Professor Michael W. Deem: Publications

MICHAEL W. DEEM

PUBLICATIONS
(Reprint links may work if your institution subscribes to the journal)

H. Zhou, R. Pophale, and M. W. Deem, ``Computer-Assisted Vaccine Design,'' in Influenza: Molecular Virology, Horizon Scientific Press, edited by Qinghua Wang and Yizhi Jane Tao, 2009.
E. T. Munoz, J.-M. Park, and M. W. Deem, ``Quasispecies Theory for Horizontal Gene Transfer and Recombination,'' submitted.
J. Sun and M. W. Deem, ``Statistical Mechanics of the Immune Response to Vaccines,'' in Statistical Mechanics of Cellular Systems and Processes, Cambridge University Press, edited by Muhammad H. Zaman, 2008.
D. J. Earl, A. W. Burton, T. Rea, K. Ong, M. W. Deem, S.-J. Hwang, and S. I. Zones, ``Synthesis and Monte Carlo Structure Determination of SSZ-77: A New Zeolite Topology,'' with cover image, J. Phys. Chem. C 112 (2008) 9099-9105 (Reprint).
E. T. Munoz and M. W. Deem, ``Amino Acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small Library Thoroughly or a Large Library Sparsely?'' with cover image, Protein Engineering, Design and Selection 21 (2008) 311-317 (Reprint).
D. J. Earl and M. W. Deem, ``Monte Carlo Simulations,'' in Methods in Molecular Biology, vol. 443, Molecular Modelling of Proteins, edited by Andreas Kukol, Humana Press, Totowa, NJ, 2008.
J. Sun and M. W. Deem, ``Spontaneous Emergence of Modularity in a Model of Evolving Individuals,'' Phys. Rev. Lett. 99 (2007) 228107 (Reprint) (also in Virtual Journal of Biological Physics Research, 1 December 2007).
J.-M. Park and M. W. Deem, ``Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer,'' Phys. Rev. Lett. 98 (2007) 058101 (Reprint) (also in Virtual Journal of Biological Physics Research, 1 February 2007).
M. W. Deem, "Mathematical Adventures in Biology," invited feature article, with cover image, Physics Today 60 (January 2007) 42-47 (Reprint). (In Japanese) (AIP Holiday Card).
J.-M. Park and M. W. Deem, ``Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory,'' J. Stat. Phys. 125 (2006) 971-1011 (or 975-1015) (Reprint).
G. Wang and M. W. Deem, ``Physical Theory of the Competition that Allows HIV to Escape from the Immune System,'' Phys. Rev. Lett. 97 (2006) 188106 (Reprint) (also in Virtual Journal of Biological Physics Research, 15 November 2006).
Z. Li, M. C. Johnson, M. Sun, E. T. Ryan, D. J. Earl, W. Maichen, J. I. Martin, S. Li, C. M. Lew, D. I. Medina, J. Wang, M. W. Deem, M. E. Davis, and Y. Yan, ``Mechanical and Dielectric Properties of Pure-Silica-Zeolites as Low-k Materials,'' Angew. Chem. Int. Ed. 45 (2006) 6329-6332 (Reprint).
M. Yang, J.-M. Park, and M. W. Deem, ``A Theory of Multi-Site Vaccination for Cancer,'' Physica A 366 (2006) 347-364 (Reprint).
M. Yang, J.-M. Park, and M. W. Deem, ``Evolutionary Design in Biological Physics and Materials Science,'' Lect. Notes Phys. 704 (2006) 541-562 (Reprint).
D. J. Earl and M. W. Deem, ``Toward a Database of Hypothetical Zeolite Structures,'' Eduardo Glandt special issue, Ind. & Eng. Chem. Res. 45 (2006) 5449-5454 (Reprint).
V. Gupta, D. J. Earl, and M. W. Deem, ``Quantifying Influenza Vaccine Efficacy and Antigenic Distance,'' Vaccine 24 (2006) 3881-3888 (Reprint).
D. Saakian, E. T. Munoz, C-K. Hu, and M. W. Deem, ``Quasispecies Theory for Multiple-Peak Fitness Landscapes,'' Phys. Rev. E 73 (2006) 041913 (Reprint).
R. A. Curtis, R. S. Pophale, and M. W. Deem, ``Monte Carlo Simulations of the Homopolypeptide Pair Potential of Mean Force,'' John M. Prausnitz special issue, Fluid Phase Equilibria 241 (2006) 354-367 (Reprint).
H. Zhou and M. W. Deem, ``Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination,'' Vaccine 24 (2006) 2451-2459 (Reprint).
