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. David Lepzelter and Muhammad H. Zaman. Modeling persistence in mesenchymal cell motility using explicit fibers. Langmuir. 2014. In Press.
  2. Xiaofeng Liu, Diego A. Vargas, Dongyuan Lü,  Yan Zhang, Muhammad H. Zaman1, and Mian Long1 . Computational modeling of stem cell migration. Cellular and Molecular Bioengineering. 2014. In Press. (1indicates co-corresponding author).
  3. Leandro Forciniti, Jose Ybarra, Muhammad H. Zaman and Christine Schmidt. Schwann cell response on polypyrrole substrates upon electrical stimulation. Acta Biomaterialia. 2014. In Press.
  4. Alexander Bloom and Muhammad H. Zaman. Quantifying the role of the microenvironment in determining cell fatePhysiological Genomics. 2014. In Press.
  5. Yasha Sharman and  Muhammad H. Zaman. Cell migration in Three Dimensional Matrices. In “Cell and Matrix Mechanics”. Zemmel and Kaunus Editors. Taylor and Francis. 2014.
  6. Grace Wu, Jaya Srivastava and Muhammad H. Zaman. Stability measurements of antibodies stored on paper. (Accepted. In Press, Analytical Biochemistry). 2014.
  7. Kristie M. Charoen, Brian Fallica, Yolonda L. Colson, Muhammad H. Zaman1 and Mark W. Grinstaff1. Embedded Multicellular Spheroids as Biomimetic 3D Cancer Model: A system for evaluating drug and drug-device combination. Biomaterials. 2014. doi:10.1016/j.biomaterials.2013.11.038 (1indicates co-corresponding author).
  8. Parag Katira, Roger T. Bonnecaze and Muhammad H. ZamanModeling the mechanics of cancer: Effect of changes in cellular and extra-cellular mechanical properties. Frontiers in Molecular and Cellular Oncology. 2013. doi:10.3389.
  9. Muhammad H. Zaman. Engineering approaches in analyzing invasion and metastasis. Nature Reviews in Cancer. (2013. doi:10.1038/nrc3564).
  10. 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. (Accepted, PLoS ONE).
  11. Diego Alejandro Vargas, Oliver Bates and Muhammad H. ZamanComputational model to probe cellular mechanics during EMT. Cells, Tissues, Organs, DOI:10.1159/000348415.
  12. Federico Fracoli, Barry D. Hughes, Muhammad H. Zaman and Kerry Landman. A computational model for collective cellular motion in three dimensions: general framework and case study for cell pair dynamics. PLoS ONE. 8(3): e59249. doi:10.1371/journal.pone.0059249
  13. Erika 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. 2013. 41(4):837-46.
  14. Grace Wu and Muhammad H. ZamanLow-Cost Tools for HIV Testing & Monitoring in Low-Resource Settings. Bulletin of the WHO. 2012. 1:90(12) 914-20.
  15. Yusuke Sakamoto, Serge Prudhomme and Muhammad H. Zaman. Modeling of adhesion, protrusion, and contraction coordination for cell migration simulations. Journal of Mathematical Biology, 2013, DOI 0.1007/s00285-012-0634-6.
  16. Dewi Harjanto and Muhammad H. Zaman. Modeling Extracellular Matrix Reorganization in 3D Environments. PLoS One, 2013: 8: e52509.
  17. Rebecca Chisholm, Barry D. Hughes, Kerry M. Landman and Muhammad H. Zaman. Analytic study of three-dimensional single cell migration with and without proteolytic enzyme (Cellular and Molecular Bioengineering, In Press.)
  18. Brian Fallica, Joe 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. 2012. 7(10): e48024.
  19. Andrea Fernandes and Muhammad H. Zaman. The role of biomedical engineering in disaster management in resource-limited settings. Bulletin of the WHO. 2012;90:631-632.
  20. Muhammad H. Zaman. Biomedical Engineering Education in Resource Limited Settings: Creating and Innovation Eco-System. Proceedings of the Institute for Engineering and Technology Conference on Appropriate Health Technologies for the Developing Countries, London, In Press. 2012.
  21. David Lepzelter and Muhammad H. Zaman. Subdiffusion of Proteins and Oligomers On Membranes. Journal of Chemical Physics. 2012. 137, 175102.
  22. Joe Maffei and Muhammad H. Zaman. Quantifying Cell-ECM pathobiology in 3D. In “Extracellular Matrix Pathobiology and Signaling”. Karamanos Editor. De Gruyter Press. 2012.
