Research Interests

Selected Publications


Research Group



Associate Professor of Chemistry

The College of William and Mary
PO Box 8795
Williamsburg, VA 23187-8795

office phone : 757-221-2556
department fax: 757-221-2715

Ph.D. UCLA 1991; Research advisor: William M. Gelbart
Postdoctoral fellow, University of Chicago; Advisor: David W. Oxtoby
Posdoctoral fellow, Albert Einstein College of Medicine: Advisors: Steven D. Schwartz and Vern L. Schramm

My background in equilibrium and nonequilibrium statistical mechanics (and a somewhat restless nature) has led me through and to the fields of self-assembly in amphiphilic systems, crystal-growth dynamics, protein motors, enzyme inhibitor design, enzyme dynamics, and complex systems theory. I've landed, recently and firmly and enamored of it, in the grips of ecosystem science and food-web dynamics. And thanks to my collaborator Amy Dunham, currently at the Smithsonian Institution, I've finally learned that the natural world is far more fascinating than the machinations of a theorist's mind.


The food-web is one of the earliest and most fundamental concepts in ecology, yet its relation to environmental feedbacks and ecosystem processes remains largely unexplored. Our question is: Can indirect interactions via environmental feedbacks promote persistence of organisms within a food-web and do trophic structure and food-web characteristics in turn affect ecosystem processes? Our work attempts to unite food-web dynamics, ecological stoichiometry, emergent regulatory systems, and biodiversity/ecosystem functioning. In preliminary work a feedback system modeled after Lovelock's Daisyworld was embedded in otherwise conventional food-web models (food-web networks featuring predator-prey dynamics only). We are learning that, regardless of trophic structuring, daisyworld dynamics increases on average the dynamical persistence of multitrophic food-webs. The "on average" qualifier, of course, hints at the wonderful complexity of the results. Amy Dunham and I, along with my research students at The College of William and Mary, are developing scenarios by which more realistic environmental feedbacks can be embedded into multitrophic food-webs. In addition to food-web generation, predator-prey dynamics, and introduction of stoichiometric or regulatory functionality, the work features genetic-algorithm evolution of food-web structures and analysis through neural network modeling.


Biodiversity Maintenance and Vulnerability in Food Webs with Regulatory Environmental Feedbacks. C.K. Bagdassarian, A.E. Dunham, C.G. Brown, D. Rauscher, Journal of Theoretical Biology, in review.

Evolution of Rate-Promoting Oscillations in a Model Enzyme. G.S. Blair Williams, A.M. Hossain, D.E. Kranbuehl and C. K. Bagdassarian, Journal of Physical Chemistry B,107, 12527 (2003).

Evolution of a Catalytically Effective Model Enzyme: The Importance of Tuned Conformational Fluctuations. G.S. Blair Williams, A.M. Hossain, S. Shang, D.E. Kranbuehl and C. K. Bagdassarian, Journal of Theoretical and Computational Chemistry,2, 323 (2003).

Coupled Genetic Algorithm/Kohonen Neural Network (GANN) for Projection of Three-Dimensional Protein Structures Onto the Plane. K.O. Alper and C.K. Bagdassarian, Journal of Theoretical and Computational Chemistry, 1, 45 (2002).

Enzymatic Conformational Fluctuations Along the Reaction Coordinate of Cytidine Deaminase. R.C. Noonan, C.W. Carter Jr., and C.K. Bagdassarian, Protein Science, 11, 1424 (2002).

Correlated Conformational Fluctuations During Enzymatic Catalysis: Implications for Catalytic Rate Enhancement. K.O. Alper, M. Singla, J.L. Stone, and C.K. Bagdassarian, Protein Science, 10, 1319 (2001).

Conformational Fluctuations and Protein Function: the Thermodynamics of a Brownian Motor. C.K. Bagdassarian and R.D. Astumian, in Thermodynamics in Biology, ed E. Di Cera, Oxford (2000).

Prostanoid Receptors: Subtypes and Signaling. R. M. Breyer, C. K. Bagdassarian, S. A. Meyers, and M. D. Breyer, Ann. Rev. Pharmacology and Toxicology, 41, 661 (2001).

