Michael W. Deem: Publications

• F. Daeyaert and M. W. Deem, ``De Novo Design of Organic Structure Directing Agents for the Synthesis of Zeolites,'' in AI-Guided Design and Property Prediction for Zeolites and Nanoporous Materials, ISBN 9781119819783, edited by German Sastre and Frits Daeyaert, Wiley, January 2023, ch. 2, pp. 33-59, 10.1002/9781119819783.ch2 (Reprint).
• S. M. Moosavi, F. Daeyaert, M. W. Deem, and G. Sastre, ``Overview of AI in the Understanding and Design of Nanoporous Materials,'' in AI-Guided Design and Property Prediction for Zeolites and Nanoporous Materials, ISBN 9781119819783, edited by German Sastre and Frits Daeyaert, Wiley, January 2023, ch. 15, pp. 411-424, 10.1002/9781119819783.ch15 (Reprint).
• J. H. Kang, L. B. McCusker, M. W. Deem, C. Baerlochere, and M. E. Davis, ``Further Investigations of Racemic and Chiral Molecular Sieves of STW Topology,'' Chem. Mater. 33 (2021) 1752-1759 (Reprint).
• F. Daeyaert and M. W. Deem, ``Design of Organic Structure Directing Agents to Guide the Synthesis of Zeolites for the Separation of Ethylene-Ethane Mixtures,'' RSC Adv. 10 (2020) 20313-20321 (Reprint).
• V. A. Blatov, O. A. Blatova, F. Daeyaert, and M. W. Deem, ``Nanoporous Materials with Predicted Zeolite Topologies,'' RSC Adv. 10 (2020) 17760-17767 (Reprint).
• M. W. Deem, ``CRISPR Recognizes as Many Phage Types as Possible Without Overwhelming the Cas Machinery,'' Proc. Natl. Acad. Sci. USA 117 (2020) 7550-7552 (Reprint).
• F. Daeyaert and M. W. Deem, ``Design of Organic Structure Directing Agents for the Controlled Synthesis of Zeolites for Use in Carbon Dioxide/Methane Membrane Separations,'' with cover feature, ChemPlusChem 85 (2020) 277-284 (Reprint).
• F. Daeyaert and M. W. Deem, ``Design of Organic Structure Directing Agents to Control the Synthesis of Zeolites for Carbon Capture and Storage,'' RSC Adv. 9 (2019) 41934-41942 (Reprint).
• M. E. Bonomo, R. Y. Kim, and M. W. Deem, ``Prediction of Influenza A(H3N2) Quasispecies Dominance and Vaccine Effectiveness Using a Novel pEpitope Model: Application to 2018-2019 Season,'' Vaccine 37 (2019) 3154-3158 (Reprint).
• F. Daeyaert and M. W. Deem, ``Design of Organic Structure Directing Agents for Chiral Zeolite Beta A,'' ChemistrySelect 4 (2019) 3531-3537 (Reprint).
• F. Daeyaert and M. W. Deem, ``Design of Organic Structure Directing Agents for Polymorph A Zeolite Beta,'' J. Mater. Chem. A 7 (2019) 9854-9866 (Reprint).
• F. Daeyaert, F. Ye, and M. W. Deem, ``A Machine Learning Approach to the Design of OSDAs for Zeolite Beta,'' Proc. Natl. Acad. Sci. USA 116 (2019) 3413-3418 (Reprint).
• M. E. Bonomo and M. W. Deem, ``Reply to Xu and Ye: On the Sufficiency of the pEpitope Method,'' Clin. Infect. Dis. 2 (2019) 247 (Reprint).
• M. W. Deem, M. E. Bonomo, and K. R. W. Matthews, ``Improving the Effectiveness of the Annual Flu Vaccine,'' Policy Brief, Rice University's Baker Institute for Public Policy, 29 October 2018 (Reprint).
• F. Daeyaert and M. W. Deem, ``In silico Design of Chiral Dimers to Direct the Synthesis of a Chiral Zeolite ,'' Molec. Phys., Daan Frenkel special issue, 116 (2018) 2836-2855 (Reprint).
