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I am interested in developing new computational techniques for modeling biological systems. I am currently developing a method for modeling molecular reaction-diffusion systems using agent based modeling. My initial work focuses on exploring transport across the nuclear pore complex using this model.

Personal Website
Publications:
·Azimi M, Mofrad MRK. Social Bookmarking and Recommendation Engines in Bioengineering Education. ASME SBC 2010
·Jamali Y, Azimi M, Mofrad MRK. A Sub-Cellular Viscoelastic Model for Cell Population Mechanics. PLoS ONE 2010, 5(8): e12097.

My projects focus on applications of molecular dynamics and related computational techniques in cellular biomechanics. The focus is on understanding the link between structure and function in molecules that play a critical role in regulating the cells response to mechanical stimulation.

Publications:
·Golji J, Lam J, and Mofrad MRK. Vinculin Activation Is Necessary for Complete Talin Binding. Biophysical J 2011, 100 (2) 332-340
·Golji J and Mofrad MRK. A Molecular Dynamics Investigation of Vinculin Activation. Biophysical J 2010, 99 (4) 1073-81
·Golji J, Collins R, and Mofrad MRK. Molecular Mechanics of the alpha-actinin rod domain: bending, torsional, and extensional behavior. PLOS Computational Biology 2009, 5 (5): e1000389

I find it elevating and exhilirating to discover that we live in a universe which permits the evolution of molecular machines as intricate and subtle as we.

Assisting the investigations of vinculin and integrin activation via umbrella sampling of free energy changes using GROMACS.

I endeavor to find better ways of applying the recent revolution in computing machines to the study of complex biological systems.

Exploring the Interaction between the Nuclear Pore Protein Tpr and the Exportin Crm1: A Computational Method of Finding Protein-Protein Binding Sites

I am a Mechanical Engineering graduate student, and I performed my undergraduate studies at Virginia Tech.

My project seeks to investigate the mechanical behavior of cross-linked microtubule bundles relevant to axonal injury. This is performed using a custom computational model.

I currently have a B.S in Bioengineering from UC Berkeley. I aspire to relate the interactions at the atomic level to larger scale events through computational simulations. I am also an avid badminton and piano player.

My current work involves discovering the consequences of key residue mutation on the auto-inhibition of vinculin.

I got my BS in physics from University of Tehran and continued my master's study in the same field at Sharif University of Technology. Now I am working as a PhD student in AS&T.

I am currenctly working of alpha-actinin, an actin binding protein and the mechanism of its interactions with other focal adhesion agents.

Publications:
·H. Shams, J. Golji, Mofrad M.R.K. Umbrella sampling molecular dynamics studies of alpha-actinin. To be submitted to Biophysical Journal

My main interest is computational approach to subcellular-scale biological systems. Right now, I am developing a biophysical coarse-grained model for the whole structure of the NPC, and conducting Brownian dynamics simulations. Using this model, we can transcend the current limits of spatiotemporal resolution in the most novel imaging techniques.

Publications:
·R. Moussavi-Baygi, Y. Jamali, R. Karimi, M.R.K. Mofrad, Biophysical Coarse-Grained Modeling Provides Insights into Transport through the Nuclear Pore Complex, Biophysical Journal, 2011.

I got my BS, MS, and PhD in Mechanical Engineering from Sharif University of Technology.

I use molecular dynamics simulations to model the protein-protein interactions present in nucleocytoplasmic transport processes.

Contact: mahboobi (at) berkeley (dot) edu