  23. David Lepzelter, Oliver Bates and Muhammad H. ZamanIntegrin Clustering in Two and Three Dimensions. Langmuir, 2012. 28(12):5379-5386. Cover Article.
  24. Parag Katira, Muhammad H. Zaman and Roger T. Bonnecaze. How Changes in cell mechanical properties induce cancerous behavior. Physical Review Letters, 2012. 108,028103.
  25. David Lepzelter and Muhammad H. Zaman. Cell Receptor and Matrix Interactions. In “Nano and Cell Mechanics”. Espinosa and Bao Editor. 2012.
  26. Muhammad H. Zaman. The role of Biomedical Engineering Education in improving East African Health. EAPHLN Bulletin. 2012.
  27. Dewi Harjanto, Joeseph Maffei and Muhammad H. ZamanQuantitative Analysis of the Effect of Cancer Invasiveness and Collagen Concentration on 3D Matrix Remodeling. PLoS One, 2011, 6(9): e24891.
  28. Daniel Lustick and Muhammad H. Zaman. “Biomedical engineering education and practice challenges and opportunities in improving health in developing countries” Science and Innovation Policy, 2011 Atlanta Conference on , vol., no., pp.1-5, 15-17 Sept. 2011
  29. Yusuke Sakamoto, Serge Prudhomme and Muhammad H. ZamanViscoelastic gel-strip model for the simulation of migrating cells. Annals of Biomedical Engineering, 2011. DOI: 10.1007/s10439-011-0360z.
  30. Erin Baker, Jaya Srivastava, Dihua Yu, Roger Bonnecaze and Muhammad H. ZamanCancer cell migration: Integrated roles of matrix mechanics and transforming potential. PLoS One, 2011, 6, 5, e20355.
  31. Dhananjay T. Tambe, C. Corey Hardin, Thomas E. Angelini, Kavitha Rajendran, Xavier Serra-Picamal, Muhammad H. Zaman, James P. Butler, David A. Weitz, Jeffrey J. Fredberg and Xavier Trepat. Cooperative intercellular forces in collective cell migration. Nature Materials. 2011. 10, 469.
  32. Diego Alejandro Vargas and Muhammad H. ZamanA computational model for migration of a cell-cluster in three dimensional matrices. Annals of Biomedical Engineering, 2011, 39(7):2068-79.
  33. Brian Fallica, Guy Makin and Muhammad H. ZamanBioengineering approaches to multi-drug resistance in tumor cells. Integrative Biology, 2011, 3(5):529-39.
  34. Darash Desai, Grace Wu and Muhammad H. ZamanTackling HIV through Robust Diagnostics in the Developing World:  Current Status and Future Opportunities. Lab on a Chip. 2011. 11(2): 194-211.
  35. Dewi Harjanto and Muhammad H. Zaman. Biophysics of 3D Cell Motility. In “Comprehensive Reviews of Biophysics”. Wirtz Editor. Cell Press. 2011.
  36. Muhammad H. Zaman. Engineering Education in the Developing World: The Case for Biological Engineering. Proceedings of IEEE EDUCON Conference on Engineering Education. Madrid. 2010.
  37. David Lepzelter and Muhammad H. ZamanClustered Diffusion of Integrins. Biophysical Journal. 2010. 99(12): L106-L108.
  38. Erin Baker, Jing Lu, Dihua Yu, Roger T. Bonnecaze and Muhammad H. ZamanCancer Cell Stiffness in 3D: Integrated roles of matrix stiffness and transforming potential. Biophysical Journal. 2010. 99 (7):  2048-57.
  39. 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.
  40. Tianyi Yang and Muhammad H. ZamanEstimation of cellular adhesion forces using mean field theory. Cellular and Molecular Bioengineering. 2010. 3(2), 190-194.
  41. Ge Wang and Muhammad H. ZamanHamiltonian Regulated Cell Signaling Network. Journal of Chemical Physics. 2010. 132 (12): 121103.
  42. Dewi Harjanto and Muhammad H. ZamanComputational study of proteolysis driven single cell migration in a three-dimensional matrix. Annals of Biomedical Engineering. (2010), 38 (5), 1815-25.
  43. Erin Baker and Muhammad H. ZamanThe biomechanical integrin. Journal of Biomechanics (2010) 43 (10) 38-44.
  44. Dewi Harjanto and Muhammad H. Zaman. Matrix Mechanics and Receptor-Ligand interactions in Cell Adhesion. Organic and Biomolecular Chemistry (2010) 8(2) 299-304.
