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Michael Deem
Professor
John W. Cox Professor of Biochemical and Genetic Engineering and Professor of Physics & Astronomy
 
e-mail:mwdeem@rice.edu
 
  • B.S. Chemical Engineering (1991) California Institute of Technology
  • Ph.D. Chemical Engineering (1994) University of California at Berkeley
 
Primary Department
   Department of Bioengineering
Picture
 
Department Affiliations
 
  • Department of Physics and Astronomy
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  • Ken Kennedy Institute for Information Technology
  • Rice Quantum Institute
  • Systems, Synthetic, and Physical Biology
  •  
    Websites
     DEEM GROUP HOME PAGE
     
    Research Areas
     Immune response to variable or multi-strain viruses and vaccine. Physical theories of pathogen evolution. Vaccine design. Newton's laws of biology. Personalized critical care.
     
    Deem Research Group
     

    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



    1. Immune response to variable or multi-strain viruses and vaccines

    2. Physical theories of pathogen evolution.

    3. Vaccine design.

    4. Structure and function of cystine-knot peptide antimicrobials.

    5. Newton's laws of biology.

    6. Structure, nucleation, and function 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, the Defense Advanced Research Projects Agency, and the National Science Foundation.

     
    Selected Publications
     Refereed articles
     

    A. T. Liu, C. Lew, D. Xie, A. Benin, S. Elomari, S. I. Zones, and M. W. Deem "Computationally-Guided Synthesis of SSZ-52, a Zeolite for Engine Exhaust Clean-up." Chem. Mater., 28 (2015) : 708-711.

     
     

    B. W. Boal, J. E. Schmidt, M. A. Deimund, M. W. Deem, L. Henling, A. M. Sunol, S. K. Brand, , S. I. Zones, and M. E. Davis "Facile Synthesis and Catalysis of Pure-Silica and Heteroatom LTA." Chem. Mater., 27 (2015) : 7774-7779.

     
     

    C. Simon, J. Kim, D. A. Gomez-Gualdron, J. S. Camp, Y. G. Chung, R. Martin, R. Mercado, M. W. Deem, D. Gunter, M. Haranczyk, D. S. Sholl, R. Q. Snurr, and B. Smit "Computer-Aided Search for Materials to Store Natural Gas for Vehicles." Frontiers for Young Minds, section ``Understanding the Earth and its Resources,'', doi:10.3389/frym.2015.00011 (2015)

     
     

    C. Simon, J. Kim, D. A. Gomez-Gualdron, J. S. Camp, Y. G. Chung, R. Martin, R. Mercado, M. W. Deem, D. Gunter, M. Haranczyk, D. S. Sholl, R. Q. Snurr, and B. Smit "The Materials Genome in Action: Identifying the Performance Limits for Methane Storage." Energy & Envi. Sci., 8 (2015) : 1190-1199.

     
     

    J. E. Schmidt, M. W. Deem, C. M. Lew, and T. M. Davis "Computationally-Guided Synthesis of the 8-Ring Zeolite AEI." Top. Catal., 58 (2015) : 410-415.

     
     

    J.-M. Park, L. R. Niestemski, and M. W. Deem "Quasispecies Theory for Evolution of Modularity." Phys. Rev. E, 91 (2015) : 012714.

     
     

    J.-M. Park, M. Chen, D. Wang, and M. W. Deem "Modularity Enhances the Rate of Evolution in a Rugged Fitness Landscape." Phys. Biol., 12 (2015) : 025001.In Press

     
     

    M. Chen and M. W. Deem "Development of Modularity in the Neural Activity of Children's Brains." Phys. Biol., 12 (2015) : 016009.

     
     

    P. Bai, M.-Y. Jeon, L. Ren, C. Knight, M. W. Deem, M. Tsapatsis, and J. I. Siepmann "Discovery of Optimal Zeolites for Challenging Separations and Chemical Transformations using Predictive Materials Modeling." Nature Comm, 6 (2015) : 5912.

     
     

    P. Bai, M.-Y. Jeon, L. Ren, C. Knight, M. W. Deem, M. Tsapatsis, and J. I. Siepmann "Predictive Materials Discovery: Finding Optimal Zeolites for Challenging Separations and Chemical Conversions." Nature Comm., 6 (2015) : 5912.

     
     

    S. Tripathi and M. W. Deem "Hierarchy in Gene Expression is Predictive of Risk, Progression, and Outcome in Adult Acute Myeloid Leukemia." Phys. Biol., 12 (2015) : 016016.In Press

     
     

    Y. Bao, R. L. Martin, C. Simon, M. Haranczyk, B. Smit, and M. W. Deem "In Silico Discovery of High Deliverable Capacity Metal-Organic Frameworks." J. Phys. Chem. C, 119 (2015) : 186-195.


    DOI 10.1021/jp5123486
     
     

    Y. Bao, R. L. Martin, M. Haranczyk, and M. W. Deem "In Silico Prediction of MOFs with High Deliverable Capacity or Internal Surface Area." Phys. Chem. Chem. Phys., 17 (2015) : 11962-11973.

     
     

    J. E. Schmidt, M. W. Deem, and M. E. Davis "Synthesis of a Specified, Silica Molecular Sieve using Computationally Predicted Organic Structure Directing Agents." Angew. Chem. Int. Ed., 53 (2014) : 8372-8374.

     
     

    S. O. Odoh, M. W. Deem, and L. Gagliardi "Preferential Location of Ge in the UTL and IPC-2a Zeolites."  J. Phys. Chem. C , 118 (2014) : 26939-26946.

