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Muhammad H. Zaman Assistant Professor

Muhammad H. Zaman

Assistant Professor

• Department of Biomedical Engineering
  The University of Texas at Austin
  Austin, Texas 78712
  Phone: (512) 471-4205
  
• Lab Website

Research Focus

Tumor cell migration and cell-matrix interactions in 3D matrices. Combined theoretical and high-throughput experimental approaches to study cancer cell invasion, cellular and matrix mechanics, metastasis and cell-cell communication

Research Interests

Research in my group is broadly focused on understanding how cancer cells interact with the extra cellular matrices in native environments. We use a combination of computational and experimental methods to study tumor cell invasion, communication and proliferation. In general we employ computational and experimental tools of biophysics, cell biology, mechanics and chemistry to study cancer related problems. On the experimental side, we develop and implement high-resolution and high-throughput migration assays in two and three-dimensional matrices, and combine them with micro and bulk rheology studies of the extracellular matrices to understand the role of mechanical and biophysical gradients in tumor cell migration. These experimental studies are combined with multi-scale simulations to get biophysical insights into the migration and invasion process. We simulate protein-ligand and protein-protein interactions using molecular dynamics and langevin dynamics simulations, study single cell migration using stochastic differential equations and Finite Element methods and model cell-cell interactions using monte carlo simulations. These hybrid computational-experimental approaches allow us to track cancer cell migration at a variety of length and timescales and approach problems that can not be tracked using just experimental or computational methods.

Other problems that we are interested in include protein-folding and protein energetics. We employ tools of statistical mechanics and combine them with novel computational strategies to study protein-protein interactions and dynamics and thermodynamics of peptides in solution. We are also interested in simulating the bulk and molecular behavior of novel biomaterials to study their mechanical and biochemical properties. Another problem of interest is pattern formation during cell-migration and we are collaborating with a group in CS to develop pattern recognition software that will allow us to track tumor cellular patterns in 3D environments.

Selected Publications

• Muhammad H. Zaman, Paul T. Matsudaira and Douglas A. Lauffenburger. Effects of MMPs and matrix organization on persistence in three-dimensional cell migration (In Press. Annals of Biomedical Engineering)
• 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. (In Press. Molecular Systems Biology).
• Muhammad H. Zaman. A multiscale probabilistic framework to model tumor metastasis. To appear in IEE Proceedings of Systems Biology. 2006.
• 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)
• 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).
• Muhammad H. Zaman Misfolding Dynamics of Human Prion Protein. (Molecular and Cellular Biomechanics, Vol 2. 2005. 179-190)
• 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).
• 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).
• 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).
• 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.
• 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.
• 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
• 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.