Publications

Books

  1. Muhammad H. Zaman, Ed. Statistical Mechanics of Cellular Systems and Processes, Cambridge University Press. March 2009. [Amazon]

Publications from Zaman Lab

  1. Zohar Weinstein and Muhammad H. Zaman. Quantitative bioassay to identify antimicrobial drugs through drug interaction analysis. Scientific Reports, In Press (2017).
  2. Meng Sun and Muhammad H. Zaman. Modeling, signaling and cytoskeleton dynamics: integrated modeling-experimental frameworks in cell migration. Wiley Interdisciplinary Reviews: Systems Biology and Medicine (2016). [Online]
  3. Fabian Spill, Zohar B. Weinstein, Atena Irani Shemirani, Nga Ho, Darash Desai and Muhammad H. Zaman. Controlling uncertainty in aptamer selection. Proceedings of the National Academy of Sciences 201605086 (2016). [Online]
  4. Fabian Spill, Daniel S Reynolds, Roger D Kamm and Muhammad H. Zaman. Impact of the physical microenvironment on tumor progression and metastasis. Current Opinion in Biotechnology 40, 41–48 (2016). [Online]
  5. Diego A. Vargas, Meng Sun, Khikmet Sadykov, Maria A. Kukuruzinska and Muhammad H. Zaman. The Integrated Role of Wnt/β-Catenin, N-Glycosylation, and E-Cadherin-Mediated Adhesion in Network Dynamics. PLOS Computational Biology 12, e1005007 (2016). [Online]
  6. Meng Sun, Fabian Spill and Muhammad H. Zaman. A Computational Model of YAP/TAZ Mechanosensing. Biophysical Journal 110, 2540–2550 (2016). [Online]
  7. Michael Mak, Fabian Spill, Roger D. Kamm and Muhammad H. Zaman. Single-cell migration in complex microenvironments: mechanics and signaling dynamics. Journal of biomechanical engineering 138, 21004 (2016).
  8. Katie L. Clifford and Muhammad H. Zaman. Engineering, global health, and inclusive innovation: focus on partnership, system strengthening, and local impact for SDGs. Global Health Action 9, (2016). [Online]
  9. Michael Mak, Muhammad H. Zaman, Roger D. Kamm and Taeyoon Kim. Interplay of active processes modulates tension and drives phase transition in self-renewing, motor-driven cytoskeletal networks. Nature Communications 7, 10323 (2016). [Online]
  10. Mehdi Bourouba, Ahmed Amine Zergoun, Joseph Maffei, Sarah Leila Sellam, Samir Ouraghi, Djamel Djennaoui, Zine-Charaf Amir-Tidadini, Chafia Touil-Boukoffa and Muhammad H. Zaman. ID24: Inhibition of the TNF-aNOS2 inflammatory pathway alters nasopharyngeal carcinoma tumor growth. Cytokine 76, 68 (2015). [Online]
  11. Michael Mak, Taeyoon Kim, Muhammad H. Zaman and Roger D. Kamm. Active Mechanics of Cytoskeletal Networks of Single and Collective Cells. Tissue Engineering Part A 21, S372–S372 (2015).
  12. Meng Sun, Alexander B. Bloom and Muhammad H. Zaman. Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity. PLOS ONE 10, e0131814 (2015). [Online]
  13. Mehdi Bourouba, Ahmed-Amine Zergoun, Joseph S. Maffei, Dalia Chila, Djamel Djennaoui, Fatima Asselah, Zine-Charef Amir-Tidadini, Chafia Touil-Boukoffa and Muhammad H. Zaman. TNFα antagonization alters NOS2 dependent nasopharyngeal carcinoma tumor growth. Cytokine 74, 157–163 (2015). [Online]
  14. Fabian Spill, Vivi Andasari, Michael Mak, Roger D. Kamm and Muhammad H. Zaman. Effects of 3D geometries on cellular gradient sensing and polarization. Preprint (2015).