     
     

    X. Li and M. W. Deem "Why Zeolites Have So Few 7-Membered Rings." J. Phys. Chem. C , 118 (2014) : 15835-15839.

     
     

    C. Zhang and M. W. Deem "Multicanonical Molecular Dynamics by Variable-Temperature Thermostats and Variable-Pressure Barostats." J. Chem. Phys., 138 (2013) : 034103.

     
     

    D. M. Lorenz, J.-M. Park, and M. W. Deem "Evolutionary Processes in Finite Populations." Phys. Rev. E, 02270487 (2013) : 022704.

     
     

    M. Chen and M. W. Deem "Hierarchy of Gene Expression Data is Predictive of Future Breast Cancer Outcome." Phys. Biol., 10 (2013) : 056006.

     
     

    M. Chen, L. R. Niestemski, R. Prevost, M. McRae, S. Cholleti, G. Najarro, T. G. Buchman, and M. W. Deem "Prediction of Heart Rate Response to Conclusion of Spontaneous Breathing Trial by Fluctuation Dissipation Theory." Phys. Biol., 10 (2013) : 016006.

     
     

    M. W. Deem "Evolution: Life has Evolved to Evolve." Phys. Life Rev., 10 (2013) : 333-335.

     
     

    P. Bai, J. I. Siepmann, and M. W. Deem "Adsorption of Glucose into Zeolite Beta from Aqueous Solution." AIChE J., 59 (2013) : 3523-3529.

     
     

    P. Han, L. R. Niestemski, and M. W. Deem "Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System." Phys. Biol., 10 (2013) : 025004.

     
     

    R. Pophale, F. Daeyaert, and M. W. Deem "Computational Prediction of Chemically-Synthesizable Organic Structure Directing Agents for Zeolites." J. Mater. Chem. A, 1 (2013) : 6750-6760.

     
     

    D. B. Saakian, M. W. Deem, and C.-K. Hu "Finite Population Size Effects in Quasispecies Models with Single-Peak Fitness Landscape." Euro. Phys. Lett., 98 (2012) : 18001..

     
     

    D. M. Lorenz, J.-M. Park, and M. W. Deem "Evolutionary Processes in Finite Populations." Submitted

     
     

    J.-M. Park and M. W. Deem "Short-Time Response Function of the Modular Dilute SK Model, with Application to Evolution." Submitted

     
     

    J.-M. Park and M. W. Deem "Theory for the Emergence of Modularity in Complex Systems." Submitted

     
     

    L.-C. Lin, A. H. Berger, R. L. Martin, J. Kim, J. A. Swisher, K. Jariwala, C. H. Rycroft, A. S. Bhown, M. W. Deem, M. Haranczyk, and B. Smit "In Silico Screening of Carbon Capture Materials." Nature Materials, 11 (2012) : 633-641.

     
     

    M. Chen and M. W. Deem "Hierarchy of Gene Expression as a Biomarker for Breast Cancer Prognosis." Submitted

     
     

    M. Chen, L. R. Niestemski, R. Prevost, M. McRae, S. Cholleti, G. Najarro, T. G. Buchman, and M. W. Deem, "Prediction of Heart Rate Response to Conclusion of Spontaneous Breathing Trial by Fluctuation Dissipation Theory." Submitted

     
     

    P. Bai, J. I. Siepmann, and M. W. Deem "Adsorption of Glucose into Zeolite Beta from Aqueous Solution." Submitted

     
     

    P. Han, L. R. Niestemski, and M. W. Deem "hysical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System." Submitted

     
     

    Q. Fang, S. Gu, Q. Liu, J. Zheng, G. Chow, J. Wang, W. Maichen, M. W. Deem, S. Qiu, and Y. Yan "An Adamantane-Based 3D Covalent Organic Framework as HF-Resistant Ultra-Low Dielectric Constant Material." Submitted

     
     

    R. Pophale, F. Daeyaert, and M. W. Deem "Computational Prediction of Chemically-Synthesizable Organic Structure Directing Agents for Zeolites." Submitted

     
     

    T. Paixao, D. M. Lorenz, J. Songhurst, M. W. Deem, R. Azecott, T. F. Cooper, and R. B. R. Azevedo "Clonal Interference Can Lead to Evolutionary Farsightedness." Submitted

     
     

    D. Lorenz, A. Jeng, and M. W. Deem "The Emergence of Modularity in Biological Systems." Physics of Life Reviews, 8 (2011) : 167-168.

     
     

    J. Long, R. V. Bushnell, J. K. Tobin, K. Pan, M. W. Deem, P. L. Nara, and G. J. Tobin "Evolution of H3N2 Influenza Virus in a Guinea Pig Model." PLoS ONE, 6 (2011) : e20130.

     
     

    K. Pan and M. W. Deem "A Multi-Scale Model for Correlation in B Cell VDJ Usage of Zebrafish." Phys. Biol., 8 (2011) : 055006.

     
     

    K. Pan and M. W. Deem "Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation." J. Chem. Theory Comput., 7 (2011) : 1259-1272.

     
     

    K. Pan and M. W. Deem "Quantifying Selection and Diversity in Viruses by Entropy Methods, with Application to the Hemagglutinin of H3N2 Influenza." J. R. Soc. Interface, 7 (2011) : 1644-1653.

     
     

    K. Pan, J. Long, H. Sun, G. J. Tobin, P. L. Nara, and M. W. Deem "Selective Pressure to Increase Charge in Immunodominant Epitopes of H3 Hemagglutinin Influenza Protein." J. Mol. Evol., 72 (2011) : 90-103.

     
     

    K. Pan, K. C. Subieta, and M. W. Deem "A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains." Protein Engineering, Design & Selection, 24 (2011) : 291-299.

     
     

    R. Pophale, P. A. Cheeseman, and M. W. Deem "A Database of New Zeolite-Like Materials." Phys. Chem. Chem. Phys., 13 (2011) : 12407-12412.

