.02 MB) - PS (3.05 MB)
     
  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.
    More Information - PDF (902 KB) - PS (2.00 MB)
     
  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).
    More Information - PDF (551 KB) - PS (2.08 MB)
     
  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).
    More Information - PDF (1.9 MB) - PS (3.7 MB)
     
  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).
    More Information - PDF (2.29 MB) - PS (4.31 MB)
     
  91. “Viscous Instabilities in Flowing Foams: a Cellular Potts Model Approach,” Soma Sanyal and James A Glazier, J. Stat. Mech. P10008 (2006).
    More Information - PDF (539 KB) - PS (1.37 MB)
     
  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).
    More Information - PDF (988 KB) - PS (2.41 MB)
     
  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).


Invited Lectures

On Biophysics:

  1. Academia Sinica, Taipei, Taiwan, February 1992.
  2. International Conference on Complexity, Kyoto University, May 1992.
  3. University of Science and Technology of China, Heifei, PRC, June 1992.
  4. Harbin Teacher's University, Harbin, PRC, June 1992.
  5. Conference on the Biology of Hydra, National Institute of Genetics, Mishima, Japan,October 1992.
  6. AT&T Bell Laboratories, February 1993.
  7. Rockefeller University, Physics Seminar, March 1993.
  8. University of Notre Dame, Department of Biochemistry, April 1993.
  9. University of Notre Dame, Department of Physics, April 1993.
  10. Materials Research Society, December 1993.
  11. Ecole Normale Superiore, Paris, France, January 1994.
  12. N.E.C. Research Laboratories, Princeton, NJ, January 1994.
  13. Ecolede Physique Theorique, Les Houches, France, February 1994.
  14. University of Notre Dame, Department of Chemistry, February 1994.
  15. James Frank Institute, University of Chicago, Chicago, Illinois, February 1994.
  16. University of New Hampshire, Department of Physics, May 1994.
  17. Instituto Superior Técnico, Lisbon, Portugal, May 1994.
  18. University of Barcelona, Barcelona, Spain, May 1994.
  19. Rockefeller University, Physics Seminar, New York, NY, October 1994.
  20. International Conference on Complexity, Kyoto University, Japan, July 1995.
  21. NSF/IMM Workshop, Rockwell Science Center, Thousand Oak, CA, November 1995.
  22. APS March Meeting, St. Louis, MO, March 1996.
  23. Institute of Nonlinear Science, University of California, San Diego, La Jolla, CA,April 1996.
  24. University of California, Irvine, CA, April 1996.
  25. University of Houston, Department of Physics, April 1996.
  26. University of Notre Dame, Department of Chemistry, April 1996.
  27. Laboratory of Experimental Hydrodynamics, Ecole Polytechnique, Paris, France, May 1996.
  28. Institute for Nonlinear Studies, CNRS, Nice, France, May 1996.
  29. Laboratoire Louis Neel, CNRS, Grenoble, France, June 1996.
  30. Second Workshop on Theoretical and Computational Biology, LBNL, Berkeley, CA, August 1996.
  31. University of Science and Technology of China, Physics Department, Hefei, Anhui Province,PRC, January 1997.
  32. Universite P.M. Curie, Department of Physics, Paris, France, March 12, 1997.
  33. NATO Winter Workshop, Dynamical Networks in Physics & Biology, Centre De Physiquedes Houches, Les Houches, France, March 19, 1997.
  34. Myriad Genetics Corporation, Salt Lake City, Utah, April 28, 1997.
  35. Hong Kong University of Science and Technology, Department of Physics, Hong Kong, PRC, July 28, 1997.
  36. Academia Sinica, Department of Physics, Taipei, Taiwan, July 30, 1997.
  37. Universida de Federal do Rio Grande do Sul, Porto Alegre, Brazil, September 25, 1997.
  38. Fifth Latin American Workshop on Nonlinear Phenomena, Canela, Brazil, October 2, 1997.
  39. Northwestern University, Evanston, Illinois, October 15, 1997.
  40. Purdue University, West Lafayette, Indiana, December 4, 1997.
  41. Indiana-Purdue University, Indianapolis, Indiana, January 29, 1998.
  42. Ohio State University, Columbus, Ohio, February 4, 1998.
  43. University of Pittsburgh, Department of Physics, Pittsburgh, Pennsylvania, April 30, 1998.