  15. Nga. T. Ho, Darash Desai and Muhammad H. Zaman. Rapid and Specific Drug Quality Testing Assay for Artemisinin and Its Derivatives Using a Luminescent Reaction and Novel Microfluidic Technology. American Journal of Tropical Medicine and Hygiene 92, 24–30 (2015). [Online]
  16. Muhammad H. Zaman. Maternal Health in Developing Countries: Engineering approaches and future outlook. IEEE Pulse 6, 25–27 (2015). [Online]
  17. Grace Wu and Muhammad H. Zaman. Integration of a paper-based electrochemical device with a commercial glucose meter for ethanol measurements. Talanata, Journal of Biotechnology 134, 194–9 (2015).
  18. Yasha Sharma, Diego A. Vargas, Adrian F. Pegoraro, David Lepzelter, David A. Weitz and Muhammad H. Zaman. Collective motion of mammalian cell cohorts in 3D. Integr. Biol. 7, 1526–1533 (2015). [Online]
  19. Michael Mak, Taeyoon Kim, Muhammad H. Zaman and Roger D. Kamm. Multiscale mechanobiology: computational models for integrating molecules to multicellular systems. Integr. Biol. 7, 1093–1108 (2015). [Online]
  20. Darash Desai and Muhammad H. Zaman. Continuous flow microfluidic solution for quantitative analysis of active pharmaceutical ingredient content and kinetic release. Anal. Methods 7, 1914–1923 (2015). [Online]
  21. Grace Wu, Jaya Srivastava and Muhammad H. Zaman. Stability measurements of antibodies stored on paper. Analytical Biochemistry 449, 147–154 (2014). [Online]
  22. Yusuke Sakamoto, Serge Prudhomme and Muhammad H. Zaman. Modeling of adhesion, protrusion, and contraction coordination for cell migration simulations. Journal of Mathematical Biology 68, 267–302 (2014). [Online]
  23. Michael Mak, Roger D. Kamm and Muhammad H. Zaman. Impact of Dimensionality and Network Disruption on Microrheology of Cancer Cells in 3D Environments. PLoS Computational Biology 10, e1003959 (2014). [Online]
  24. Joseph S. Maffei, Jaya Srivastava, Brian Fallica and Muhammad H. Zaman. Combinative in vitro studies and computational model to predict 3D cell migration response to drug insult. Integr. Biol. 6, 957–972 (2014). [Online]
  25. Xiaofeng Liu, Diego A. Vargas, Dongyuan Lü, Yan Zhang, Muhammad H. Zaman and Mian Long. Computational Modeling of Stem Cell Migration: A Mini Review. Cellular and Molecular Bioengineering 7, 196–204 (2014). [Online]
  26. David Lepzelter and Muhammad H. Zaman. Modeling Persistence in Mesenchymal Cell Motility Using Explicit Fibers. Langmuir 30, 5506–5509 (2014). [Online]
  27. Patricia Garcia, Robert Armstrong, Muhammad H. Zaman and others. Models of education in medicine, public health, and engineering. Science 345, 1281–1283 (2014).
  28. Leandro Forciniti, Jose Ybarra, Muhammad H. Zaman and Christine E. Schmidt. Schwann cell response on polypyrrole substrates upon electrical stimulation. Acta Biomaterialia 10, 2423–2433 (2014). [Online]
  29. Kristie M. Charoen, Brian Fallica, Yolonda L. Colson, Muhammad H. Zaman and Mark W. Grinstaff. Embedded multicellular spheroids as a biomimetic 3D cancer model for evaluating drug and drug-device combinations. Biomaterials 35, 2264–2271 (2014). [Online]
  30. Alexander. B. Bloom and Muhammad H. Zaman. Influence of the microenvironment on cell fate determination and migration. Physiological Genomics 46, 309–314 (2014). [Online]
  31. Muhammad H. Zaman. The role of engineering approaches in analysing cancer invasion and metastasis. Nature Reviews Cancer 13, 596–603 (2013).
  32. Muhammad H. Zaman. The role of engineering approaches in analysing cancer invasion and metastasis. Nature Reviews Cancer 13, 596–603 (2013).