     
     

    D. Lorenz, A. Jeng, and M. W. Deem "The Emergence of Modularity in Biological Systems." Physics of Life ReviewsIn Press

     
     

    J. He and M. W. Deem "Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)." Phys. Rev. Lett., 105 (2010) : 128102.

     
     

    J. He and M. W. Deem "Low-Dimensional Clustering Detects Incipient Dominant Influenza Strain Clusters." Protein Engineering, Design & Selection, 23 (2010) : 935-946.

     
     

    J. He and M. W. Deem "Structure and Response in the World Trade Network." Phys. Rev. Lett., 105 (2010) : 198701.

     
     

    J.-M. Park, E. T. Munoz, and M. W. Deem "Quasispecies theory for finite populations." , 81 (2010) : 011902.

     
     

    K. Pan, J. Long, H. Sun, G. J. Tobin, P. L. Nara, and M. W. Deem "Selective Pressure to Increase Charge in Immunodominant Epitopes of H3 Hemagglutinin Influenza Protein." J. Mol. Evol. (2010)

     
     

    K. Pan, K. C. Subieta, and M. W. Deem "A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains." Protein Engineering, Design & Selection (2010)

     
     

    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." J. Stat. Phys., 135 (2009) : 429-465.

     
     

    J. He and M. W. Deem "Hierarchical Evolution of Animal Body Plans." Dev. Biol., 337 (2009) : 157-161.

     
     

    J. He, J. Sun, and M. W. Deem "Spontaneous Emergence of Modularity in a Model of Evolving Individuals and in Real Networks." Phys. Rev. E, 79 (2009) : 031907.

     
     

    K. Pan and M. W. Deem "Comment on Ndifon et al, `On the use of hemagglutination-inhibition for influenza surveillance: Surveillance data are predictive of influenza vaccine effectiveness'." Vaccine, 27 (2009) : 5033-5034.

     
     

    K. Pan and M. W. Deem "The Epitope Regions of H1-Subtype Influenza A, with Application to Vaccine Efficacy." Protein Engineering, Design & Selection, 22 (2009) : 543-546.

     
     

    M. W. Deem, R. Pophale, P. A. Cheeseman, and D. J. Earl "Computational Discovery of New Zeolite-Like Materials." J. Phys. Chem. C, 113 (2009) : 2135321360.

     
     

    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., 24 (2009) : 347-361.

     
     

    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 ." Micropor. Mesopor. Mater. , 123 (2009) : 10-14.

     
     

    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.

     
     

    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 & Selection, 21 (2008) : 311-317.

     
     

    E. T. Munoz, J.-M. Park, and M. W. Deem "Quasispecies Theory for Horizontal Gene Transfer and Recombination." Phys. Rev. E, 78 (2008) : 061921.

     
     

    J. Sun and M. W. Deem, "Spontaneous Emergence of Modularity in a Model of Evolving Individuals,'' Phys. Rev. Lett., 99 (2007) 228107

     
     

    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

     
     

    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

     
     

    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

     
     

    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

     
     

    H. Zhou and M. W. Deem, "Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination,'' Vaccine 24 (2006) 2451-2459

     
     

    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

     
     

    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.

     
     

    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

     
     

    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

     
     V. Gupta, D. J. Earl, and M. W. Deem, ``Quantifying Influenza Vaccine Efficacy and Antigenic Distance,'' Vaccine 24 (2006) 3881-3888
     
     

    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

     
     

    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.

     
     

    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.

     
     

    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.

     
     

    T. Tan, D. Frenkel, V. Gupta, and M. W. Deem "Length, Protein-Protein Interactions, and Complexity." Physica A, 350 (2005) : 52-62.

     
     Book chapters
     

    M. Chen and M. W. Deem "Modularity, Plasticity, and Development of Brain Function." The Cognitive Neurosciences V (2014) : 119-128.

     
     

    M. W. Deem "Statistical Mechanics of Modularity and Horizontal Gene Transfer." Annual Review of Condensed Matter Physics, 4 (2013) : 287-311.

     
     

    P. Hejazi and M. W. Deem "Theoretical Aspects of Immunity." Annual Review of Chemical and Biomolecular Engineering, 1 (2010) : 247-276.

     
     

    H. Zhou, R. Pophale, and M. W. Deem "Computer-Assisted Vaccine Design." Influenza: Molecular Virology (2009) : 173-191.

     
     

    J. Sun and M. W. Deem "Statistical Mechanics of the Immune Response to Vaccines." tatistical Mechanics of Cellular Systems and Processes (2009) : 177-213.

     
     

    D. J. Earl and M. W. Deem "Monte Carlo Simulations." Methods in Molecular Biology: Molecular Modelling of Proteins, 443 (2008) : 25-36.

     
     Book reviews
     

    M. W. Deem "Book Review: Introduction to Mathematical Methods in Bioinformatics."  (October 2005) : 83-84.

     
     Refereed conference papers
     E.Walker, D.J.Earl, and M.W. Deem, "How to Run a Million Jobs in Six Months on the NSF TeraGrid," TeraGrid Conference, 2007, Madison, WI.
     
     P.A. Cheeseman, M.W. Deem, D.J. Earl, and W.I. Whitson, "Adapting an Application for Use in a Condor Based Parameter Sweep on TeraGrid," TeraGrid Conference, 2007, Madison, WI.
     
