Books    |    UT Austin work    |    Graduate school and Post-doc work

PUBLICATIONS

Peer Reviewed Publications

Books

  1. Muhammad H. Zaman, Ed.  Statistical Mechanics of Cellular Systems and Processes, Cambridge University Press.  To appear, June 2008.

Papers from work at University of Texas at Austin (Fall 2006 -- to date )

  1. Tianyi Yang and Muhammad H. Zaman. Equilibrium and non-equilibrium thermodynamic processes in cell-matrix interactions. (To appear. Journal of Non-Equilibrium Thermodynamics. 2008).
  2. Muhammad H. Zaman. Integrating the role of matrix mechanics, receptor conformation and ligand dynamics in cell adhesion. (To appear. Organic and Biomolecular Chemistry. 2008)
  3. 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. In press. Biophysical Journal.
  4. Heiko Enderling, Nelson Alexander, Emily Clark, Lourdes Estrada, Cornelia Crooke, Jerome Jourquin, Nichole Lobdell, Muhammad H. Zaman, Alexander R.A. Anderson, and Alissa Weaver. A cellular automaton model of invadopodia-ECM interactions. In press. Biophysical Journal.
  5. Rajagopal Rangarajan and Muhammad H. Zaman. Modeling cell-adhesion and cell-migration in native like 3D matrices. (In press. Cell Adhesion and Migration. 2008).
  6. Tianyi Yang and Muhammad H. Zaman. Thermodynamics of clustered and unclustered systems in cell adhesion. Chemical Physics Letters. 2008. 454.362-366. [PDF reprint]
  7. Muhammad H. Zaman. Computer simulations and mathematical models for cell-matrix interactions. (Journal of Connective Tissue Research. To appear, 2008)
  8. Muhammad H. Zaman. A multiscale probabilistic framework to model early steps in tumor metastasis. Molecular and Cellular Biomechanics. 2007. 4. 133-141. [PDF reprint]
  9. Tianyi Yang and Muhammad H. Zaman. Regulation of cell adhesion free energy and forces by external sliding velocities. Journal of Experimental Mechanics. 2007. [PDF reprint]
  10. Tianyi Yang and Muhammad H. Zaman. The free energy landscape of receptor mediated cell adhesion. (Journal of Chemical Physics, 2007,126(4):045103). [PDF reprint]
  11. Muhammad H. Zaman. Understanding the molecular basis for differential binding of integrins to collagen and gelatin. Biophysical Journal. 2007. 15;92(2):L17-9. [PDF reprint]
  12. Muhammad H. Zaman. Multiscale modeling of tumor cell migration. AIP Proc. Vol. 851. 117-122.
  13. Tianyi Yang and Muhammad H. Zaman. Computational model of cell adhesion to nano ligands: Effects of ligand size and concentration in solution. Submitted.
  14. Leandro Forciniti, Christine E. Schmidt and Muhammad H. Zaman. Understanding Hippocampal Neurons distinct behavior to chemical and topographical cues using computational and experimental methods. Submitted.
  15. Tianyi Yang and Muhammad H. Zaman. Estimation of cell adhesion forces using mean field theory. Submitted.
  16. Rajagopal Rangarajan, Insuk Lee, Edward Marcotte and Muhammad H. Zaman. Entropic classification of complex biological networks. Submitted.
  17. Ralf B. Lukner and Muhammad H. Zaman. Modeling cell-cell and cell-matrix interactions in cellular networks. Submitted.

Papers from work during post-doctoral research (MIT and Whitehead Institute 2003-2006) and graduate school (University of Chicago, 1999-2003)

  1. Muhammad H. Zaman, Paul T. Matsudaira and Douglas A. Lauffenburger. Effects of MMPs and matrix organization on persistence in three-dimensional cell migration (Ann. Biomed. Engr. 2007. 35(1):91-100). [PDF reprint]
  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. 2:54). [PDF reprint]
  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) [PDF reprint]
  4. Muhammad H. Zaman, Linda M. Trapani, Alisha Siemeski, Alan Wells, Douglas A. Lauffenburger and Paul T. Matsudaira. Cell Migration in Three-dimensional Matrices Is Inversely-dependent on Cell-matrix Adhesiveness and Matrix Stiffness (Poc. Natl. Acad. Sci. USA. 2006, 103; 10889-10894). [PDF reprint]
  5. Muhammad H. Zaman. Misfolding Dynamics of Human Prion Protein. (Molecular and Cellular Biomechanics, Vol 2. 2005. 179-190) [PDF reprint]
  6. Abhishek K. Jha, Andres Colubri, Muhammad H. Zaman, Karl F. Freed and Tobin R. Sosnick. Helix and sheet propensities, the predominance of polyproline II and strong nearest neighbor effects observed in a restricted coil library. (Biochemistry, 2005. 44(28):9691-702). [PDF reprint]
  7. Muhammad H. Zaman, Paul T. Matsudaira, Roger D. Kamm and Douglas A. Lauffenburger. A computational model for cell migration in 3D matrices. (Biophysical Journal. 2005. 89(2):1389-97). [PDF reprint]
  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. [PDF reprint]
  10. Muhammad H. Zaman, Tobin R. Sosnick and R. Stephen Berry. Temperature dependencereactions with multiple pathways. Physical Chemistry Chemical Physics (PCCP). 2003, 5, 2589-2594. [PDF reprint]
  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 [PDF reprint]
  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. [PDF reprint]