  45. Michael Schwartz, Robert E. Rogers, Benjamin D. Fairbanks, Rajagopal Rangarajan, Muhammad H. Zaman and Kristi S. Anseth. A synthetic strategy for mimicking the extracellular matrix provides new insight about in vivo tumor cell migration. Integrative Biology (2010) 2, 32-40.
  46. 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.
  47. Diego A. Vargas and Muhammad H. ZamanSerine at Phosphorylation Site Regulates the Mechanical and Structural Behavior of Fascin. Cellular and Molecular Bioengineering (2009) 2, (4) 504-513.
  48. Erin L. Baker, Roger T. Bonnecaze and Muhammad H. Zaman. Extracellular Matrix Stiffness and Architecture Govern Intracellular Rheology in Cancer Biophysical Journal (2009) 97 (4) 1013-1021.
  49. Mark Kness, Ge Wang and Muhammad H. ZamanRobustness of integrin signaling network. Journal of Chemical Physics (2009) 130 (23) 235103.
  50. 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.
  51. Leandro Forciniti, Ge Wang and Muhammad H. ZamanActin-Fascin bundle formation under pressure. Cellular and Molecular Bioengineering (2009) 2 (1), 2-12.
  52. Leandro Forciniti, Christine E. Schmidt and Muhammad H. ZamanComputational model provides insight into the distinct responses of neurons to chemical and topographical cues. Annals of Biomedical Engineering (2009) 37(2):363-374.
  53. Tianyi Yang and Muhammad H. ZamanEquilibrium and non-equilibrium thermodynamic processes in cell-matrix interactions. Journal of Non-Equilibrium Thermodynamics (2009) 34, 195-217.
  54. Tianyi Yang and Muhammad H. ZamanCell adhesion to nanoligands: Effects of ligand size and concentration in solution. Langmuir (2008) 24 (20), 11819–11827.
  55. Brendan A Harley, Hyung-Do Kim, Muhammad H Zaman, Ioannis V Yannas, Douglas A. Lauffenburger, and Lorna J Gibson, Micro-architecture of three-dimensional scaffolds influences cell migration behavior via junction interactions. Biophysical Journal (2008) 95 (8), 4013-24.
  56. Rajagopal Rangarajan and Muhammad H. ZamanModeling cell migration in 3D: Status and Challenges. Cell Adhesion and Migration (2008) 2, (2) 95-105.
  57. Heiko Enderling, Nelson Alexander, Emily Clark, Lourdes Estrada, Cornelia Crooke, Jerome Jourquin, Nichole Lobdell, Muhammad H. Zaman, Alexander R.A. Anderson, and Alissa Weaver. Dependence of invadopodia function on collagen fiber spacing and cross-linking: computational modeling and experimental evidence. Biophysical Journal (2008) 95(5):2203-18.
  58. Tianyi Yang and Muhammad H. ZamanThermodynamics of clustered and unclustered systems in cell adhesion. Chemical Physics Letters (2008) 454.362-366.
  59. Muhammad H. ZamanComputer simulations in connective tissue research: Successes and challenges. Connective Tissue Research (2008) 49(3):162-4.
  60. Muhammad H. ZamanA multiscale probabilistic framework to model early steps in tumor metastasis. Molecular and Cellular Biomechanics (2007) 4. 133-141.
  61. Tianyi Yang and Muhammad H. ZamanRegulation of cell adhesion free energy by external sliding forces. Experimental Mechanics. (2009) 49 (1) 57-63.
  62. Tianyi Yang and Muhammad H. Zaman. The free energy landscape of receptor mediated cell adhesion. Journal of Chemical Physics, (2007) 126(4):045103.
  63. Muhammad H. ZamanUnderstanding the molecular basis of differential binding of integrin to collagen and gelatin. Biophysical Journal. (2007) 15;92(2):L17-9.
  64. Muhammad H. ZamanMultiscale modeling of tumor cell migration. AIP Conf. Proc. Vol. 851. 117-122.

Publications from Post-Doctoral, Graduate and Undergraduate Work

  1. Muhammad H. Zaman, Paul T. 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 (2007) Vol 25, 91-100.
  2. Alejandro Wolf-Yadlin, Yi Zhang, Neil Kumar, Sampsa Hautaniemi, Muhammad H. Zaman, Hyung-Do Kim, Viara Grantcharova, Douglas A. Lauffenburger and Forest M. White. Quantitative phosphoproteomic analysis of HER2-overexpression effects on cell signaling networks governing proliferation and migration.Molecular Systems Biology (2006) 1-15.
  3. 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 (2006) 91; L32-L34.