    Presentations
     Invited Talks
     

    "Emergence of Modularity in Biology." coffee@beyond, The Beyond Institute, Arizona State University, Tempe, AZ. (2 November 2015)

     
     

    "Emergence of Modularity in Biology." session Laws of Life: Exploring Universal Biology Through Computer Simulation, The Origins and Subsequent Evolution of Life, Astrobiology Science Conference 2015, Chicago, IL. (15-19 June 2015)

     
     

    "Hierarchy of Gene Expression Data is Predictive of Future Breast Cancer Outcom." 2015 NCTS International Workshop on Critical Phenomena and Complex Systems, National Tsing Hua University, Hsinchu, Taiwan. (15-17 August 2015)

     
     

    "In Silico Discovery of High Deliverable Capacity Metal-Organic Frameworks." 2nd Fudan-UC Berkeley Workshop on Materials Beyond, Fudan Univesity, Shanghai, China. (27 April 2015)

     
     

    M. W. Deem, “In Silico Discovery of High Deliverable Capacity Metal-Organic
    Frameworks,” Department of Chemistry, University of California, Berkeley, CA, (17
    February 2015)

     
     

    M. W. Deem, “Prediction of High Deliverable Capacity Metal-Organic Frameworks with
    an Evolutionary Algorithm,” in session Inverse Design of Materials: The Genomic
    Approach, 249th ACS National Meeting, Denver, CO, (22–26 March 2015)

     
     

    M. W. Deem, “Statistical Mechanics: From Surface Science to Zeolites to the Immune
    System,” in Workshop in Honor of W. Henry Weinberg, Santa Barbara, CA, (3 January
    2015)

     
     

    M. W. Deem, “The Challenges of Vaccine Design for Influenza and Dengue Fever,”
    Department of Biomedical Engineering, Texas A & M University, (30 March 2015)

     
     

    "Computational Prediction of Chemically-Synthesizable Organic Structure Directing Agents for Zeolites." 247th ACS National Meeting, Dallas, TX. (16-20 March 2014)

     
     

    "Emergence of Modularity in Biology." 9th European Conference on Mathematical and Theoretical Biology, Gothenburg, Sweden. (15-16 June 2014 )

     
     

    "Fundamental Laws." BAASiC/Predictive Pathophysiology Consortium, Emory University Hospital, Atlanta, GA. (15-17 September 2014)

     
     

    "Heterogeneity in Cancer and in the Immune Response." U.S.--China Physical Sciences--Oncology Alliance, Complex Adaptive Systems (CAS) Institute and the Biodesign Institute, Arizona State University, Tempe, AZ. (21-22 November 2014.)

     
     

    "Heterogeneity in the Immune Response to the Influenza Virus." 3rd Annual Influenza Research and Development Conference, Boston, MA. (9-11 July 2014)

     
     

    "Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System." StatPhys-Taiwan-2014: The 12th Taiwan International Symposium on Statistical Physics and Complex Systems, Institute of Physics of Academia Sinica , Taipei, Taiwan. (28-30 June 2014)

     
     

    "Physics of the Immune System and the Emergence of Disease." Conference on Complex Adaptive Matter, Hong Kong University of Science and Technology, Hong Kong. (15-19 December 2014)

     
     

    "Physics of the Immune System and the Emergence of Disease." Institute of Physics of Academia Sinica, Taipei, Taiwan. (16 December 2014)

     
     

    "Design of Predicted Nanoporous Materials." Chemical Theory, University of Minnesota, Minneapolis, MN. (12 September 2013)

     
     

    "Evolution in the Bacterial, Archaeal, and Jawed Vertebrate Immune Systems." Marquette University, Milwaukee, WI. (12 April 2013)

     
     

    "Evolution in the Bacterial, Archaeal, and Jawed Vertebrate Immune Systems." Ohio Wesleyan University, Delaware, OH. (5 April 2013)

     
     

    "Evolution in the Immune System." Iowa State University, Ames, IA. (6 March 2013)

     
     

    "Evolution of Modularity in Biological Systems." University of California, Berkeley, CA. (11-13 January 2013)

     
     

    "Impacting Climate Change: New Materials for Carbon Capture." The University at Albany, Albany, NY. (12 March 2013)

     
     

    "In Search of Fundamental Mathematical Laws of Biology." Ohio Wesleyan University, Delaware, OH. (6 April 2013)

     
     

    "In Search of Fundamental Mathematical Laws of Biology." University of Oklahoma, Oklahoma City, OK. (29 January 2013)

     
     

    "In Search of Fundamental Mathematical Laws of Biology." University of Tulsa, Tulsa, OK. (31 January 2013)

     
     

    "In Search of Fundamental Mathematical Laws of Biology." The University at Albany, Albany, NY. (12 March 2013)

     
     

    "Modularity and Evolvability,." Sage Center for the Study of the Mind, UC Santa Barbara, Lake Tahoe, CA. (25-26 June 2013)

     
     

    "Physical Theory of the Immune Response to Vaccines." Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX. (16 April 2013)

     
     

    "Properties, Predicted Materials, and Propensity for Growth." Nanoporous Materials & Their Applications, Gordon Research Conference, Holderness, NH. ( 11-16 August 2013)

     
     

    "The Adaptive, Heritable Bacterial Immune System: Heterogeneous Diversity of Spacers within CRISPR." University of Oklahoma, Oklahoma City, OK. (30 January 2013)

     
     

    "Theoretical Aspects of Immunity,." University of Tulsa, Tulsa, OK. (31 January 2013)

     
     

    "Zeolites: New Materials for Carbon Capture." Iowa State University, Ames, IA. (6 March 2013)

     
     

    M. W. Deem, ``A Database of Computationally-Predicted Zeolite-Like Materials,'' American Mathematical Society, 2012 Spring Southeastern Section Meeting, University of South Florida, Tampa, FL, 10-11 March 2012.

