B.S. Chemical Engineering (1991) California Institute of Technology
Ph.D. Chemical Engineering (1994) University of California at Berkeley
Immune response to variable or multi-strain viruses and vaccine. Physical theories of pathogen evolution. Vaccine design. Newton's laws of biology.
Email: mwdeem@rice.edu
Phone:
Office: Keck Hall, 130
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Michael W. Deem
John W. Cox Professor of Biochemical and Genetic Engineering and Professor of Physics & Astronomy
DEEM GROUP HOME PAGE Theoretical methods of statistical mechanics are developed and applied at Rice to study the collective properties of biological systems. Both computational and analytical methods are of interest. Natural systems from our world and engineered systems from biotechnology offer a wide variety of phenomena for study. New field-theoretic techniques, new computer simulation methods, and new random energy models have resulted. Current areas of interest include - Immune response to variable or multi-strain viruses and vaccines.
- Physical theories of evolution.
- Cystine-knot antimicrobials and the innate immune system.
- Structure and nucleation of zeolites.
Of particular interest are those biological issues involving randomness, diversity, and correlations. The group has developed methods to quantify vaccine effectiveness and antigenic distance for influenza, methods to sculpt the immune system to mitigate immunodominance in dengue fever, a physical theory of the competition that allows HIV to escape from the immune system, and the first exact solution of a mathematical model of evolution that accounts for cross-species genetic exchange. The adaptive immune response to viruses and vaccines is studied with a variety of random energy models. Field theories are used to analyze physical theories of evolution. In the materials field, the group has developed a number of widely-used Monte Carlo methods in structure, nucleation, and function of zeolites and remains interested in these areas. Our research is supported by the National Institutes of Health, the Department of Energy Office of Basic Energy Sciences, and the National Science Foundation.
Selected Publications
Abstract
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?." Protein Engineering, Design and Selection, 21 (2008): 311-317.
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
Article
J. He, J. Sun, and M. W. Deem "Spontaneous Emergence of Modularity in a Model of Evolving Individuals and in Real Networks." .(Submitted)
E. T. Munoz, J.-M. Park, and M. W. Deem "Solution of the Crow-Kimura and Eigen Models for Alphabets of Arbitrary Size by Schwinger Spin Coherent States." .(Submitted)
J.-M. Park, E. T. Munoz, and M. W. Deem "Quasispecies theory for finite populations." .(Submitted)
Y. Lu, A. Burykin, M. W. Deem, and T. G. Buchman "Predicting Clinical Physiology: A Markov Chain Model of Heart Rate Recovery After Spontaneous Breathing Trials in Mechanically Ventilated Patients." J. Crit. Care..(In Press)
Y. Yan, M. Sun, W. Maichen, R. Pophale, Y. Liu, R. Cai, C. M. Lew, H. Hunt, M. W. Deem, and M. E. Davis "Dielectric Constant Measurement of Zeolite Powders by Time Domain Reflectometry
." .(Submitted)
E. T. Munoz, J.-M. Park, and M. W. Deem "Quasispecies Theory for Horizontal Gene Transfer and Recombination." Phys. Rev. E, 78 (2008): 061921.
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." J. Phys. Chem. C, 112 (2008): 9099-9105.
Book chapter
D. J. Earl and M. W. Deem "Monte Carlo Simulations." Methods in Molecular Biology: Molecular Modelling of Proteins, 443 (2008): 25-36.
H. Zhou, R. Pophale, and M. W. Deem "Computer-Assisted Vaccine Design." Influenza: Molecular Virology (2009).(In Press)
J. Sun and M. W. Deem "Statistical Mechanics of the Immune Response to Vaccines." tatistical Mechanics of Cellular Systems and Processes (2009).(In Press)
Book review
M. W. Deem "Book Review: Introduction to Mathematical Methods in Bioinformatics." (October 2005): 83-84.
Refereed Article
M. W. Deem, "Mathematical Adventures in Biology," Physics Today, to appear.
J. Sun and M. W. Deem, ``Spontaneous Emergence of Modularity in a Model of Evolving Individuals,'' Phys. Rev. Lett., to appear.