• M. E. Bonomo and M. W. Deem, ``The Physicist's Guide to One of Biotechnology's Hottest New Topics: CRISPR-Cas,'' Physical Biology 15 (2018) 041002 (Reprint).
• M. E. Bonomo and M. W. Deem, ``Predicting Influenza H3N2 Vaccine Efficacy from Evolution of the Dominant Epitope,'' Clin. Infect. Dis. 67 (2018) 1129-1131. (Reprint).
• S. Tripathi and M. W. Deem, ``The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences,'' J. Mol. Evol. 86 (2018) 325-339 (Reprint).
• S. Tripathi, M. K. Jolly, W. A. Woodward, H. Levine, and M. W. Deem, ``Analysis of Hierarchical Organization in Gene Expression Networks Reveals Underlying Principles of Collective Tumor Cell Dissemination and Metastatic Aggressiveness of Inflammatory Breast Cancer,'' Frontiers in Oncology (2018) doi.org/10.3389/fonc.2018.00244 (Reprint).
• F. Ye, D. Jia, M. Lu, H. Levine, and M. W. Deem, ``Modularity of the Metabolic Gene Network as a Prognostic Biomarker for Hepatocellular Carcinoma,'' Oncotarget 9 (2018) 15015-15026 (Reprint).
• L. Zhao, L. Deng, G. Li, H. Jin, J. Cai, H. Shang, Y. Li, H. Wu, W. Xu, L. Zeng, R. Zhang, H. Zhao, P. Wu, Z. Zhou, J. Zheng, P. Ezanno, A.-X. Yang, Q. Yan, M. W. Deem, J.-K. He, ``Single Molecule Sequencing of M13 Virus Genome Without Amplification,'' PLOS One 12 (2017) e0188181 (Reprint).
• M. E. Bonomo and M. W. Deem, ``How the Other Half Lives: CRISPR-Cas's Influence on Bacteriophages,'' in Evolutionary Biology : Self, Non-Self Evolution, Species and Complex Traits; Evolution, Methods and Concepts, ISBN 978-3-319-61569-1, edited by Pierre Pontarotti, Springer Nature, September 2017, pp. 63-85 (Reprint).
• A. I. Ramos-Nuez, S. Fischer-Baum, R. Martin, Q.-H. Yue, F.-D. Ye, and M. W. Deem, ``Static and Dynamic Measures of Human Brain Connectivity Predict Complementary Aspects of Human Cognitive Performance,'' Frontiers in Human Neuroscience (2017) doi: 10.3389/fnhum.2017.00420 (Reprint).
• Q.-H. Yue, R. Martin, S. Fischer-Baum, A. I. Ramos-Nuez, F.-D. Ye, and M. W. Deem, ``Brain Modularity Mediates the Relation of Cognitive Performance to Task Complexity,'' J. Cog. Neurosci. 29 (2017) 1532-1546. (Reprint).
• S. K. Brand, J. E. Schmidt, M. W. Deem, F. Daeyaert, Y. Ma, O. Terasaki, M. Orazova, and M. E. Davis, ``Enantiomerically Enriched, Polycrystalline Molecular Sieves,'' Proc. Natl. Acad. Sci. USA 114 (2017) 5101-5106 (Reprint).
• F. Daeyaert and M. W. Deem, ``A Pareto Algorithm for Efficient De Novo Design of Multi-Functional Molecules,'' Molecular Informatics 36 (2017) 1600044 (Reprint).
• P. Han and M. W. Deem, ``A Non-Classical Phase Diagram for Virus-Bacterial Co-Evolution Mediated by CRISPR,'' J. Roy. Soc. Interface 14 (2017) 20160905 (Reprint).
• Y. Gao, L.-W. Deng, Q. Yan, Y.-Q. Gao, Z.-D. Wu, J.-S. Cai, D.R. Ji, G.-L. Li, P. Wu, H.-A. Jin, L.-Y. Zhao, S. Liu, L.-J. Ge, M. W. Deem, and J. K. He, ``Single Molecule Targeted Sequencing for Cancer Gene Mutation Detection,'' Scientific Reports 6 (2016) 26110 (Reprint).