     
     

    M. W. Deem, ``Emergence of Modularity in Biology,'' Department of Physics, National University of Singapore, Singapore, 19 December 2012

     
     

    M. W. Deem, ``Emergence of Modularity in Biology,'' in session Analogy in Applications of Mathematics and Statistics to Other Disciplines, AAAS Annual Meeting, Vancouver, Canada, 16-20 February 2012.

     
     

    M. W. Deem, ``Evolution and the Immune System,'' 6th Annual Vaccine Renaissance Conference, Institute for Immunology and Informatics, Biotechnology Center, University of Rhode Island, Providence, RI, 15-17 October 2012.

     
     

    M. W. Deem, ``Evolution in the Bacterial, Archaeal, and Jawed Vertebrate Immune Systems,'' Computational Biology & Bioinformatics PhD Program, Center for Theoretical and Mathematical Science, Duke University, Durham, NC, 24 September 2012.

     
     

    M. W. Deem, ``Evolution of Modularity in Biological Systems,'' in International Conference on Stochastic Processes in Systems Biology, Genetics and Evolution, Department of Statistics, Rice University, Houston, TX, 22-25 August 2012

     
     

    M. W. Deem, ``Evolution of Modularity in Biological Systems,'' Colloquium in Physics, Pontifical Catholic University of Chile, Santiago, Chile, 3 August 2012.

     
     

    M. W. Deem, ``Immune Response to and Evolution of Influenza Virus,'' Keck Seminar, Rice University, Houston, TX, 16 March 2012

     
     

    M. W. Deem, ``In Search of Fundamental Mathematical Laws of Biology,'' Phi Beta Kappa Visiting Scholar, University of Hawaii at Manoa, Honolulu, HI, 19 September 2012

     
     

    M. W. Deem, ``P",'' Texas Section APS meeting, Texas Tech University, Lubbock, TX, 26-27 October 2012

     
     

    M. W. Deem, ``Principles of Least Action in Biological Evolution from Bosonic Quantum Field Theories,'' in TAMU-Casper College Summer School on Quantum Science and Engineering, Casper, Wyoming, 16-20 July 2012

     
     

    M. W. Deem, ``Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination,'' Investigative Workshop on Dengue Modeling, National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee, 23-24 July 2012

     
     

    M. W. Deem, ``The Adaptive, Heritable Bacterial Immune System: Heterogeneous Diversity of Spacers within CRISPR,'' Phi Beta Kappa Visiting Scholar, University of Hawaii at Manoa, Honolulu, HI, 19 September 2012

     
     

    M. W. Deem, ``Zeolites as Nanosensors,'' OMICS Group conference on Biosensors & Bioelectronics Conference, Las Vegas, NV, 14-16 May 2012

     
     

    M. W. Deem, ``Zeolites: New Materials for Carbon Capture,'' Phi Beta Kappa Visiting Scholar, University of Hawaii at Manoa, Honolulu, HI, 18 September 2012

     
     

    M. W. Deem, ``A Database of New Zeolite-Like Materials,'' in workshop Physical Frameworks for Sampling Chemical Compound Space, Institute for Pure and Applied Mathematics, University of California, Los Angeles, CA, 16-20 May 2011.

     
     

    M. W. Deem, ``Emergence of Modularity in an Evolving System,'' in Telluride Science Research Center workshop Rise of the Machines: Integration of Experiment, Simulation and Theory for a Mechanistic Understanding of Biomolecular Machines, Telluride, CO, 8-11 August 2011.

     
     

    M. W. Deem, ``F = m a of Biology?,'' Professional Progress Award Lecture, AIChE Annual Meeting, Minneapolis, MN, 16-21 October 2011.

     
     

    M. W. Deem, ``F = ma of Biology?'', Nanjing University of Science and Technology, Nanjing, China, 4 November 2011.

     
     

    M. W. Deem, ``Heterogeneous Diversity of Spacers within CRISPR,'' in 5th q-bio Conference on Cellular Information Processing, Santa Fe, NM, 10-14 August 2011.

     
     

    M. W. Deem, ``Immune Response to and Evolution of Influenza Virus,'' in Mathematical Modeling of Infectious Diseases: Bridging Data and Models, Institute for Mathematical Behavioral Sciences, 28-29 October 2011

     
     

    M. W. Deem, ``In Search of Fundamental Mathematical Laws of Biology,'' Institute of Physics of Academia Sinica, Taipei, Taiwan, 13 December 2011.

     
     

    M. W. Deem, ``Modularity and Heterogeneity of Tumor Structures,'' in Workshop of the Physics of Tumor Heterogeneity, Physical Sciences-Oncology Center, Princeton University, Princeton, NJ, 5-7 June 2011.

     
     

    M. W. Deem, ``Modularity as a Principled Tool for Network Analysis,'' Biologically Inspired Security and Resilience, Institute for Human & Machine Cognition, Ocala, FL, 27-29 March 2011.

     
     

    M. W. Deem, ``Statistical Mechanics, Sequence, and Zoonosis,'' in DTRA workshop Anticipating the Species Jump: Bioinformatics and Information Sharing, Science Applications International Corporation, McLean, VA, 29-30 March 2011.