J.-M. Park and M. W. Deem, ``Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer,'' Phys. Rev. Lett. 98 (2007) 058101
M. W. Deem, "Mathematical Adventures in Biology," invited feature article, Physics Today 60 (January 2007) 42-47
M. W. Deem "Complexity in the Immune System." Comput. Chem. Eng., 29 (2005): 437-446.
M. W. Deem "Entropy, Disease, and New Opportunities for Chemical Engineering Research." AIChE J., 51 (2005): 3086-3090.
E. T. Munoz and M. W. Deem "Epitope Analysis for Influenza Vaccine Design." Vaccine, 19 (2005): 1144-1148.
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.
T. Tan, D. Frenkel, V. Gupta, and M. W. Deem "Length, Protein-Protein Interactions, and Complexity." Physica A, 350 (2005): 52-62.
D. J. Earl and M. W. Deem "Markov Chains of Infinite Order and Asymptotic Satisfaction of Balance: Application to the Adaptive Integration Method." J. Phys. Chem. B, 109 (2005): 6701-6704.
D. J. Earl and M. W. Deem "Parallel Tempering: Theory, Applications, and New Perspectives." Phys. Chem. Chem. Phys., 7 (2005): 3910-3916.
M. Yang, J.-M. Park, and M. W. Deem, ``A Theory of Multi-Site Vaccination for Cancer,'' Physica A 366 (2006) 347-364
M. Yang, J.-M. Park, and M. W. Deem, ``Evolutionary Design in Biological Physics and Materials Science,'' Lect. Notes Phys. 704 (2006) 527-548
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
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
G. Wang and M. W. Deem, ``A Physical Theory of the Competition that Allows HIV to Escape from the Immune System,'' Phys. Rev. Lett. 97 (2006) 188106
V. Gupta, D. J. Earl, and M. W. Deem, ``Quantifying Influenza Vaccine Efficacy and Antigenic Distance,'' Vaccine 24 (2006) 3881-3888
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
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.
H. Zhou and M. W. Deem, ``Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination,'' Vaccine 24 (2006) 2451-2459
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
Presentations
Invited Talk
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Biological Physics Seminar, Department of Physics, Arizona State University, Tempe, AZ. (28 November 2007)
"Evolutionary Design in Materials Science and Biological Physics." Seminar in Chemical Engineering, University of California, Santa Barbara, CA. (11 January 2006)
"How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Greater Boston Theoretical Lecture Series, Massachusetts Institute of Technology, Cambridge, MA. (5 November 2008)
"Localization in Antibody Sequence Space-A Mechanism for Original Antigenic Sin." Mini Statistical Mechanics Meeting, Berkeley, CA. (7-8 January 2005)
"Functional Integrals for the Parallel and Eigen Models of Virus Evolution." DARPA meeting on path integrals in biology, Johns Hopkins University, Baltimore, MD. (15 February 2006)
"Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Seminar in Computer Science Department, University of Chicago, Chicago, IL. (11 February 2005)
"Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination." Ehrlich II-2nd World Conference on Magic Bullets Celebrating the 100th Anniversary of the Nobel Prize Award to Paul Ehrlich, Nurnberg, Germany. (3-5 October 2008)
"Some Mathematical Adventures in Biology." eminar in Biomedical Engineering, Boston University, Boston, MA. (9 November 2007)
"Life has Evolved to Evolve (Evolvability is a Selectable Trait)." Colloquium in Physics, Johns Hopkins University, Baltimore, MD. (23 February 2006)
"Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Center for Theoretical Biological Physics, San Diego, CA. (4 March 2005)
"Physical Aspects of Vaccine Design for Influenza and Dengue Fever." eminar in Physical Chemistry, Harvard University, Cambridge, MA. (25 October 2007)
"Vaccine Design for Influenza and Dengue Fever." IChemE Distinguished Speakers Seminar Series, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom. (15 September 2008)
"Life has Evolved to Evolve." n seminar session The Experimental and Theoretical Foundations of Evolution, APS March Meeting, Baltimore, MD. (13-17 March 2006)
