Publications

Books

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

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.
   

Refereed Journal Articles

1. Ge Wang and Muhammad H. Zaman. Hamiltonian Regulated Cell Signaling Network. Journal of Chemical Physics. In Press. 2010.

2. Dewi Harjanto and Muhammad H. Zaman, Computational study of proteolysis driven single cell migration in a three-dimensional matrix. Annals of Biomedical Engineering. In Press. 2010.

3. Erin Baker and Muhammad H. Zaman. The biomechanical integrin. Journal of Biomechanics (2010) 43 (10) 38-44.

4. Dewi Harjanto and Muhammad H. Zaman. Matrix Mechanics and Receptor-Ligand interactions in Cell Adhesion. Organic and Biomolecular Chemistry (2010) 8(2) 299-304.

5. 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.

6. Diego A. Vargas and Muhammad H. Zaman. Serine at Phosphorylation Site Regulates the Mechanical and Structural Behavior of Fascin. Cellular and Molecular Bioengineering (2009) 2, (4) 504-513.

7. 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.

8. Mark Kness, Ge Wang and Muhammad H. Zaman. Robustness of integrin signaling network. Journal of Chemical Physics (2009) 130 (23) 235103.
   

9. Leandro Forciniti, Ge Wang and Muhammad H. Zaman. Actin-Fascin bundle formation under pressure. Cellular and Molecular Bioengineering (2009) 2 (1), 2-12.

10. 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 (2009) 37(2):363-374.

11. Tianyi Yang and Muhammad H. Zaman. Equilibrium and non-equilibrium thermodynamic processes in cell-matrix interactions. Journal of Non-Equilibrium Thermodynamics (2009) 34, 195-217.

12. Tianyi Yang and Muhammad H. Zaman. Cell adhesion to nanoligands: Effects of ligand size and concentration in solution. Langmuir (2008) 24 (20), 11819–11827.

13. 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.

14. Rajagopal Rangarajan and Muhammad H. Zaman. Modeling cell migration in 3D: Status and Challenges. Cell Adhesion and Migration (2008) 2, (2) 95-105.

15. 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.

16. Tianyi Yang and Muhammad H. Zaman. Thermodynamics of clustered and unclustered systems in cell adhesion. Chemical Physics Letters (2008) 454.362-366.

17. Muhammad H. Zaman. Computer simulations in connective tissue research: Successes and challenges. Connective Tissue Research (2008) 49(3):162-4.

18. Muhammad H. Zaman. A multiscale probabilistic framework to model early steps in tumor metastasis. Molecular and Cellular Biomechanics (2007) 4. 133-141.

19. Tianyi Yang and Muhammad H. Zaman Regulation of cell adhesion free energy by external sliding forces. Experimental Mechanics. (2009) 49 (1) 57-63.

20. Tianyi Yang and Muhammad H. Zaman. The free energy landscape of receptor mediated cell adhesion. Journal of Chemical Physics, (2007) 126(4):045103.

21. Muhammad H. Zaman. Understanding the molecular basis of differential binding of integrin to collagen and gelatin. Biophysical Journal. (2007) 15;92(2):L17-9.

22. Muhammad H. Zaman. Multiscale modeling of tumor cell migration. AIP Conf. Proc. Vol. 851. 117-122.

23. Tianyi Yang and Muhammad H. Zaman. Estimation of cellular adhesion forces using mean field theory. Submitted.

24. Rajagopal Rangarajan, Edward Marcotte and Muhammad H. Zaman. MMP regulation of integrin activity. (Submitted)

25. Yusuke Sakamoto, Serge Prudhomme and Muhammad H. Zaman. Amoeboid Cell motility in 3D matrices. (Submitted)

26. Jaya Srivasta and Muhammad H. Zaman. Regulation of FAK activity in 3D environments. (Submitted)

27. Erin Baker, Jing Lu, Dihua Yu, Roger T. Bonnecaze and Muhammad H. Zaman. Transforming Potential Couples with Matrix Stiffness to Dictate the Intracellular Mechanical State of Mammary Epithelial Cells. Submitted to Cancer Research. (Submitted).

Publications in Engineering Education

28. Muhammad H. Zaman. Engineering Education in the Developing World: The Case for Biological Engineering. Proceedings of IEEE EDUCON Conference on Engineering Education. Madrid. 2010.

Work for Post-Doctoral, Graduate and Undergraduate Years (1999-2006)

29. 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.

30. 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.
    

31. 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.

32. 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.
    

33. Muhammad H. Zaman Misfolding Dynamics of Human Prion Protein. (Molecular and Cellular Biomechanics, Vol 2. (2005) 179-190.

34. 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.

35. 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.
    

36. 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).

37. 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

38. 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.

39. 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. Times cited: 20

40. 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.

41. 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.

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