     
     

    "Computational Discovery of New Zeolite-Like Materials." Cheminformatics Tools and High-Throughput Approaches for the Discovery of New Materials Symposium, 239th ACS National Meeting, San Francisco, CA. (21-25 March 2010)

     
     

    "Computational Systems Biology of the Immune System." CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China. (17 June 2010)

     
     

    "Evolution in the Bacterial, Archaeal, and Jawed Vertebrate Immune Systems." he Physics of Evolution Summer School, Center for Theoretical Biological Physics, University of California, San Diego, CA. (29 August-2 September 2010)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." The Physics of Evolution Summer School, Center for Theoretical Biological Physics, University of California, San Diego, CA. (29 August-2 September 2010)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Colloquium in Physics, Emory University, Atlanta, GA. (17 September 2010)

     
     

    "Measurement of Hierarchy Demonstrates that Structure in the World Trade Network Increases after Global Recessions." Networks Cluster Seminar, Departments of Biology, Biochemistry, Mathematics, and Physics, University of Houston, Houston, TX. (13 May 2010)

     
     

    "Measurement of Hierarchy Demonstrates that Structure in the World Trade Network Increases after Global Recessions." Institute of Physics of Academia Sinica, Taipei, Taiwan. (21 June 2010)

     
     

    "The Adaptive, Heritable Bacterial Immune System: Heterogeneous Diversity of Spacers within CRISPR." Frontiers in Quantitative Biology, Department of Bioengineering, Stanford University, Stanford, CA. (7 October 2010)

     
     

    "The Adaptive, Heritable Bacterial Immune System: Heterogeneous Diversity of Spacers within CRISPR." 104th Statistical Mechanics Conference, Department of Mathematics, Rutgers University, Piscataway, NJ. ( 19 December 2010)

     
     

    "Vaccine Design for Influenza." in symposium Advances and Impact in Computational Biology, AAAS SWARM meeting Expanding Frontiers through the Advancement of Science, Houston, TX. (8-10 April 2010)

     
     

    "Vaccine Design for Influenza." seminar in Chemical Engineering, Penn State University, University Park, PA. (4 February 2010)

     
     

    "Antigenic Distance and Pre-Dominant Strain Detection for H1N1." 7th Annual Conference Vaccines: All Things Considered, Washington, DC. (9-10 November 2009)

     
     

    "Computational Discovery of New Zeolite-Like Materials." CCP5 annual meeting on Structure Prediction from First Principles, University College London, London, United Kingdom. (7-9 September 2009)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Seminar in Physics, Korea Institute for Advanced Study, Seoul, South Korea. (4 April 2009)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Seminar in Physics, Universita di Roma ``La Sapienza,'', Rome, Italy. (8 June 2009)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Seminar in Physics, University of Houston, Clear Lake, TX. (23 February 2009)

     
     

    "Physical Theory of Vaccine Design for Influenza and Dengue Fever." Colloquium in Theoretical Chemistry, Department of Chemistry, Cambridge University, Cambridge, United Kingdom. (16 June 2009)

     
     

    "Physical Theory of Vaccine Design for Influenza and Dengue Fever." Seminar Session Physics of the Immune System, APS March Meeting, Pittsburgh, PA. (16-20 March 2009)

     
     

    "Spontaneous Emergence of Modularity in an Evolving System: Nucleation of Biology from Chemistry." Workshop on Evolution: Foundations, Fundamentals, and Disease, Hong Kong University of Science and Technology, Hong Kong. (8-11 December 2009)

     
     

    "The Effects of Recombination and Finite Population Size on Viral Evolution." Stochastic Dynamics in Population Biology of SIAM Conference on Applications of Dynamical Systems, Snowbird, UT. (17-21 May 2009)

     
     

    "The pepitope Method." Strategies to Predict the Antigenic Evolution of H1N1pdm, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ. (5 August 2009)

     
     

    "Vaccine Design for Influenza and Dengue Fever." Seminar in Chemical Engineering, Ohio State University, Columbus, OH. (5 February 2009)

     
     

    "Vaccine Design for Influenza and Dengue Fever." Quantitative Biology Seminar Series, Los Alamos National Lab, Los Alamos, NM. (28 April 2009)

     
     

    "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 2008)

     
     

    "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)

     
     

    "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)

     
     

    "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)

     
     

    "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)

     
     

    "How is the Landscape Upon Which Life Evolves Selected: Spontaneous Emergence of Modularity." Department of Mathematics, Stanford University, Stanford, CA. (20 February 2008)

     
     

    "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)

     
     

    "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 2008)

     
     

    "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)

     
     

    "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." Colloquium in Physics, Department of Physics, Washington University in St. Louis, St. Louis, MO. (18 March 2008)

     
     

    "Spontaneous Emergence of Modularity as a Law in Biology,'' in session Fundamental Laws of Biology." Society of Complexity in Acute Illness, Atlanta, GA. (10 September 2010)

     
     

    "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)

     
     

    "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)

     
     

    "Vaccine Design for Influenza and Dengue Fever." seminar in Chemical Engineering, University of California, Los Angeles, CA. (11 April 2008)

     
     

    "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)

     
     

    "Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Seminar in Chemical Physics, National Institutes of Health, Bethesda, MD. (4 October 2007)

     
     

    "Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Colloquium in Physics, University of Illinois, Urbana-Champaign, IL. (8 February 2007)

     
     

    "Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Joint Seminar in Physics, Biology, and Center for Systems Biology, Duke University, Durham, NC. (20 March 2007)

     
     

    "Antigenic Distance, Glassy Dynamics, and Localization in the Immune System." Biological Physics Seminar, Department of Physics, Arizona State University, Tempe, AZ. (28 November 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)

     
     

    "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)

     
     

    "Phase Diagrams of Quasispecies Theory with Recombination and Horizontal Gene Transfer." Seminar in Biological Physics, University of Illinois, Urbana-Champaign, IL. (9 February 2007)

     
     

    "Physical Aspects of Vaccine Design for Influenza and Dengue Fever." Seminar in Physical Chemistry, Harvard University, Cambridge, MA. (25 October 2007)

     
     

    "Some Mathematical Adventures in Biology." Robert W. Vaughan Lectureship in Chemical Engineering, California Institute of Technology, Pasadena, CA. (5 April 2007)