"Spontaneous Emergence of Modularity in a Model of Evolving Individuals." Seminar in Interdisciplinary Program in Networks, University of Houston, Houston, TX. (19 October 2007)
"Study of Zeolite Nucleation Kinetics." Catalysis in Fuel Chemistry Symposium, 229th ACS National Meeting, San Diego, CA. (13-17 March 2005)
"The Monte Carlo Sampling Approach to Construction of a Database of Hypothetical Zeolite Frameworks." CECAM Workshop on Surfactant Templated Porous Materials: Synthesis and Characterisation, EPFL, Zurich, Switzerland. (10-12 September 2008)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Seminar in Chemical Physics, National Institutes of Health, Bethesda, MD. (4 October 2007)
"Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Colloquium in Mathematics, Rice University, Houston, TX. (17 March 2005)
"Path Integral Representation of Evolution." DARPA Fundamental Laws of Biology Program Annual Meeting, Santa Barbara, CA. (10-12 May 2006)
"The Monte Carlo Sampling Approach to Construction of a Database of Hypothetical Zeolite Frameworks." International Center for Materials Research Workshop on Design and Synthesis of New Materials, Univesity of California, Santa Barbara, CA. (1-2 August 2008)
"Mitigating Immunodominance in Multi-Epitope Tumor Vaccines by Polytopic Vaccination." Cancer Biology and Therapy Modeling, SIAM Conference on the Life Sciences, Raleigh, NC. (31 July-4 August 2006)
"Modeling Original Antigenic Sin and Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Bioprocess Research & Development Lecture Series, Merck & Co., West Point, PA. (2 June 2005)
"Monte Carlo Approach to Generate Hypothetical Zeolite Topologies." CECAM Workshop on Energy landscape of solids: from (hypothetical) topologies to materials properties, EPFL, Lausanne, Switzerland. (23-25 July 2008)
"The Monte Carlo Sampling Approach to Construction of a Database of Hypothetical Zeolite Frameworks." CECAM Workshop on Theoretical Aspects of Design of Periodic Materials, Ecole Normale Superieure, Lyon, France. (19-20 July 2007)
"Exact Solutions to Some Infinite Dimensional Quasispecies Theories of Evolution." Nonlinear and Stochastic Dynamics for Infinite Dimensional Dynamical Systems of SIAM Conference on Applications of Dynamical Systems,, Snowbird, UT. (28 May-1 June 2007)
"How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Taiwan International Symposium on Statistical Physics Institute of Physics of Academia Sinica, Taipei, Taiwan. (8-12 July 2008)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." International Institute for Applied Systems Analysis Workshop on Multidisciplinary Approaches to Studying Pandemic Flu, Laxenburg, Austria. (4-5 August 2006)
"Statistical Mechanics Modeling of Complex Systems,." Alliance for Nanohealth Working Group, MD Anderson Cancer Center, Houston, TX. (2 June 2005)
"Quasispecies Theory for Horizontal Gene Transfer and Recombination,." Workshop on Critical Phenomena and Complex Systems Chung-Yuan Christian University, Chung Li, Taiwan. (5-7 July)
"Sculpting the Immune Response to T Cell Vaccines for Viruses and Cancers." Distinguished Lecture, Center for Cancer Immunology Research, Department of Immunology, Houston, TX. (27 June 2005)
"Some Mathematical Adventures in Biology." Seminar in Physical Chemistry, University of California, Los Angeles, CA. (30 April 2007)
"Toward a Database of Hypothetical Zeolite Structures." CECAM Workshop on Computational Aspects of Building Blocks, Nucleation, and Synthesis of Porous Materials Ecole Normale Superieure, Lyon, France. (29-31 August 2006)
"Amino Acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small Library Thoroughly or a Large Library Sparsely?." Workshop on Critical Phenomena and Complex Systems Chung-Yuan Christian University, Chung Li, Taiwan. (5-7 July)
"Evolutionary Design in Biological Physics and Materials Science." International School of Solid State Physics, 34th Course: Computer Simulations in Condensed Matter: From Materials to Chemical Biology, Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Sicily, Italy. (20 July - 1 August 2005)