• D. Wang and M. W. Deem, ``Modular Knowledge Systems Accelerate Human Migration in Asymmetric Random Environments,'' J. Roy. Soc. Interface 13 (2016) 20160778 (Reprint).
• J. E. Schmidt, D.-L. Fu, M. W. Deem, and B. M. Weckhuysen, ``Template-Framework Interactions in Tetraethylammonium Directed Zeolite Synthesis,'' Angew. Chem. Int. Ed. 55 (2016) 16044-16048 (Reprint).
• Y. Tong, Z.-F. Li, H. Zhang, L.-G. Xia, M. Zhang, Y. Xu, Z.-H. Wang, M. W. Deem, X.-J. Sun, J.-K. He, ``T Cell Repertoire Diversity Is Decreased in Type 1 Diabetes,'' Genomics, Proteomics & Bioinformatics 14 (2016) 338-348 (Reprint).
• Y. Pan and M. W. Deem, ``Prediction of Influenza B Vaccine Effectiveness from Sequence Data,'' Vaccine 34 (2016) 4610-4617 (Reprint).
• X. Li and M. W. Deem, ``Influenza Evolution and H3N2 Vaccine Effectiveness, with Application to the 2014/2015 Season,'' Protein Engineering, Design & Selection 29 (2016) 309-315 (Reprint).
• B. W. Boal, M. W. Deem, D. Xie, J.-H. Kang, M. E. Davis, and S. I. Zones, ``Synthesis of Germanosilicate Molecular Sieves from Mono- and Di-Quaternary Ammonium OSDAs Constructed from Benzyl Imidazolium Derivatives: Stabilization of Large Micropore Volumes Including New Molecular Sieve CIT-13,'' Chem. Mater. 28 (2016) 2158-2164 (Reprint).
• T. M. Davis, 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 (2016) 708-711 (Reprint).
• 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 (Reprint).
• 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,'' 2015, doi:10.3389/frym.2015.00011 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• 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) 6912 (Reprint).
• J.-M. Park, L. R. Niestemski, and M. W. Deem, ``Quasispecies Theory for Evolution of Modularity,'' Phys. Rev. E 91 (2015) 012714 (Reprint).
• 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 (Reprint).
• M. Chen and M. W. Deem, ``Development of Modularity in the Neural Activity of Children's Brains,'' Phys. Biol. 12 (2015) 016009 (Reprint).
• 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 (Reprint).
• X. Li and M. W. Deem, ``Why Zeolites Have So Few 7-Membered Rings,'' J. Phys. Chem. C 118 (2014) 15835-15839 (Reprint).
• 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 (Reprint).
• M. Chen and M. W. Deem, ``Modularity, Plasticity, and Development of Brain Function,'' in section Plasticity of Learning, The Cognitive Neurosciences V, edited by Michael S. Gazzaniga and George R. Mangun, MIT Press, 2014, pp. 119-128.
• M. W. Deem, ``Evolution: Life has Evolved to Evolve,'' Physics of Life Reviews 10 (2013) 333-335 (Reprint).
• R. Pophale, F. Daeyaert, and M. W. Deem, ``Computational Prediction of Chemically-Synthesizable Organic Structure Directing Agents for Zeolites,'' with cover image, J. Mater. Chem. A 1 (2013) 6750-6760 (Reprint).
• P. Bai, J. I. Siepmann, and M. W. Deem, ``Adsorption of Glucose into Zeolite Beta from Aqueous Solution,'' AIChE J., special Amundson issue, 59 (2013) 3523-3529 (Reprint).
• P. Han, L. R. Niestemski, J. E. Barrick, and M. W. Deem, ``Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System,'' a Highlight of 2013, Phys. Biol. 10 (2013) 025004 (Reprint).
• M. Chen and M. W. Deem, ``Hierarchy of Gene Expression Data is Predictive of Future Breast Cancer Outcome,'' Phys. Biol. 10 (2013) 056006 (Reprint).
• 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 (Reprint).
• D. M. Lorenz, J.-M. Park, and M. W. Deem, ``Evolutionary Processes in Finite Populations,'' Phys. Rev. E 87 (2013) 022704 (Reprint).