     
     

    "Some Mathematical Adventures in Biology." Seminar in Physical Chemistry, University of California, Los Angeles, CA. (30 April 2007)

     
     

    "Some Mathematical Adventures in Biology." Seminar in Biomedical Engineering, Boston University, Boston, MA. (9 November 2007)

     
     

    "Spontaneous Emergence of Modularity in a Model of Evolving Individuals." Seminar in Interdisciplinary Program in Networks, University of Houston, Houston, TX. (19 October 2007)

     
     

    "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)

     
     

    "Statistical Mechanics of Pathogen Escape from the Immune System." Controlling Pathogen Evolution DARPA Workshop, Arlington, VA. (27 March 2007)

     
     

    "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)

     
     

    "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)

     
     

    "Evolutionary Design in Materials Science and Biological Physics." Seminar in Chemical Engineering, University of California, Santa Barbara, CA. (11 January 2006)

     
     

    "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)

     
     

    "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)

     
     

    "Life has Evolved to Evolve." n seminar session The Experimental and Theoretical Foundations of Evolution, APS March Meeting, Baltimore, MD. (13-17 March 2006)

     
     

    "Life has Evolved to Evolve (Evolvability is a Selectable Trait)." Colloquium in Physics, Johns Hopkins University, Baltimore, MD. (23 February 2006)

     
     

    "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)

     
     

    "Path Integral Representation of Evolution." DARPA Fundamental Laws of Biology Program Annual Meeting, Santa Barbara, CA. (10-12 May 2006)

     
     

    "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)

     
     

    "Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Seminar in Structural and Quantitative Biology, University of California, Berkeley, CA. (2 October 2006)

     
     

    "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)

     
     

    "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)

     
     

    "Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Ashland Inc. Distinguished Lecture Series, Department of Chemical Engineering, University of Kentucky, Lexington, KY. (20 October 2006.)

     
     

    "Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Seminar in Synthetic and System Biology, University of Texas, Austin, TX. (4 December 2006)

     
     

    "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)

     
     

    "Some Mathematical Adventures in Biology." Institute of Physics of Academia Sinica, Taipei, Taiwan. (18 December 2006)

     
     

    "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)

     
     

    "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)

     
     

    "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)

     
     

    "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)

     
     

    "Antigenic Distance, Glassy Dynamics, and Localization 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." Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA. (7 October 2005)

     
     

    "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." National Center for Theoretical Sciences, National Taiwan University, and Institute of Physics of Academia Sinica, Taipei, Taiwan. (27-29 July 2005)

     
     

    "Glassy Dynamics in the Adaptive Immune Response Prevents Autoimmune Disease." Computer and Information Technology Institute Luncheon Lecture, Rice University, Houston, TX. (2 September 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)

     
     

    "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)

     
     

    "Life has Evolved to Evolve." Colloquium in Physics and Genetics, Institute of Theoretical Physics, University of Cologne, Cologne, Germany. (25 October 2005)

     
     

    "Localization in Antibody Sequence Space-A Mechanism for Original Antigenic Sin." Mini Statistical Mechanics Meeting, Berkeley, CA. (7-8 January 2005)

     
     

    "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)

     
     

    "Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." seminar in Physics, Oxford University, Oxford, United Kingdom. (7 December 2005)

     
     

    "Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Center for Theoretical Biological Physics, San Diego, CA. (4 March 2005)

     
     

    "Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Colloquium in Mathematics, Rice University, Houston, TX. (17 March 2005)

     
     

    "Negative Correlations, Immunodominance, and Original Antigenic Sin in the Immune System." Seminar in Computer Science Department, University of Chicago, Chicago, IL. (11 February 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)

     
     

    "Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Keck Seminar, Rice University, Houston, TX. (18 November 2005)

     
     

    "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)

     
     

    "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)

     
     

    "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)

     
     

    "Statistical Mechanics Modeling of Complex Systems,." Alliance for Nanohealth Working Group, MD Anderson Cancer Center, Houston, TX. (2 June 2005)

     
     

    "Study of Zeolite Nucleation Kinetics." Catalysis in Fuel Chemistry Symposium, 229th ACS National Meeting, San Diego, CA. (13-17 March 2005)

     
     Keynote Speaker
     

    "Heterogeneity in the Immune Response to Viruses." ``Dynamical Systems applied to Biology and Natural Sciences'' at the Centro de Matematica e Aplicacoes Fundamentais (CMAF), Lisbon University, Lisbon, Portugal. (13-15 February 2013)

     
     

    "Hierarchy of Gene Expression Data is Predictive of Future Breast Cancer Outcome." 5th Annual International Conference on Computational and Systems Biology, South University of Science and Technology of China, Shenzhen, China. (13-17 November 2013)

     
     

    "Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination." Keynote Speech in Dengue Vaccines, BIT Life Sciences 1st World Congress of Virus and Infections 2010, Seoul, South Korea. (31 July-3 August 2010)

     
     

    "Sculpting the Immunological Response to Dengue Fever by Polytopic Vaccination." BIT Life Sciences 2nd Annual World Summit of Antiviral, Beijing, China. (18-20 July 2009)

     
     

    "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)

     
     Lectures
     

    "A Physical Theory of the Competition that Allows HIV to Escape from the Immune System." APS March Meeting, Denver, CO. (5-9 March 2007)

     
     

    "Quantifying Influenza Vaccine Efficacy and Antigenic Distance." Rice Computational and Theoretical Biology Symposium, Houston, TX. (8-10 December 2006)

     
     

    "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)

     
     Panelist
     

    "Global Health: Influenza and Dengue Fever." Collaborative Research Center, Trevisio Conference Center, Houston, TX. (28 November 2006)

     
     