  44. Tohoku University, Research Institute of Electrical Communication, Sendai, Japan, May 19, 1998.
  45. Tokyo University, Department of Physics, Tokyo, Japan, July 1, 1998.
  46. Instituto Superior Technico, Department of Materials Engineering, Lisbon, Portugal,March 10, 1999.
  47. International Workshop on Dynamics of Interfaces, Patterns and Domains '99, Los Alamos National Laboratory, Los Alamos, NM, April 22, 1999.
  48. CIRCS, Northeastern University, Boston, MA, June 8, 1999.
  49. Emory University, Department of Physics, Colloquium, Atlanta GA, February 4, 2000.
  50. New York University, Department of Biology, New York, NY, February 10, 2000.
  51. University of South Florida, Department of Physics, Tampa, FL, March 24, 2000.
  52. Department of Biology, University of Utrecht, Utrecht, the Netherlands, June 14, 2000.
  53. Workshop on "Models of Biological Motion," Collegium Budapest, Budapest, Hungary, June 19, 2000.
  54. International Center for Complex Systems and Department of Physics, Universidade Federaldo Rio Grande do Notre, Natal, Brazil, July 17, 2000.
  55. Department of Statistical Mechanics and Department of Biophysics, University of Sao Paolo, Sao Paolo, Brazil, July 19, 2000.
  56. Modelling Dictyostelium Morphogenesis, Symposium, Department of Theoretical Biology, University of Utrecht, Utrecht, Holland, October, 16, 2000.
  57. From Physics to Biology, Symposium, Departments of Physics, Biology and Instituteof Integrative Genomics, Princeton University, Princeton, NJ, October 21,2000.
  58. Laboratoirede Spectrometrie Physique, University Joseph Fourier, Grenoble, Grenoble, France, November 14, 2000.
  59. International Conference on Dynamical Aspects of Complex Systems, from Cells to Brain,Sendai International Center, Sendai, Japan, November 30, 2000.
  60. Laboratory of Complex Materials and Interfaces, Université de Marne la Vallée, Marne-la-Vallée, France, December 19, 2000.
  61. Laboratoirede Physique des Solides, Universite Paris-Sud, Orsay, France, December 20, 2000.
  62. Department of Physics Colloquium, Indiana University, Bloomington, IN, March 28, 2001.
  63. Department of Physics Colloquium, Kent State University, Kent, OH, April 5, 2001.
  64. Department of Biomathematics W. M. Keck Seminar in Computational Biology, University of California Los Angeles, Los Angeles, CA, April 19, 2001.
  65. Wellcome Institute of Biological Sciences, University of Dundee, Dundee, Scotland, June 1, 2001.
  66. Department of Physics Biophysics Colloquium, University of Illinois, Chicago, Chicago,IL, November 29, 2001.
  67. Department of Physics Colloquium, Carnegie Mellon University, Pittsburgh, PA, January 22, 2002.
  68. Department of Physics, Biophysics Seminar, Indiana University, Bloomington, IN, January 25, 2002.
  69. Department of Physics, O. M. Stewart Colloquium, University of Missouri, Columbia, MO, February 18, 2002.
  70. College of Engineering, Special Seminar, University of Missouri, Columbia, MO, February 19, 2002.
  71. Department of Physics, Physics Colloquium, Washington University, St. Louis, MO, March 12, 2002.
  72. ECMTB 2002, Milan, Italy, July 3, 2002.
  73. GEOMES Workshop, Max Planck Institute, Dresden, Germany, October 16, 2002.
  74. Department of Applied Mathematics, Max Planck Institute, Leipzig, Germany, October 21, 2002.
  75. Department of Bioengineering, Rice University, Houston, TX, February 17, 2003.
  76. Department of Physics, University of Houston, Houston, TX, February 18, 2003.
  77. DARPA ReGenesis Concept Development Workshop, San Diego, CA, March 18, 2003.
  78. Department of Physics Colloquium, IUPUI, Indianapolis, IN, March 27, 2003.
  79. Center for Nonlinear Dynamics, Department of Physics, University of Texas, Austin, TX, April 21, 2003.
  80. Department of Mathematics, University of Minnesota, Minneapolis, MN, April 24, 2003.
  81. Department of Physics, Princeton University, Princeton, NJ, April 28, 2003.
  82. Biomedical Engineering Society Annual Fall Meeting, Philadelphia, PA, October 16th, 2004.
  83. Keynote Address, ACRI 2004, Sixth International Conference on Cellular Automata for Research and Industry, Amsterdam, the Netherlands, October 26th, 2004.