  33. Diego A. Vargas, Oliver Bates and Muhammad H. Zaman. Computational Model to Probe Cellular Mechanics during Epithelial-Mesenchymal Transition. Cells Tissues Organs 197, 435–444 (2013). [Online]
  34. Michael P. Schwartz, Samir P. Singh, Justin Y. Lee, Samuel G. Loveland, Justin T. Koepsel, Robert E. Rogers, Sara I. Montanez-Sauri, Kyung E. Sung, Eric K. Sackmann, Emi Y. Tokuda, Lydia M. Everhart, Eric H. Nguyen, Yasha Sharma, Muhammad H. Zaman, David J. Beebe, Natalie G. Ahn, William L. Murphy and Kristi S. Anseth. A comparison between primary and transformed cells reveals a unique migration mode with mixed mesenchymal and amoeboid character. PLoS ONE 8, (2013).
  35. Parag Katira, Roger T. Bonnecaze and Muhammad H. Zaman. Modeling the Mechanics of Cancer: Effect of Changes in Cellular and Extra-Cellular Mechanical Properties. Frontiers in Oncology 3, (2013). [Online]
  36. Dewi Harjanto and Muhammad H. Zaman. Modeling extracellular matrix reorganization in 3D environments. PloS one 8, e52509 (2013).
  37. Federico Frascoli, Barry D. Hughes, Muhammad H. Zaman and Kerry A. Landman. A Computational Model for Collective Cellular Motion in Three Dimensions: General Framework and Case Study for Cell Pair Dynamics. PLoS ONE 8, e59249 (2013). [Online]
  38. Erika J. Fong, Yasha Sharma, Brian Fallica, Dylan B. Tierney, Sarah M. Fortune and Muhammad H. Zaman. Decoupling Directed and Passive Motion in Dynamic Systems: Particle Tracking Microrheology of Sputum. Annals of Biomedical Engineering 41, 837–846 (2013). [Online]
  39. Rebecca H. Chisholm, Barry D. Hughes, Kerry A. Landman and Muhammad H. Zaman. Analytic Study of Three-Dimensional Single Cell Migration with and without Proteolytic Enzymes. Cellular and Molecular Bioengineering 6, 239–249 (2013). [Online]
  40. Muhammad H. Zaman. Biomedical Engineering Education in resource-limited settings: Creating an innovation eco-system. in Appropriate Healthcare Technologies for Developing Countries, 7th International Conference on 1–5 (IET, 2012). [Online]
  41. Grace Wu and Muhammad H. Zaman. Low-cost tools for diagnosing and monitoring HIV infection in low-resource settings. Bulletin of the World Health Organization 90, 914–920 (2012). [Online]
  42. David Lepzelter and Muhammad H. Zaman. Subdiffusion of proteins and oligomers on membranes. The Journal of chemical physics 137, 175102 (2012).
  43. David Lepzelter, Oliver Bates and Muhammad H. Zaman. Integrin Clustering in Two and Three Dimensions. Langmuir 28, 5379–5386 (2012). [Online]
  44. Parag Katira, Muhammad H. Zaman and Roger T. Bonnecaze. How Changes in Cell Mechanical Properties Induce Cancerous Behavior. Physical Review Letters 108, (2012). [Online]
  45. Andrea Fernandes and Muhammad H. Zaman. The role of biomedical engineering in disaster management in resource-limited settings. Bulletin of the World Health Organization 90, 631–632 (2012).
