James Clarage
4309 Darsey
Bellaire, TX 77401
713.743.1520 (work)
713.669.9019 (home)
jclarage@uh.edu

Education

Ph.D. Physics 1990. Brandeis University, Waltham, MA
Thesis: Disorder in Protein Crystals

B. A. Math, B. A. Physics 1985. Illinois Wesleyan University, Bloomington, IL
Magna Cum Laude

Teaching and Research Interests

Biological Physics, Computational Science, Molecular and Crystal Dynamics, Astronomy and Astrophysics

Professional Experience

Adjunct Professor of Physics
School of Science And Computer Engineering
University of Houston – Clear Lake (2004-present)

Adjunct Professor of Physics
Department of Natural Sciences
University of Houston – Downtown (2007-present)

Team Lead, User Interface Team
Department of Web Technologies
University of Houston (2003-present)

Lecturer and Internet Developer
Information Technology
University of Houston (2000-2003)

Artist in Residence
DiverseWorks theater (2000)

Board Member
Art Institute of Houston school (1998-2001)

Scientific Programmer
Department of Biochemistry and Cell Biology
Rice University (1998-1999)

Lecturer and Research Scientist
Institute of Biosciences and Bioengineering
and Keck Center for Computational Biology
Rice University (1994-1997)

Postdoctoral Fellow,
W. M. Keck Center for Computational Biology
Rice University (1991-1994)

Assistant
Mark Evans Observatory
Bloomington, IL (1984-85)

Teaching Experience

University of Houston – Downtown (2007-present)
Physics courses including:
PHYS 1307/1308, College Physics

University of Houston – Clear Lake (2004-present)
Physics courses including:
ASTR 3131, Modern Astronomy
Workshop, Student Conference for Research and Creative Arts

University of Houston (2000-present)
Various guest lectures for courses in the Philosophy Department, School of Communication, College of Technology, including:
COMM 3353, Web Technologies I
PHIL 1361, Philosophy and the Arts
OCTE 4397, Web Page Design

Rice University (1995-1999)
Taught interdisciplinary courses with undergraduate and graduate students from physics, biology and mathematics, including:
BIOS 481, Molecular Biophysics
BIOS 482, Molecular Biophysics

Grant Support

CowParade foundation, commission for computer-driven cow sculpture, 2001

Artist in Residence, DiverseWorks, 2000

CACHH public arts grant, 1999

CO-P.I. on NSF grant 'Maximal Use of Information from Macromolecular X-ray Diffraction.'
$251,000 over three years, 1994-97.

NRSA Postdoctoral Fellowship GM-13945 from NIH.
$75,200 over three years, 1992-94

W. M. Keck Foundation Fellowship in Computational Biology.
$30,000 stipend, 1991-93

Publications

• Clarage JB, Cellular Automata models in alternative medicine. (in preparation)
• Clarage JB, Phillips GN Jr., Analysis of diffuse scattering and relation to molecular motion. Methods Enzymol. 1998;277:407-32.
• Andrews BK, Romo T, Clarage JB, Pettitt BM, Phillips GN Jr., Characterizing global substates of myoglobin. Structure. 1998 May 15;6(5):587-94
• Wall ME, Clarage JB, Phillips GN. Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure. 1997 Dec 15;5(12):1599-612.
• Romo. T. D., Clarage, J. B., Sorensen, D. C. and Phillips, G. N., Jr. Automatic Identification of Discrete Substates in Proteins: Singular Value Decomposition Analysis of Time-averaged Crystallographic Refinements. Proteins, 22:311-321, (1995)
• Clarage, J. B., Romo, T., Andrews, B. K., Pettitt, B. M. & Phillips G. N. Jr. A Sampling Problem in Molecular Dynamics Simulations of Macromolecules. Proc. Natl. Acad. Sci., USA, 92:3288-3292, (1995)
• Clarage, J. B., and Phillips, G. N., Jr. Cross-validation Tests of Time-averaged Molecular Dynamics Refinements for Determination of Protein Structures by X-ray Crystallography. Acta Cryst., D50:24-36 (1994)
• Kolatkar, A., Clarage, J. B., Phillips, G. N., Jr. Analysis of Diffuse Scattering from Yeast Initiator tRNA Crystals. Acta Cryst. D50:210-218 (1994).
• Clarage, J. B., and Phillips, G. N., Jr. Protein Crystallography and Molecular Dynamics on the Connection Machine. Biophys. J. abstracts, 61:A448 (1992)
• Clarage,J.,Clarage,M.,Caspar,D. L. D. Correlation of Atomic Movements in Lysozyme Crystals, Proteins, 12:145-157 (1992)
• Caspar,D. L. D.,Clarage,J.,Salunke,D. M.,Clarage,M. Liquid-like Movements in Crystalline Insulin, Nature, 332:659-662 (1988)