On Chaos:

  1. University of Chicago, High Energy Physics Lunch Seminar (with Brian Kenny), 1986
  2. University of Chicago, J.F.I. Colloquium (with Brian Kenny), 1987.
  3. AMOCO Corporation, Naperville, Illinois, Amoco Research Center Colloquium, April 1988.
  4. University of Western Australia, Department of Geophysics Seminar, July 1989.
  5. University of Western Australia, Department of Computer Science Seminar, July 1989.
  6. University of Western Australia, Advanced Undergraduate Seminar Series, July 1989.
  7. University of Tasmania, Hobart, Australia, Australian Institute of Physics Public Lecture, July 1989.
  8. University of New South Wales, Sydney Australia, Department of Mathematics, August 1989.
  9. University of Utah, Salt Lake City, Utah, October 1989.
  10. Academia Sinica, Taipei, Taiwan, February 1992.
  11. University of Science and Technology of China, Heifei, PRC, June 1992.
  12. Harbin Teacher's University, Harbin, PRC, June 1992.
  13. Myriad Genetics Corporation, Salt Lake City, Utah, November 1993.
  14. University of Barcelona, Department of Physics, Barcelona, Spain, May 1994.
  15. XIII Max Born Symposium, Wroclaw, Poland, May 26th, 1999.
  16. Tohoku University, Research Institute of Electrical Communication, Sendai, Japan, November 17th, 1999.


On Cellular Patterns:

  1. University of Chicago, Chicago, Illinois, U. of Illinois/U. of Chicago meeting, 1987.
  2. Los Alamos National Laboratory, Los Alamos, New Mexico, Center for Nonlinear Studies Colloquium, December 1987.
  3. Gordon Conference on Physical Metallurgy, Meriden, New Hampshire, July 1988.
  4. AT&T Bell Laboratories, Murray Hill, NJ 1989.
  5. University of Western Australia, Perth, Australia, Department of Physics Seminar, July 1989.
  6. Canterbury University, Christchurch, New Zealand, Department of Physics Seminar, August 1989.
  7. Cornell University, Ithaca, New York, LASSP Solid State Seminar, October 1989.
  8. TMMMS Meetings, Indianapolis, Indiana (presented by G.S. Grest), October 1989.
  9. American Physical Society General Meeting, Anaheim, California, March 1990.
  10. Exxon Research and Engineering, Annandale, New Jersey, September 1990.
  11. University of Massachusetts, Amherst, Department Colloquium, September 1990.
  12. University of Pennsylvania, Philadelphia, Pennsylvania, February 1991.
  13. Pennsylvania State University, University Park, Pennsylvania, February 1991.
  14. Purdue University, West Lafayette, Indiana, February 1991.
  15. Notre Dame University, South Bend, Indiana, February 1991.
  16. Emory University, Atlanta, Georgia, March 1991.
  17. Trinity College, Dublin, May 1991.
  18. International Conference on Grain Growth and Recrystallization, Rome, Italy (presented by Denis Weaire) 1991.
  19. Academia Sinica, Taipei, Taiwan, February 1992.
  20. University of Science and Technology of China, Heifei, PRC, June 1992.
  21. Harbin Teacher's University, Harbin, PRC, June 1992.
  22. Department of Physics, Tohoku University, Sendai, Japan, July 1992.
  23. G.I.R.I.T. Laboratory, Sendai, Japan, August 1992.
  24. Loyola University, Chicago, IL, February 1994.
  25. Foams Euroconference, Renvyle, Ireland, March 1994.
  26. University of Barcelona, Barcelona, Spain, May 1994.
  27. NSF/IMM Workshop, Rockwell Science Center, Thousand Oaks, CA, November 1995.
  28. Gordon Conference on Foams, Plymouth, NH, August 1996.
  29. Dow Chemical Company, Freeport, TX, April 1996.
  30. Second Euroconference on Foams, Arcachon, France, May 1996.
  31. University of Chicago, Department of Physics, September 1996.
  32. Department of Materials Engineering, Instituto Superior Technico, Lisbon, Portugal, May 1997.
  33. Clarkson University, Department of Physics, Pottsdam, NY, July 7, 1997.
  34. Tohoku University, Research Institute of Electrical Communication, Sendai, Japan, July 23, 1997.
  35. Academia Sinica, Department of Physics, Taipei, Taiwan, July 30, 1997.
  36. Sandia National Laboratories, Albuquerque, New Mexico, August 6, 1997.
  37. Tsukuba University, Institute of Applied Physics, Tsukuba, Japan, July 6, 1998.
  38. Japan Fine Ceramics Center, Nagoya, Japan, July 7, 1998.
  39. Tohoku University, Research Institute of Electrical Communication, Sendai, Japan, July 8, 1998.
  40. Chuo University, Department of Physics, Tokyo, Japan, July 10, 1998.
  41. Centro Brasiliero de Pesquisas Fsicas, Rio de Janiero, Brazil, August 7, 1998.
  42. Universidade Federal do Rio Grande do Sul, Department of Physics Colloquium, Porto Alegre, Brazil, August 11, 1998.
  43. Universidade Federal So Paolo, Department of Statistical Physics, Sa Paolo, Brazil, August 14, 1998.
  44. University of Science and Technology of China, Department of Physics, Hefei, PRC, December 17, 1998.
  45. Fudan University, Department of Physics, Shanghai, PRC, December 22, 1998.
  46. Los Alamos National Laboratory, Center for Nonlinear Systems Colloquium, Los Alamos, NM, January 27, 1999.
  47. Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, June 7th, 1999.
  48. New York University, Department of Physics, Colloquium, New York, NY, February 10th, 2000.
  49. Eurofoam 2000, Technical University, Delft, Delft, the Netherlands, June 7, 2000.
  50. Leiden University, Department of Physical and Macromolecular Chemistry, Leiden, the Netherlands, June 13, 2000.
  51. National Polytechnic Institute of Grenoble, Department of Physical Engineering and Mechanics of Materials, Grenoble, France, October 12, 2000
  52. University of Lyon, Claude Bernard, Department of Materials Physics, Lyon, France, 10/13/00.
  53. University of Paris VI/VII, Jussieu, Joint Condensed Matter, Biophysics Seminar, Paris, France, November 11, 2000.
  54. Laboratoire de Physique, Ecole Normale Superieure de Lyon, Lyon, France, December 14, 2000.
  55. Department of Physics, University of South Florida, March 23, 2001.
  56. Interdisciplinary Center in Nonlinear Science, Northwestern University, Evanston, IL, December 7, 2001.
  57. Plasticity 2002, Aruba, January 7, 2002.
  58. Eurofoam 2002, Manchester, England, July 9, 2002.
  59. Foams and Minimal Surfaces, Isaac Newton Institute, Cambridge, England, August 6, 2002.
  60. GEOMES Conference, Max Planck Institute, Dresden, Germany, October 22, 2002.


On Turbulence:

  1. Workshop on Convective Turbulence, Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, CA, March 31, 2000.
  2. Department of Materials Engineering, Instituto Superior Technico, Lisbon, Portugal, May 24, 2000.
  3. Department of Physics Colloquium, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, July 11, 2000.
  4. Center for Nonlinear Science, Los Alamos National Laboratory, Los Alamos, NM, August 24th, 2000.
  5. Laboratory of Geophysics and Industry, Joint Fluid Mechanics and Magnetohydrodynamics Seminar, Grenoble, France, September 28, 2000.