    "Global Health: The challenge of Influenza." Rice BIOE EAC, Rice University, Houston, TX. (21 April 2006)

     
     Seminar Speaker
     

    "Emergence of Modularity in Biology." Physics, Massachusetts Institute of Technology, Cambridge, MA. (6 February 2013)

     
     

    "Physical Theory of the Immune System." University of Houston, Clear Lake, TX. (28 February 2013)

     
     Session Chair
     

    "Computational Genomics." AIChE Annual Meeting, San Francisco, CA. (12-17 November 2006)

     
    Editorial Positions
     Member of the Editorial Board, Bioengineering and Translational Medicine. (2015 - 2015)

     Other, BMES Representative, FASEB Publications & Communications Committee. (2011 - 2011)

     Member of the Editorial Board, Protein Engineering, Design & Selection. (2014 - 2015)

     Member of the Editorial Board, Physical Biology. (2014 - 2015)

    Supervised Theses & Dissertations
     Hao Zhou, Ph.D. Stochastic Simulation for Viral Diseases: Dengue and Avian Influenza. (2007) (Thesis or Dissertation Director)

     Andrew Nguyen, MS Targeting A549 and MCF7 with small bivalent molecules coated on bilamellar invaginated vesicles. (2007) (Committee Member)

     Jianping Chen, MS Hydration Shell Loosening Induced by Dehydron. (2007) (Committee Member)

     Xi Zhang, MS Mocular Basis of Specificity for the Druggable Kinome. (2007) (Committee Member)

     Jiankui He, M.S. Spontaneous Emergence of Modularity in a Model of Evolving Individuals and in Real Networks. (2008) (Thesis or Dissertation Director)

     Ramdas Pophale, Ph.D Zeolites to Peptides: Statistical Mechanics for Structure Solution and Propery Evaluation. (2008) (Thesis or Dissertation Director)

     Enrique Munoz, Ph.D. Modeling of Natural and in vitro protein Evolution. (2008) (Thesis or Dissertation Director)

     Enrique Munoz, Ph.D. Statistical Mechanics of Quasi-Species Theories of Evolution. (2008) (Thesis or Dissertation Director)

     Yan Lu, M.S. Predicting Clinical Physiology: A Markov Chain Model of Heart Rate Recovery after Spontaneous Breathing Trials in Mechanically Ventilated Patients. (2008) (Thesis or Dissertation Director)

     Jianping Chen, Ph.D. Molecular Basis of Gene Dosage Sensitivity. (2008) (Committee Member)

     Hao Zhou, Ph.D. Stochastic Simulation for Viral Diseases: Dengue and Avian Influenza. (2008) (Thesis or Dissertation Director)

     Xi Zhang, Ph.D. Specificity in the Druggable Kinome: Molecular Basis and its Applications. (2008) (Committee Member)

     Jiankui He, Ph.D. Spontaneous Emergence of Hierarchy in Biological Systems. (2010) (Thesis or Dissertation Director)

     Pooya Hejazi, Ph.D. The Immune System and Pathogen Coevolution. (2010) (Thesis or Dissertation Director)

     Keyao Pan, Ph.D. Predicting the Evolution of Influenza. (2011) (Thesis or Dissertation Director)

     Dirk Lorenz, Ph.D. Statistical Mechanics of Evolution. (2013) (Thesis or Dissertation Director)

     Man Chen, Ph.D. Statistical Mechanics of Networks. (2013) (Thesis or Dissertation Director)

     Man Chen, PhD Theoretical Biological Physics of Structural Dynamics in Physiology and Evolution. (2014) (Thesis or Dissertation Director)

     Pu Han, MS Statisical Mechanics of CRISPR. (2015) (Thesis or Dissertation Director)

    Awards, Prizes, & Fellowships
     Phi Beta Kappa Visiting Scholar, Phi Beta Kappa (2012-2013)

     Edith and Peter O'Donnell Award, The Academy of Medicine, Engineering, Science, and Technoloyg of Texas (12 January 2012)

     Professional Progress Award, AIChE (2010)

     Fellow of the American Association for the Advancement of Science, (2010)

     Fellow, Biomedical Engineering Society, Biomedical Engineering Society (2009)

     Vaughan Lecturship, AIChE (5 April 2007)

     Fellow of the American Physical Society, American Physical Society (November 2006)

     Fellow, American Institute for Medical and Biological Engineering (2005)

     Allan P. Colburn Award, AIChE (2004)

     Camille Dreyfus Teacher-Scholar Award, The Camille & Henry Dreyfus Foundation (2002)

     Alfred P. Sloan Research Fellowship, Alfred P. Sloan Foundation (2000)

     A Top 100 Young Innovator, MIT's Technolog Review (1999)

     NSF CAREER Award, NSF (1997)

     Northrop Grumman Outstanding Junior Faculty Research Award, UCLA (1997)

     NSF postdoctoral fellowship, NSF (1995)

     Fannie and John Hertz Fellow, Fannie and John Hertz Foundation (1991)

    Positions Held
     Editorial Board Member, Protein Engineering, Design & Selection. (2008 - 2008)

     BMES Representative on the FASEB Publications & Communications Committee. (2009 - 2009)

     Associate Editor, PLoS Computational Biology. (2008 - 2008)

     Visiting Scholar, Phi Beta Kappa. (2012 - 2013)

     Member, Board of Governors, Institute for Complex Adaptive Matter. (2008 - 2008)

     Board of Governors Member, Institute for Complex Adaptive Matter. (2012 - 2012)

     External Scientific Advisor, Princeton Physical Sciences-Oncology Center. (2012 - 2014)

     Member, Division of Biological Physics Nominating Committee, American Physical Society. (2007 - 2007)