  46. Brian Fallica, Joseph S. Maffei, Shaun Villa, Guy Makin and Muhammad H. Zaman. Alteration of Cellular Behavior and Response to PI3K Pathway Inhibition by Culture in 3D Collagen Gels. PLoS ONE 7, e48024 (2012). [Online]
  47. Diego A. Vargas and Muhammad H. Zaman. Computational Model for Migration of a Cell Cluster in Three-Dimensional Matrices. Annals of Biomedical Engineering 39, 2068–2079 (2011). [Online]
  48. Dhananjay T. Tambe, C. Corey Hardin, Thomas E. Angelini, Kavitha Rajendran, Chan Young Park, Xavier Serra-Picamal, Enhua H. Zhou, Muhammad H. Zaman, James P. Butler, David A. Weitz, Jeffrey J. Fredberg and Xavier Trepat. Collective cell guidance by cooperative intercellular forces. Nature Materials 10, 469–475 (2011). [Online]
  49. Yusuke Sakamoto, Serge Prudhomme and Muhammad H. Zaman. Viscoelastic Gel-Strip Model for the Simulation of Migrating Cells. Annals of Biomedical Engineering 39, 2735–2749 (2011). [Online]
  50. Daniel R. Lustick and Muhammad H. Zaman. Biomedical Engineering Education and Practice Challenges and opportunities in improving health in developing countries. in Science and Innovation Policy, 2011 Atlanta Conference on 1–5 (IEEE, 2011). [Online]
  51. Dewi Harjanto, Joseph S. Maffei and Muhammad H. Zaman. Quantitative Analysis of the Effect of Cancer Invasiveness and Collagen Concentration on 3D Matrix Remodeling. PLoS ONE 6, e24891 (2011). [Online]
  52. Brian Fallica, Guy Makin and Muhammad H. Zaman. Bioengineering approaches to study multidrug resistance in tumor cells. Integrative Biology 3, 529 (2011). [Online]
  53. Darash Desai, Grace Wu and Muhammad H. Zaman. Tackling HIV through robust diagnostics in the developing world: current status and future opportunities. Lab Chip 11, 194–211 (2011). [Online]
  54. Erin L. Baker, Jaya Srivastava, Dihua Yu, Roger T. Bonnecaze and Muhammad H. Zaman. Cancer Cell Migration: Integrated Roles of Matrix Mechanics and Transforming Potential. PLoS ONE 6, e20355 (2011). [Online]
  55. Muhammad H. Zaman. Engineering education in the developing world: The case for biological engineering. in Education Engineering (EDUCON), 2010 IEEE 1047–1050 (IEEE, 2010). [Online]
  56. Tianyi Yang and Muhammad H. Zaman. Estimation of Cellular Adhesion Forces Using Mean Field Theory. Cellular and Molecular Bioengineering 3, 190–194 (2010). [Online]
  57. Ge Wang and Muhammad H. Zaman. Communications: Hamiltonian regulated cell signaling network. The Journal of Chemical Physics 132, 121103 (2010). [Online]
  58. Michael P. Schwartz, Benjamin D. Fairbanks, Robert E. Rogers, Rajagopal Rangarajan, Muhammad H. Zaman and Kristi S. Anseth. A synthetic strategy for mimicking the extracellular matrix provides new insight about tumor cell migration. Integr. Biol. 2, 32–40 (2010). [Online]
  59. David Lepzelter and Muhammad H. Zaman. Clustered Diffusion of Integrins. Biophysical Journal 99, L106–L108 (2010). [Online]
  60. Dewi Harjanto and Muhammad H. Zaman. Matrix mechanics and receptor–ligand interactions in cell adhesion. Org. Biomol. Chem. 8, 299–304 (2010). [Online]
  61. Dewi Harjanto and Muhammad H. Zaman. Computational Study of Proteolysis-Driven Single Cell Migration in a Three-Dimensional Matrix. Annals of Biomedical Engineering 38, 1815–1825 (2010). [Online]
  62. Erin L. Baker and Muhammad H. Zaman. The biomechanical integrin. Journal of Biomechanics 43, 38–44 (2010). [Online]
  63. Erin L. Baker, Jing Lu, Dihua Yu, Roger T. Bonnecaze and Muhammad H. Zaman. Cancer Cell Stiffness: Integrated Roles of Three-Dimensional Matrix Stiffness and Transforming Potential. Biophysical Journal 99, 2048–2057 (2010). [Online]
  64. Tianyi Yang and Muhammad H. Zaman. Regulation of Cell Adhesion Free Energy by External Sliding Forces. Experimental Mechanics 49, 57–63 (2009). [Online]
  65. Tianyi Yang and Muhammad H. Zaman. Equilibrium and non-equilibrium thermodynamic processes in cell-matrix interactions. Journal of Non-Equilibrium Thermodynamics 34, 195–217 (2009).