J. Sun, D. J. Earl, and M. W. Deem, ``Localization and Glassy Dynamics in the Immune System,'' invited review, Mod. Phys. Lett. B 20 (2006) 63-95 (Reprint).
M. W. Deem, ``Entropy, Disease, and New Opportunities for Chemical Engineering Research,'' Perspective, invited, with cover image, AIChE J. 51 (2005) 3086-3090 (Reprint).
D. J. Earl and M. W. Deem, ``Parallel Tempering: Theory, Applications, and New Perspectives,'' invited review, with cover, image Phys. Chem. Chem. Phys. 7 (2005) 3910-3916 (Reprint) (Hot article).
M. W. Deem, ``Book Review: Introduction to Mathematical Methods in Bioinformatics,'' invited review, Physics Today, October 2005, 83-84.
J. Sun, D. J. Earl, and M. W. Deem, ``Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease,'' Phys. Rev. Lett. 95 (2005) 148104 (Reprint) (Highlight).
D. J. Earl and M. W. Deem, ``Markov Chains of Infinite Order and Asymptotic Satisfaction of Balance: Application to the Adaptive Integration Method,'' David Chandler Festschrift, J. Phys. Chem. B 109 (2005) 6701-6704 (Reprint).
M. W. Deem, ``Complexity in the Immune System,'' Systems Engineering Challenges and Opportunities in Biology issue, invited, Comput. Chem. Eng. 29 (2005) 437-446 (Reprint).
T. Tan, D. Frenkel, V. Gupta, and M. W. Deem, ``Length, Protein-Protein Interactions, and Complexity,'' Physica A 350 (2005) 52-62 (Reprint).
E. T. Munoz and M. W. Deem, ``Epitope Analysis for Influenza Vaccine Design,'' Vaccine 23 (2005) 1144-1148 (Reprint).
T. Tan, L. D. Bogarad, and M. W. Deem, ``Modulation of Base Specific Mutation and Recombination Rates Enables Functional Adaptation within the Context of the Genetic Code,'' J. Mol. Evol. 59 (2004) 385-399 (Reprint).
D. J. Earl and M. W. Deem, ``Evolvability is a Selectable Trait,'' Proc. Natl. Acad. Sci. USA 101 (2004) 11531-11536 (Reprint) (News and Commentary) (In Brief).
J.-M. Park and M. W. Deem, ``Correlations in the T Cell Response to Altered Peptide Ligands,'' Physica A 341 (2004) 455-470 (Reprint).
D. J. Earl and M. W. Deem, ``Optimal Allocation of Replicas to Processors in Parallel Tempering Simulations,'' Hans C. Andersen Festschrift, J. Phys. Chem. B 108 (2004) 6844-6849 (Reprint).
E. T. Munoz, L. D. Bogarad, and M. W. Deem, ``Microarray and EST Database Estimates of mRNA Expression Levels Differ: The Protein Length versus Expression Curve for C. elegans,'' BMC Genomics 5 (2004) 30 (Reprint).
M. W. Deem, ``Complexity in the Immune System: New Opportunities for Chemical Engineering Research,'' Perspective, invited, with cover image, AIChE J. 50 (2004) 734-738 (Reprint).
M. W. Deem, ``Evolution and Evolvability of Proteins in the Laboratory,'' Commentary, invited, Proc. Natl. Acad. Sci. USA 101 (2004) 3997-3998 (Reprint).
L. Chen and M. W. Deem, ``Two-Dimensional Diffusion in the Presence of Topological Disorder,'' Phys. Rev. E 68 (2003) 021107 (Reprint).
J.-M. Park and M. W. Deem, ``A Statistical Theory of Isotropic Turbulence Well-Defined within the Context of the epsilon Expansion,'' Eur. Phys. J. B 34 (2003) 105-114 (Reprint).
R. A. Curtis and M. W. Deem, ``A Statistical Mechanics Study of Ring Size, Ring Shape, and the Relation to Pores Found in Zeolites,'' J. Phys. Chem. B 107 (2003) 8612-8620 (Reprint).
M. W. Deem and H. Y. Lee, ``Sequence Space Localization in the Immune System Response to Vaccination and Disease,'' Phys. Rev. Lett. 91 (2003) 068101 (Reprint).
M. W. Deem, ``The Monte Carlo Approach to Library Design and Redesign,'' chapter, invited, in Experimental Design for Combinatorial and High Throughput Materials Development, John Wiley & Sons, 2003, pp. 239-276 (Reprint and Review).

ARXIV PREPRINT SEARCH: Quantitative Biology or Condensed Matter
The most recent publications above are archived in an electronic, downloadable format.

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