Michael W. Deem: Publications
MICHAEL
W.
DEEM
PUBLICATIONS
(Reprint links may work if your institution subscribes to the journal)
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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F. Daeyaert and M. W. Deem,
``Design of Organic Structure Directing Agents for Chiral Zeolite Beta A,''
ChemistrySelect 4 (2019) 3531-3537
(Reprint).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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D. Wang and M. W. Deem,
``Modular Knowledge Systems Accelerate Human Migration in Asymmetric Random
Environments,''
J. Roy. Soc. Interface 13 (2016) 20160778
(Reprint).
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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).
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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).
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Y. Pan and M. W. Deem,
``Prediction of Influenza B Vaccine Effectiveness from Sequence Data,''
Vaccine 34 (2016) 4610-4617
(Reprint).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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J.-M. Park, L. R. Niestemski, and M. W. Deem,
``Quasispecies Theory for Evolution of Modularity,''
Phys. Rev. E 91 (2015) 012714
(Reprint).
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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).
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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).
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X. Li and M. W. Deem,
``Why Zeolites Have So Few 7-Membered Rings,''
J. Phys. Chem. C 118 (2014) 15835-15839
(Reprint).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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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.
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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).
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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).
ARXIV
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