  4. Muhammad H. Zaman, Linda M. Trapani, Alisha Sieminski, Alan Wells, Douglas A. Lauffenburger and Paul T. Matsudaira. Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc. Natl. Acad. Sci. USA. (2006) 103; 10889-10894.
  5. Muhammad H. ZamanMisfolding Dynamics of Human Prion Protein. (Molecular and Cellular Biomechanics, Vol 2. (2005) 179-190.
  6. Abhishek K. Jha, Andres Colubri, Muhammad H. Zaman, Karl F. Freed and Tobin R. Sosnick. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry, (2005) 44(28):9691-702.
  7. Muhammad H. Zaman, Paul T. Matsudaira, Roger D. Kamm and Douglas A. Lauffenburger. Computational model for cell migration in 3D matrices. Biophysical Journal. (2005) 89(2):1389-97.
  8. Muhammad H. Zaman and Mohammad R. Kaazempur-Mofrad. How flexible is α-actinin’s rod domain? (Mechanics and Chemistry of Biosystems, 2004. Vol 1. No. 4. 291-302).
  9. 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. (Cover Article). 2003, 331, 693-711.Times cited: 65
  10. Muhammad H. Zaman, Tobin R. Sosnick and R. Stephen Berry. Temperature dependence reactions with multiple pathways. Physical Chemistry Chemical Physics (PCCP). 2003, 5, 2589-2594.
  11. Muhammad H. Zaman, Min-yi Shen, R. Stephen Berry and Karl F. Freed. Computer Simulations of Met-Enkephalin using Explicit and United Atom Force-Fields : Similarities, Differences and Suggestions for Improvement. Journal of Physical Chemistry B. 2003. 107(7); 1685-1691.
  12. Muhammad H. Zaman, R. Stephen Berry and Tobin R. Sosnick. The entropic benefit  of a cross-link in protein association. Proteins: Structure, Function and Genetics. 2002. 48: 341-351.
  13. Scott Jordan and Muhammad H. Zaman. Using SAS Macros to Develop Confidence Intervals for the Weibull and Extreme Value Distribution Using Type II Censored Data. Proceedings of the 24th Annual SAS Users Group International Conference. Miami Beach, FL. 1999.

Submitted

  1. Joseph Maffei, Jaya Srivastava, Brian Fallica and Muhammad H. ZamanIntegrin-β1 and membrane type 1 matrix metalloproteinase (MT1-MMP) influence HT-1080 cell migration in 3D matrices via Rho kinase (ROCK) mediated extracellular signal-regulated kinase (ERK) activation. (Submitted to PLoS One; In Revision)
  2. Yasha Sharma, David Lepzelter, Adrian Pegoraro, David Weitz and Muhammad H. Zaman. Cell Flocking in three-dimensional cell cultures. (Submitted to Biophysical Journal)
  3. Joseph 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 (Submitted to Integrative Biology.)
  4. Nicoletta Bertani, Giorgia Volpi, Laura Pazzaglia, Maria Serena Benassi, Sabrina Cattaruzza, Piero Picci, Maria Teresa Mucignat, Elisa Carra, Alessio Malcevski, Gaetano Magro, Michela Ori, Paolo Malatesta, Muhammad H. Zaman and Roberto Perris.  DEP domain-containing XTP1 and SDP35 link cell shape to malignancy (Submitted to Cell Reports; In revision)
  5. Nga Ho, Darash Desai and Muhammad H. Zaman Rapid, robust, sensitive, and specific drug quality testing assay for antimalarials using luminescent reaction and novel microfluidic technology (Submitted to American Journal of Tropical Medicine and Hygiene. In Revision.)
  6. Darash Desai, Nga Ho and Muhammad H. Zaman.  Field testing of solid and injectable anti-malarial quality testing in Ghana with PharmaChk: Comparisons with field and gold standard. (Submitted to PLoS One)
  7. Grace Wu and Muhammad H. Zaman. Integration of a paper-based electrochemical device with a commercial glucose meter for ethanol measurements(Submitted to Journal of Biotechnology)
  8. Grace Wu and Muhammad H. Zaman A novel method to detect misoprostol on an enzymatic paper-based electrochemical device (Submitted to Lab on a Chip)
  9. Diego A. Vargas, Maria Kukuruzinska and Muhammad H. ZamanQuantifying the effect of canonical Wnt signaling in stability of adherens junctions through numerical simulations and multivariate data analysis (Submitted to Proc. Natl. Acad. Sci. USA)
  10. Leandro Forciniti, Jose Ybarra, Muhammad H. Zaman and Christine Schmidt. Schwann cell response on polypyrrole substrates upon electrical stimulation. (Submitted to Acta Biomaterialia).