Personnel


Visitors:

Prof. Jose Mombach ---March 1994 - April 1995
Centro de Ciencias Exatas e Tecnologicas Unisinos
Homepage: http://www.inf.unisinos.br/~mombach/
E-mail: mombach [at] exatas (dot) unisinos (dot) br
Dr. Emma Stott  August 1997 - November 1997

Dr. Florence Elias  March 1998 - May, 1998
Laboratoire des Milieux Désordonnés et Hétérogènes
University of Paris 6
Lab: http://www.ccr.jussieu.fr/lab/p6/ufr925/lab14/d.html
University: http://www.jussieu.fr/
E-mail: elias [at] ccr (dot) jussieu (dot) fr
Dr. Simon Cox  October 1999 - December 1999
Department of Physics
Trinity College, Dublin
Homepage: http://www.maths.tcd.ie/~simoncox/
E-mail: coxs [at] tcd (dot) ie
Prof. Rita de Almeida  November 1999 - January 2000
Instituto de Fisica
Universidade Federal do Rio Grande do Sul
Institute: http://www.if.ufrgs.br/
E-mail: rita [at] if (dot) ufrgs (dot) br
Prof. Nestor Oiwa  November 1999 - February 2001
Instituto de Física da Universidade de São Paulo
http://www.if.usp.br/
http://www.fge.if.usp.br
E-mail: oiwa [at] fge (dot) if (dot) usp (dot) br
Deilson de Melo Tavares  September 2000 - January 2001
Universidade Federal do Rio Grande do Norte
http://www.ufrn.br/
E-mail: deilson [at] dfte (dot) ufrn (dot) br
Isabelle Cantat  October 2002 - November 2002
Universite de Rennes 1, France
http://www.univ-rennes1.fr/
isabelle (dot) cantat [at] univ-rennes1 (dot) fr
Manuel Balaguera  November 2002 - Present


Postdoctoral Fellows:

Dr. Constantinos Gonatas ---June 1993 - January 1994  
Dr. Claudia Mohr  September 1995 - August 1997  
Dr. Igor Veretennikov   September 1996 - September 2002 http://www.nd.edu/~ivereten/
Igor.N.Veretennikov.1 [at] nd (dot) edu
Prof. Gilberto Thomas  September 2000 - October 2002  

Ph.D. Students:

Cheryl Berthelsen, Ph.D. June, 1993 University of Mississippi
    (co-supervised with Mark Skolnick)
Yi Jiang, Ph.D. November, 1998 Los Alamos National Laboratories
Sridhar Raghavachari, Ph.D. June, 1999 Brandeis University
Burkhard Prause, Ph.D. May, 2000 Max-Planck Institute, Tübingen
Arpita Uphadhyaya, Ph.D. May, 2000 Massachusetts Institute of Technology
Mark Zajac, Ph.D. August, 2002 Co-supervised with Prof. G. Jones
Marius Asipauskas   NASA Glenn Research Laboratory
SengKai Wong Current Indiana University, Bloomington
Cheng Cui Current Indiana University, Bloomington
Zheng Wei Current Indiana University, Bloomington
Dragos Amarie Current Indiana University, Bloomington
Wendy Zhang Current Indiana University, Bloomington
Kun Chen Current Indiana University, Bloomington


Undergraduate Students:

Mike Bradshaw ---June 1993 - August 1994
Richard Raphael  June 1993 - December 1998
Deborah Denton  June 1994 - August 1994
Daniel Eklund  June 1994 - August 1995
Wendy Strech  May 1995 - August 1995
Richard Waltz  January 1996 - August 1996
Richard Hasty  June 1998 - August 1998
Kimberly Uchman  June 1998 - August 1998
Jeff Doucette  May 1999 - August 1999
Robert Lillis  May 1999 - September 1999
Brian Foley  May 1999 - September 1999
Candice Bookwalter   
Austin Gerig   
Carrie Williams   
Justin Robinson   
David Landy  June 2001 - September 2001
Ronan Lynch  June 2001 - September 2001
Karl Fedje  May 2001 - August 2001
Troy Anderson  May 2002 - August 2002
Christopher Lloyd  May 2002 - August 2002
Gabriel Benman  May 2003 - Present


High School Students:

John Clark ---June 1994 - August 1994
Jeff Doucette  March 1996 - April 1996
High Carell  March 1997 - August 1997
Buko Abele  May 1999 - August 1999
Greg Harris  March 2001 - April 2001
Medardo Rosario  May 2001 - July 2001