Director and Principal Investigator
Current Members
    Mohammad Azimi

    Mohammad Azimi

    (graduate student)

    Jack Bulat

    Jack Bulat

    (graduate student)

    Karen Burtt

    Karen Burtt

    (undergrad student)

    Kiavash Garakani

    Kiavash Garakani

    (undergrad student)

    Haoming Huang

    Haoming Huang

    (undergrad student)

    Zeinab Jahed

    Zeinab Jahed

    (graduate student)

    Hanif Mahboobi

    Hanif Mahboobi

    (post-doc)

    Mehrdad Mehrbod

    Mehrdad Mehrbod

    (graduate student)

    R. Moussavi-Baygi

    R. Moussavi-Baygi

    (graduate student)

    Michael Nasr

    Michael Nasr

    (undergrad student)

    Brenden Petersen

    Brenden Petersen

    (rotation grad student)

    H. Pezeshgi

    H. Pezeshgi

    (visiting scholar)

    Alejandro Schuler

    Alejandro Schuler

    (undergrad student)

    H. Shams

    H. Shams

    (graduate student)

    Stephen Trisno

    Stephen Trisno

    (undergrad student)

    Tiffany Truong

    Tiffany Truong

    (undergraduate student)

    Yinyin Wang

    Yinyin Wang

    (undergraduate student)

    Ramin Zareian

    Ramin Zareian

    (post-doc)

Alumni
Former PhD Students
  • Dr. Reza Karimi (presently Research Scientist at Philips Healthcare)
  • Dr. Javad Golji (presently Research Scientist at Roche)
  • Dr. Sang-Hee Yoon (presently assistant professor of Mechanical Engineering at Inha University, Korea)
  • Dr. Joe Leach (presently at UCSF Medical School)
  • Dr. Eli Weinberg (presently Strategy Consultant at Monitor Group)
  • Dr. Nur Aida Abdul Rahim (presently Technology Expert at InnovationXchange)
  • Dr. Seung Lee (presently at Boston Consulting Group)
  • Dr. Helene Karcher, PhD (presently Senior Scientist at Novartis)
Former Masters Students
  • Janice Tan (presently at National University of Singapore Hospital)
  • Sephalie Patel (presently at Emory Medical School)
  • Ting Zhu (presently PhD student at MIT)
  • Alyx Chau (presently PhD student at MIT)
  • Ahmad "Mo" Khalil (presently Assistant Professor of BME at Boston University)
  • Kranthi K. Mandadapu (presently PhD student at UCB ME)
  • Daniel Shreter (presently Senior Manager, Marketing Strategy at Microsoft)
  • Peter White (presently Product Marketing Manager at KLA-Tencor)
  • Kevin Kolahi (presently MD/PhD student at Oregon Health Sciences University)
  • Charles Zhao (presently PhD student at Georgia Tech)
  • Amer Abdullah (presently MD student at UCLA)
  • Steve Peter (presently R&D scientist at Medtronic)
Former Bachelor Students
  • Robert Collins (presently at Medical School)
  • Allison Deppe (presently PhD student at UCSD)
  • Heather Bowerman (currently a graduate student at Harvard)
  • Elise Nguyen (presently MD student at UMD)
  • Hamideh Emrani (presently PhD student at U. Toronto)
  • Alen Zamanyan (presently graduate student at UCLA)
  • Ivy Lin (presently PhD student at U. Pennsylvania)
  • Kevin Kolahi (presently MD/PhD student at Oregon Health Sciences University)
  • Harvey Chen (presently at Albert Einstein School of Medicine)
  • Amanda Laska(presently MD student at USUHS)
  • Rustin Massoudi (presently MD student at UCSD)
  • Tim Fei(presently MD student at U. Hawai)
  • Dena Shahriari (presently Research Associate at Zymo Research)
  • Johnny Lam (presently PhD student at Rice University)
  • Vinh Ho (presently PhD student at UIUC)
  • Kevin Shiuan (presently PhD student at Boston University)
  • Anwaar Al-Zireeni (presently CEO and Founder of a Medical Device Start-up)
Profile coming soon!
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

Departments of Bioengineering and Mechanical Engineering
Graduate Programs in Biophysics, Chemical Biology, and Applied Science & Technology
University of California, Berkeley
208A Stanley Hall #1762, Berkeley, CA 94720
Phone: (510) 643-8165 | fax: (510) 642-5835

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