Association Entropy in Adsorption Processes. N. Ben-Tal, B. Honig, C. K. Bagdassarian, and A. Ben-Shaul, Biophys. J. 79, 1180 (2000).

Quantum Neural Networks Can Predict Binding Free Energy for Enzymatic Inhibitors. B. B. Braunheim, C. K. Bagdassarian, V. L. Schramm, and S. D. Schwartz, Int. J. of Quant. Chem.,78, 195 (2000).

Synthesis of Surface-Metallized Polymeric Films by in situ Reduction of (4,4,4-triflouro-1-(2-thienyl)-1,3-butanedionato) silver(I) in a Polyamide Matrix. R. E. Southward, C. K. Bagdassarian, C. J. Sudol, J. L. Wasyk, S. H. Sproul, S. T. Broadwater, J. L. Scott, and D. W. Thompson, J. Mat. Res. 14, 2897 (1999).

Purine Nucleoside Phosphorylase. Transition State Structure, Transition State Inhibitors and One-Third-The-Sites Reactivity. R. W. Miles, P. C. Tyler, R. H. Furneaux, C. K. Bagdassarian, and V. L. Schramm, in Enzymatic Mechanisms, eds. P. A. Frey and D. B. Northrop, IOS Press (1999).

Deamination of Nucleosides and Nucleotides and Related Reactions. V. L. Schramm and C.K.Bagdassarian, in Comprehensive Natural Products Chemistry, eds. Sir D. Barton, K. Nakanishi, and C. D. Poulter, Elsevier Science, Oxford (1999).

One-Third-the-Sites Transition-State Inhibitors for Purine Nucleoside Phosphorylase. R. W. Miles, P.C. Tyler, R. H. Furneaux, C. K. Bagdassarian, and V. L. Schramm, Biochemistry, 37, 8615 (1998).

Pre-Steady-State Kinetic Analysis of the Reactions of Alternative Substrates with Dialkylglycine Decarboxylase. S. Sun, C. K. Bagdassarian, and Michael D. Toney, Biochemistry, 37, 3876 (1998).

Molecular Electrostatic Potential Analysis for Enzymatic Substrates, Competitive Inhibitors, and Transition-State Inhibitors. C. K. Bagdassarian, V. L. Schramm, and S. D. Schwartz, J. Am. Chem. Soc. 118, 8825 (1996).

Quantitative Measures of Molecular Similarity: Methods to Analyze Transition State Analogs for Enzymatic Reactions. C. K. Bagdassarian, B. B. Braunheim, V. L. Schramm, and S. D. Schwartz, Int. J. of Quant. Chem.: Quant. Biol. Symp.23, 1797 (1996).

Enzymatic Transition States and Inhibitor Design from Principles of Classical and Quantum Chemsitry. V. L.Schramm, B. A. Horenstein, C. K. Bagdassarian, S. D. Schwartz, P. Berti, K. A. Rising, J. Scheuring, P. C. Kline, D. W. Parkin, and D. J. Merkler, Int. J. of Quant. Chem.: Quant. Biol. Symp.23, 81 (1996).

Trypanosomal Nucleoside Hydrolase. Resonance Raman Spectroscopy of a Transition-State Inhibitor Complex. H. Deng, A. W.-Y. Chan, C. K. Bagdassarian, B. Estupinan, B. Ganem, R. H. Callender, and V. L. Schramm, Biochemistry35, 6037 (1996).


Thomas Jefferson Teaching Award, William and Mary, 2003
Phi Beta Kappa Faculty Award for the Advancement of Scholarship, W&M, 2002




I typically work with 2 to 3 research students at a time, who come to speed during the summer prior to their senior year.

My present undergraduate students are Monica Tremont, Will Green, and Natalie Herring. Armen Sharabian is a Master's degree student.




This will take you to courses offered at William and Mary's Chemistry Department. Below are lecture classes I've taught and teach. The syllabi you'll find, through the link above, are those of the current instructors. In all my courses, especially Biophysical Chemistry, I work in a good deal of complex systems theory and emergent behavior. Additionally, I'm involved in the general and physical chemistry laboratories.

Chemistry 341: Principles of Biophysical Chemistry
Chemistry 301: Physical Chemistry I
Chemistry 308: General Chemistry II
Chemistry 335: Chemical Principles


Coming soon