Arneh Babakhani, Ph.D.



University of California at San Diego

Department of Chemistry & Biochemistry

9500 Gilman Drive MC 0365

La Jolla, CA 92093-0365

ababakha@mccammon.ucsd.edu

http://www.arneh.net



Education & Research



Ph.D., Chemistry, University of California at San Diego (05/2009)

  • Degree: Chemistry, with specialization in Computational Science
  • Dissertation: “Computational and Pharmacological Modeling of Membrane Proteins”
  • Adviser: Prof. J. Andrew McCammon
  • 7 manuscripts (6 published + 1 submitted)
  • Conducted research in peptide-membrane simulations, protein-ligand docking,
    • free energy calculations, and virtual screening methodologies
  • Collaborated with 3 different experimental research groups
  • Conducted wet-lab experimental binding assays in verification of computational work
  • Attended and presented at 6 conferences
  • Organized 3 UCSD Physical Chemistry seminars for visiting faculty


    • M.S., University of California at San Diego (03/2007)

  • Completed graduate coursework in chemistry, mathematics, and computational science
  • Served as teaching assistant for 4 courses [Link to teaching evaluations]


    • B.S., Chemistry, University of California at Berkeley (12/2000)



    Lawrence Berkeley National Lab/Center for Functional Imaging (08/1998-06/2001)

  • Project: “Synthesis of Atipamezole and Rotenone Derivatives”
  • Advisers: Dr. Henry F. VanBrocklin , Dr. Andrew R. Gibbs
  • Formulated/conducted small molecule synthesis reactions, chromatographic
    • and separation procedures, analyzed spectral data.


    University of California at Berkeley, Department of Chemistry (01/2000-12/2000)

  • Project: “Expression of the Glycosyl Sulfotransferases”
  • Adviser: Prof. Carolyn R. Bertozzi
  • Formulated/conducted molecular biology protocols, maintained cell cultures


    • Military & Leadership Experience (United States Navy)



    Executive Officer (XO), NMORA 1994 Unit, San Diego, CA (02/2007-06/2009)

  • #2 in Command, Manage a division of 24 sailors, chiefs and junior officers
  • Coordinate administrative items & logistics for monthly drills and annual training activities.
  • Manage evaluations, awards, disciplinary items, security clearances


    • Lieutenant (O-3), United States Naval Reserve, San Diego, CA (08/2005-06/2009)

  • Drilling Reservist (SELRES), Naval METOC Reserve Activity 1994
  • Train in the usage of imagery for environmental analysis and mission planning


    • Lieutenant Junior Grade (O-2), Mobile Environmental Team (02/2004-08/2005)

  • Division Officer, managed a division of 16 enlisted personnel
  • Oversight of deployments throughout the world
  • Provided tactical oceanographic products and support to U.S. Naval assets.


    • Ensign (O-1), Naval Pacific Oceanography Center San Diego, CA (04/2002-02/2004)

  • Command Duty Officer, supervised a division of 10 enlisted personnel
  • Managed watchfloor operations, forecasted for U.S. Third Fleet assets.


    • Commissioned (06/11/2001)



    Publications



    Burke, J.; Babakhani, A.; Gorfe, A. A.; Kokotos, G.; Li, S.; Woods, V. L.; McCammon, J. A.; Dennis, E. A. Location of inhibitor bound of group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry. Journal of the American Chemical Society 2009, Accepted, In press.


    Babakhani, A.; Talley, T. T.; Taylor, P.; McCammon, J. A. A virtual screening study of the acetylcholine binding protein using a relaxed complex approach. Computational Biology and Chemistry 2009, 33, 160-170.


    Babakhani, A.; Gorfe, A. A.; Kim, J. E.; McCammon, J. A.Thermodynamics of peptide insertion and aggregation in a lipid bilayer. Journal of Physical Chemistry B 2008, 112, 10528-10534.


    Gorfe, A. A.; Babakhani, A.; McCammon, J. A. H-ras protein in a bilayer: interaction and structure perturbation. Journal of the American Chemical Society 2007, 129, 12280-12286.


    Gorfe, A. A.; Babakhani, A.; McCammon, J. A. Free energy profile of H-ras membrane anchor upon membrane insertion. Angewandte Chemie International Edition 2007, 46, 8234-8237.


    Babakhani, A.; Gorfe, A. A.; Gullingsrud, J.; Kim, J. E.; McCammon, J. A. Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulation. Biopolymers 2007, 85, 5-6, 490-497.


    Gullingsrud, J.; Babakhani, A.; McCammon, J. A. Computational investigation of pressure profiles in lipid bilayers with embedded proteins. Molecular Simulation 2006, 32, 831-838.


    Transcripts, manuscripts, references, details regarding military assignments and security clearances are all available upon request.