  66. Diego A. Vargas and Muhammad H. Zaman. Serine at Phosphorylation Site Regulates the Mechanical and Structural Behavior of Fascin. Cellular and Molecular Bioengineering 2, 504–513 (2009). [Online]
  67. Mark Kness, Ge Wang and Muhammad H. Zaman. Robustness of integrin signaling network. The Journal of Chemical Physics 130, 235103 (2009). [Online]
  68. Leandro Forciniti, Ge Wang and Muhammad H. Zaman. Actin–Fascin Bundle Formation Under Pressure. Cellular and Molecular Bioengineering 2, 2–12 (2009). [Online]
  69. Leandro Forciniti, Christine E. Schmidt and Muhammad H. Zaman. Computational Model Provides Insight into the Distinct Responses of Neurons to Chemical and Topographical Cues. Annals of Biomedical Engineering 37, 363–374 (2009). [Online]
  70. Erin L. Baker, Roger T. Bonnecaze and Muhammad H. Zaman. Extracellular Matrix Stiffness and Architecture Govern Intracellular Rheology in Cancer. Biophysical Journal 97, 1013–1021 (2009). [Online]
  71. Muhammad H. Zaman. Computer simulations in connective tissue research: successes and challenges. Connect. Tissue Res. 49, 162–164 (2008). [Online]
  72. Tianyi Yang and Muhammad H. Zaman. Thermodynamics of clustered and unclustered receptor systems in cell adhesion. Chemical Physics Letters 454, 362–366 (2008). [Online]
  73. Tianyi Yang and Muhammad H. Zaman. Cell adhesion to nanoligands: effects of ligand size and concentration in solution. Langmuir 24, 11819–11827 (2008).
  74. Rajagopal Rangarajan and Muhammad H. Zaman. Modeling cell migration in 3D: Status and challenges. Cell adhesion & migration 2, 106–109 (2008).
  75. Brendan A.C. Harley, Hyung-Do Kim, Muhammad H. Zaman, Ioannis V. Yannas, Douglas A. Lauffenburger and Lorna J. Gibson. Microarchitecture of Three-Dimensional Scaffolds Influences Cell Migration Behavior via Junction Interactions. Biophysical Journal 95, 4013–4024 (2008). [Online]
  76. Heiko Enderling, Nelson R. Alexander, Emily S. Clark, Kevin M. Branch, Lourdes Estrada, Cornelia Crooke, Jérôme Jourquin, Nichole Lobdell, Muhammad H. Zaman, Scott A. Guelcher, Alexander R.A. Anderson and Alissa M. Weaver. Dependence of Invadopodia Function on Collagen Fiber Spacing and Cross-Linking: Computational Modeling and Experimental Evidence. Biophysical Journal 95, 2203–2218 (2008). [Online]
  77. Muhammad H. Zaman. Understanding the Molecular Basis for Differential Binding of Integrins to Collagen and Gelatin. Biophysical Journal 92, L17–L19 (2007). [Online]
  78. Muhammad H. Zaman. Cell adhesion & migration. Cell adhesion & migration 2, 53–54 (2007).
  79. Muhammad H. Zaman. A multiscale probabilisitic framework to model early steps in tumor metastasis. Mol Cell Biomech 4, 133–141 (2007).
  80. Tianyi Yang and Muhammad H. Zaman. Free energy landscape of receptor-mediated cell adhesion. The Journal of Chemical Physics 126, 045103 (2007). [Online]
  81. Muhammad H. Zaman. Multiscale Modeling of Tumor Cell Migration. in 851, 117–122 (AIP, 2006). [Online]
  82. Muhammad H. Zaman, Linda M. Trapani, Alisha Sieminski, Drew MacKellar, Haiyan Gong, Roger D. Kamm, Alan Wells, Douglas A. Lauffenburger and Paul Matsudaira. Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proceedings of the National Academy of Sciences 103, 10889–10894 (2006). [Online]
  83. Muhammad H. Zaman, Paul Matsudaira and Douglas A. Lauffenburger. Understanding Effects of Matrix Protease and Matrix Organization on Directional Persistence and Translational Speed in Three-Dimensional Cell Migration. Annals of Biomedical Engineering 35, 91–100 (2006). [Online]
  84. Alejandro Wolf-Yadlin, Neil Kumar, Yi Zhang, Sampsa Hautaniemi, Muhammad H. Zaman, Hyung-Do Kim, Viara Grantcharova, Douglas A Lauffenburger and Forest M White. Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Molecular Systems Biology 2, (2006). [Online]
  85. Neil Kumar, Muhammad H. Zaman, Hyung-Do Kim and Douglas A. Lauffenburger. A High-Throughput Migration Assay Reveals HER2-Mediated Cell Migration Arising from Increased Directional Persistence. Biophysical Journal 91, L32–L34 (2006). [Online]