"Evolvability is a Selectable Trait (Life has Evolved to Evolve)." Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey. (7 September 2006)
"Spontaneous Emergence of Modularity in a Model of Evolving Proteins." Varenna Evolvability Conference, ``Piero Caldirola'' Center for the Promotion of Science, Varenna, Italy. (15-17 April 2007)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Colloquium in Physics, Department of Physics, North Carolina State University, Raleigh, NC. (21 April 2008)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Workshop on Macromolecules and Biological Systems, National Center for Theoretical Sciences, National Taiwan University, and Institute of Physics of Academia Sinica, Taipei, Taiwan. (27-29 July 2005)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." New Frontiers in Chemical Engineering Seminar Series, Department of Chemical Engineering, Texas Tech University, Lubbock, TX. (15 September 2006)
"Some Mathematical Adventures in Biology." Robert W. Vaughan Lectureship in Chemical Engineering, California Institute of Technology, Pasadena, CA. (5 April 2007)
"Evolvability is a Selectable Trait." National Center for Theoretical Sciences, National Taiwan University, and Institute of Physics of Academia Sinica, Taipei, Taiwan. (27-29 July 2005)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Seminar in Structural and Quantitative Biology, University of California, Berkeley, CA. (2 October 2006)
"Statistical Mechanics of Pathogen Escape from the Immune System." Controlling Pathogen Evolution DARPA Workshop, Arlington, VA. (27 March 2007)
"Vaccine Design for Influenza and Dengue Fever." seminar in Chemical Engineering, University of California, Los Angeles, CA. (11 April 2008)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." oint Seminar in Physics, Biology, and Center for Systems Biology, Duke University, Durham, NC. (20 March 2007)
"Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease." National Center for Theoretical Sciences, National Taiwan University, and Institute of Physics of Academia Sinica, Taipei, Taiwan. (27-29 July 2005)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Ashland Inc. Distinguished Lecture Series, Department of Chemical Engineering, University of Kentucky, Lexington, KY. (20 October 2006.)
"Some Mathematical Adventures in Biology,." Colloquium in Physics, Department of Physics, Washington University in St. Louis, St. Louis, MO. (18 March 2008)
"How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Department of Mathematics, Stanford University, Stanford, CA. (20 February 2008)
"Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer." Seminar in Applied Mathematics and Computer Science, University of Pennsylvania, Philadelphia, PA. (16 February 2007)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Seminar in Synthetic and System Biology, University of Texas, Austin, TX. (4 December 2006)
"A Physical Theory of the Competition that Allows HIV to Escape from the Immune System." Workshop on Critical Phenomena and Complex Systems, National Center for Theoretical Studies, and Department of Physics, National Taiwan University, Taipei, Taiwan. (15-16 December 2006)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." seminar in Institute for Mathematical Behavioral Sciences, University of California, Irvine, CA. (7 February 2008)
"Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease." Computer and Information Technology Institute Luncheon Lecture, Rice University, Houston, TX. (2 September 2005)
"Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer." Seminar in Biological Physics, University of Illinois, Urbana-Champaign, IL. (9 February 2007)
"A Database of Hypothetical Zeolite Structures." CECAM Workshop Towards New Methods to Design Catalytic and Separation Processes in Nanoporous Materials, Ecole Normale Superieure,, Lyon, France. (5-7 September 2005)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Colloquium in Physics, University of Illinois, Urbana-Champaign, IL. (8 February 2007)
"Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer." Workshop on Critical Phenomena and Complex Systems, National Center for Theoretical Studies, and Department of Physics, National Taiwan University, Taipei, Taiwan. (15-16 December 2006)
"Sculpting the Immune Response to T Cell Vaccines for Viruses and Cancers." workshop, Viral Paradigms: Molecules, Populations, Ecosystems, and Infectious Disease, Department of Biology, Georgia Tech, Atlanta, GA. (14-16 January 2008)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA. (7 October 2005)
"Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory." Workshop on Critical Phenomena and Complex Systems, National Center for Theoretical Studies, and Department of Physics, National Taiwan University, Taipei, Taiwan. (15-16 December 2006)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Research Workshop on Physics Based Approach to Immunology and Gene Expression Analysis, International Centre for Condensed Matter Physics, University of Brasilia, Brasilia, Brazil. (13-22 October 2005)
"Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease." Research Workshop on Physics Based Approach to Immunology and Gene Expression Analysis, International Centre for Condensed Matter Physics, University of Brasilia, Brasilia, Brazil. (13-22 October 2005)
"A Theory of Cancer Mutation, Escape, and Control by the Immune System." Research Workshop on Physics Based Approach to Immunology and Gene Expression Analysis, International Centre for Condensed Matter Physics, University of Brasilia, Brasilia, Brazil. (13-22 October 2005)
"Life has Evolved to Evolve." Colloquium in Physics and Genetics, Institute of Theoretical Physics, University of Cologne, Cologne, Germany. (25 October 2005)
"A Theory of Cancer Mutation, Escape, and Control by the Immune System." Colloquium, FOM Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands. (26 October 2005)
"Some Mathematical Adventures in Biology." Institute of Physics of Academia Sinica, Taipei, Taiwan. (18 December 2006)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Keck Seminar, Rice University, Houston, TX. (18 November 2005)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Workshop on Infectious Diseases---Old Challenges and New Solutions, London School of Hygiene and Tropical Medicine, London, United Kingdom. (5-7 December 2005)
"Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." seminar in Physics, Oxford University, Oxford, United Kingdom. (7 December 2005)
"Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." seminar in Physics, Oxford University, Oxford, United Kingdom. (7 December 2005)
Keynote Speaker
"A Theory of Cancer Mutation, Escape, and Control by the Immune System." StatPhys-Taiwan 2005, Taiwan Summer Symposium on Statistical and Nonlinear Physics, Institute of Physics of Academia Sinica, Taipei, Taiwan. (1-6 August 2005)
"Life has Evolved to Evolve." Frontiers in Physics Session, American Institute of Physics 2005 Industrial Physics Forum, Gaithersburg, MD. (6-8 November 2005)
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Presentation to Dr. Klaus Stohr, Director of WHO Global Influenza Programme, Texas Influenza Researchers Meeting, Texas Medical Center, Houston, TX. (4 November 2005)
Lecture
"Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Special seminar for visiting students from El Tecnologico en Monterrey, Nuevo Leon, Mexico, Department of Physics & Astronomy, Rice University, Houston, TX. (28 October 2005)
Session Chair
"Computational Genomics." AIChE Annual Meeting, San Francisco, CA. (12-17 November 2006)
Editorial Positions
Member of the Editorial Board, Protein Engineering, Design and Selection, (2005).
Member of the Editorial Board, Protein Engineering, Design and Selection, (2007).
Member of the Editorial Board, Protein Engineering, Design & Selection, (2008).
Associate Editor, PLoS Computational Biology, (2008).
Theses
Hao Zhou, Ph.D. "Stochastic Simulation for Viral Diseases: Dengue and Avian Influenza." (2007).(Thesis or Dissertation Director)
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