Other Publications (essays and fiction)

• Clarage. J. B. 'Udder Dada', CD rom for Houston CowParade, (2001)
• Clarage, J. B. 'Web Labyrinth', WIRED magazine, 4.08 (1996)
• Clarage, J. B. 'Is There New Art on the Internet?', Zocalo News, (1996)
• Clarage, J. B. 'Changing Experience', WIRED magazine, 3.12 (1995)
• Clarage, J. B. 'Surfing' University Blue vol. XII, (1995)
• Clarage, J. B. 'Portrait of the Artist as a Young Surfer' Trincoll Journal, April 27, (1995)
• Clarage, J. B. 'New Muse' SOC, vol. 3 (1994)
• Clarage, J. B. 'High Bawd Helena' Cyberkind (1994)
• Clarage, J. B. 'Mixing Blood with Fire' Texas Magazine (1994)
• Clarage, J. B. 'She Psyches Me up, this Mother Nature' Prophetic Witness (1993)

Invited Lectures / Presentations

• 'Dynamics of Biological Molecules,' University of Houston, Clear Lake, 2006
• 'The Golden Ratio in Physics, Art and Technology,' World Year of Physics event, University of Houston, Clear Lake, 2005
• 'Human Factors and Accessibility in Design', Disabilities Awareness Week, University of Houston, 2005
• 'Biofeedback as a User Interface', University of Houston, 2004
• 'The Golden Ratio in Art, Science, Design and Technology', University of Houston, 2003
• 'Web Accessibility', IT Training, University of Houston, 2003
• 'Tufte's Theory of Information Design', School of Communications, University of Houston, 2002
• 'Making the Internet Accessible to the Disabled', University of Houston, 2002
• 'Udder Dada', multimedia kiosk for the Houston Cow Parade, 2001
• 'Computers and Modern Art', Philosophy Department, University of Houston, 2001
• 'Jonah and the WWWhale', multimedia theater production, DiverseWorks theater, Houston, 2000
• 'Planet-X', Multimedia Exploration of Mathematics and Music, performed in collaboration with OrchestraX symphony and choir, Houston Museum of Natural Science, 1998
• 'Lives of a Protein.' Symposium on Mathematics of Quasi-Equivalence, Florida State University, 1997
• 'www.Faust', multimedia theater production, Zocalo theater, Houston 1996
• 'Chaos, Sub-states and Sampling in Protein Dynamics.' Biophysical Society. Baltimore, MD, 1996
• 'Molecular Motion in Proteins and Nucleic Acids.' Symposium on X-ray and Neutron scattering, Brookhaven National Lab, 1996
• 'A Sampling Problem in Molecular Dynamics Simulations of Macromolecules.' Biophysical Society. San Francisco, CA, 1995
• 'Studies of Diffuse Scattering Reveal Liquid-like Disorder in Protein Crystals.' International Union of Crystallography. Beijing, China, 1993
• 'Analysis of Diffuse Scattering from Proteins and Nucleic Acids.' International Union of Crystallography. Beijing, China, 1993

Software Packages in Computational Science

Biology Workbench
( workbench.sdsc.edu )
On development team of web-based genetic and structural research tool for biology and medicine. Used Perl, HTML and OpenGL to create webpages from multiple dynamic datasources, including a web version of XRayView, a browser-based crystallography teaching tool.

XCADS
(X-ray Crystallographic Analysis of Diffuse Scattering)
Suite of programs to analyze and simulate diffuse scattering due to molecular and crystal disorder.

Technical Skills

Languages: Mathematica, C, FORTRAN, PHP, SQL, Perl, Coldfusion, UNIX shell scripting, HTML, XHTML, CSS

Environments: UNIX, Apache/MySQL/PHP, Macintosh OS-X, Windows

Design: Macromedia Studio MX 2004, Adobe Creative Suite, Director, PeopleSoft Application Designer

Project Management: Microsoft Project, FastTrack, Project Management Certificate Program (35 units recognized by PMI)

Observational Astronomy: own and operate my own Celestron telescope

References

George N. Phillips Jr.
Department of Biochemistry
433 Babcock Drive
Madison, WI 53706-1544
(608) 262-3040
phillips@biochem.wisc.edu

Donald L. D. Caspar
Institute of Molecular Biophysics
Mail code 4380
Florida State University
Tallahassee, FL 32306
(850) 644-5522
caspar@sb.fsu.edu

Kim B. Andrews
Manager, Research Computing
Academic & Research Computing MS119
Rice University
6100 Main
Houston, TX 77005
(713) 348-5726
kimba@rice.edu

additional references available upon request

 

Document URL: http://www.uh.edu/~jclarage/science/vita