• C. Zhang and M. W. Deem, ``Multicanonical Molecular Dynamics by Variable-Temperature Thermostats and Variable-Pressure Barostats,'' J. Chem. Phys. 138 (2013) 034103 (Reprint).
• M. W. Deem, ``Statistical Mechanics of Modularity and Horizontal Gene Transfer,'' Annu. Rev. Condens. Matter Phys. 4 (2013) 287-311 doi:10.1146/annurev-conmatphys-030212-184316.
• 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 (Reprint).
• K. Pan and M. W. Deem, ``A Multi-Scale Model for Correlation in B Cell VDJ Usage of Zebrafish,'' Phys. Biol. 8 (2011) 055006 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• R. Pophale, P. A. Cheeseman, and M. W. Deem, ``A Database of New Zeolite-Like Materials,'' with cover image, a ``hot'' article, Phys. Chem. Chem. Phys. 13 (2011) 12407-12412 (Reprint).
• D. Lorenz, A. Jeng, and M. W. Deem, ``The Emergence of Modularity in Biological Systems,'' Physics of Life Reviews, invited review, editor Luca Peliti, 8 (2011) 129-160 (Reprint) and M. W. Deem and D. Lorenz, ``Statistical Mechanics of Biological Modularity,'' 8 (2011) 167-168 (Reprint).
• 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 (Reprint).
• 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 (Reprint).
• J. He and M. W. Deem, ``Structure and Response in the World Trade Network,'' Phys. Rev. Lett. 105 (2010) 198701, Editor's Suggestion article, highlighted in Physics. (Reprint).
• J. He and M. W. Deem, ``Low-Dimensional Clustering Detects Incipient Dominant Influenza Strain Clusters,'' with cover image, Protein Engineering, Design & Selection 23 (2010) 935-946 (Reprint).
• J. He and M. W. Deem, ``Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats),'' Phys. Rev. Lett. 105 (2010) 128102 (Reprint).
• M. W. Deem and P. Hejazi, ``Theoretical Aspects of Immunity,'' in Annual Review of Chemical and Biomolecular Engineering, vol. 1, edited by John Prausnitz, 2010, pp. 247-276.
• J.-M. Park, E. T. Munoz, and M. W. Deem, ``Quasispecies Theory for Finite Populations,'' Phys. Rev. E 81 (2010) 011902 (Reprint).
• J. He and M. W. Deem, ``Hierarchical Evolution of Animal Body Plans,'' Dev. Biol. 337 (2009) 157-161 (Reprint).
• M. W. Deem, R. Pophale, P. A. Cheeseman, and D. J. Earl, ``Computational Discovery of New Zeolite-Like Materials,'' with cover image, J. Phys. Chem. C 113 (2009) 21353-21360 (Reprint).
• M. W. Deem and K. Pan, ``The Epitope Regions of H1-Subtype Influenza A, with Application to Vaccine Efficacy,'' Protein Engineering, Design & Selection 22 (2009) 543-546 (Reprint).
• 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
• 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 (Reprint).
• M. Sun, W. Maichen, R. Pophale, Y. Liu, R. Cai, C. M. Lew, H. Hunt, M. W. Deem, M. E. Davis, and Y. Yan, ``Dielectric Constant Measurement of Zeolite Powders by Time Domain Reflectometry,''Micropor. Mesopor. Mater. 123 (2009) 10-14 (Reprint).
• 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 (Reprint) (also in Virtual Journal of Biological Physics Research, 1 April 2009).
• H. Zhou, R. Pophale, and M. W. Deem, ``Computer-Assisted Vaccine Design,'' in Influenza: Molecular Virology, Caister Academic Press (Norfolk, United Kingdom), edited by Qinghua Wang and Yizhi Jane Tao, 2009, pp. 173-191.
• 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, 2009, pp. 177-213.
• 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 (Reprint).
• E. T. Munoz, J.-M. Park, and M. W. Deem, ``Quasispecies Theory for Horizontal Gene Transfer and Recombination,'' Phys. Rev. E 78 (2008) 061921 (Reprint).
• 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, p. 25-36.
• 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) (APS Advertisement).
• 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) 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).