  86. Muhammad H. Zaman. Misfolding dynamics of human prion protein. Mol Cell Biomech 2, 179–190 (2005).
  87. Muhammad H. Zaman, Roger D. Kamm, Paul Matsudaira and Douglas A. Lauffenburger. Computational Model for Cell Migration in Three-Dimensional Matrices. Biophysical Journal 89, 1389–1397 (2005). [Online]
  88. Abhishek K. Jha, Andres Colubri, Muhammad H. Zaman, Shohei Koide, Tobin R. Sosnick and Karl F. Freed. Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library †. Biochemistry 44, 9691–9702 (2005). [Online]
  89. Muhammad H. Zaman and Mohammad R. Kaazempur-Mofrad. How flexible is alpha-actinin’s rod domain? Mech Chem Biosyst 1, 291–302 (2004).
  90. Muhammad H. Zaman, Tobin R. Sosnick and R. Stephen Berry. Temperature dependence of reactions with multiple pathways. Physical Chemistry Chemical Physics 5, 2589 (2003). [Online]
  91. Muhammad H. Zaman, Min-Yi Shen, R. Stephen Berry and Karl F. Freed. Computer Simulation of Met-Enkephalin Using Explicit Atom and United Atom Potentials: Similarities, Differences, and Suggestions for Improvement. The Journal of Physical Chemistry B 107, 1685–1691 (2003). [Online]
  92. Muhammad H. Zaman, Min-Yi Shen, R.Stephen Berry, Karl F. Freed and Tobin R. Sosnick. Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin Dynamics and the Flory Isolated-pair Hypothesis for Peptides. Journal of Molecular Biology 331, 693–711 (2003). [Online]
  93. Muhammad H. Zaman, R. Stephen Berry and Tobin R. Sosnick. Entropic benefit of a cross-link in protein association. Proteins: Structure, Function, and Genetics 48, 341–351 (2002). [Online]
  94. Muhammad H. Zaman and Scott M. Jordan. Using SAS Macros to Develop Confidence Intervals for the Weibull and Extreme Value Distribution Using Type II Censored Data. (1999).

Published Book Chapters

  1. Tianyi Yang and Muhammad H. Zaman. Statistical Mechanics of Cell Matrix Interactions. In Muhammad H. Zaman, Ed. Statistical Mechanics of Cellular Systems and Processes, Cambridge University Press. 2009.
  2. Dewi Harjanto and Muhammad H. Zaman. Multiscale modeling of cell motion in three-dimensional environments. In “Multiscale Cancer Modeling”  Deisboeck and Stamataoks Ed. Taylor and Francis Publishers. 2010.
  3. Dewi Harjanto and Muhammad H. Zaman. Biophysics of 3D Cell Motility. In “Comprehensive Reviews of Biophysics”. Wirtz Editor. Cell Press. 2011.
  4. David Lepzelter and Muhammad H. Zaman. Cell Receptor and Matrix Interactions. In “Nano and Cell Mechanics”. Espinosa and Bao Editor. 2012.
  5. Joe Maffei and Muhammad H. Zaman. Quantifying Cell-ECM pathobiology in 3D. In “Extracellular Matrix Pathobiology and Signaling”. Karamanos Editor. De Gruyter Press. 2012.
  6. Yasha Sharma and Muhammad H. Zaman. Cell migration in Three Dimensional Matrices. In “Cell and Matrix Mechanics”. Zemmel and Kaunus Editors. Taylor and Francis. 2014.
  7. Jaya Srivastava and Muhammad H. Zaman. Systems Biology of tumor cell migration in 3D. In “Mechanobiology of Cell Matrix Interactions”. Harley and Wagner Editors. Springer. 2010.
  8. Muhammad H. Zaman and Mariam Bhacker. Healthy Relationships? GCC global health engagement – a focus on Africa. In “Gulf Africa Relationship”, Eickelman and Abusharaf Editors. Gerlach Press Series on GCC, 2015.