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ANDREI TOKMAKOFF - CURRICULUM VITAE

University of Chicago Tel: 773–834–7696
Department of Chemistry E–mail: tokmakoff@uchicago.edu
929 East 57th Street, GCIS E139D Web: http:// tokmakofflab.info
Chicago, Illinois 60637  

 
EDUCATION

 
1995 Ph.D. in Chemistry, Stanford University.  Research Advisor: Michael D. Fayer
1991 M.S. in Chemistry, Stanford University
1988 B.S. in Chemistry, California State University, Sacramento

 
POSITIONS AND EMPLOYMENT

 
2013– Henry G. Dale Distinguished Service Professor, Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago
2012 Robert T. Haslam and Bradley Dewey Professor of Chemistry, Mass. Institute of Technology
2007–2012 Professor of Chemistry, Massachusetts Institute of Technology
2003–07 Associate Professor of Chemistry, Massachusetts Institute of Technology
1998–03 Assistant Professor of Chemistry, Massachusetts Institute of Technology
1996–98 National Science Foundation Postdoctoral Research Fellow with Prof. Graham Fleming. Department of Chemistry and the James Franck Institute, University of Chicago (1996-97) Department of Chemistry, University of California, Berkeley; and Lawrence Berkeley National Laboratory (1997-98)
1995–96 Alexander von Humboldt Research Fellow with Prof. Alfred Laubereau. Department of Physics, Technical University, Munich

 
AWARDS AND HONORS

 
2012 Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics (American Physical Society)
2009 Fellow of the Optical Society of America
2009 Peter B. Sherry Memorial Lecture, Georgia Institute of Technology
2003 Bryce Crawford Jr. Lecturer, University of Minnesota
2002 National Fresenius Award (Phi Lambda Upsilon)
2002 Alfred P . Sloan Research Fellowship
2002 Coblentz Award (Coblentz Society)
2001 Richard E. Heikkila Research Scholar Award (National Parkinson Foundation)
2001 Outstanding Young Investigator (Time-Resolved Vibrational Spectroscopy Conference)
2000 David and Lucile Packard Fellowship for Science and Engineering
1999 Research Corporation Research Innovation Award
1995 National Science Foundation Postdoctoral Fellowship in Chemistry
1994 Alexander von Humboldt Foundation Research Fellowship

 
PRINCIPAL RESEARCH INTERESTS

 
Molecular dynamics in solution. Development of experimental methods to study transient molecular structure and its time-evolution in molecular condensed phases and biological systems. Study of water: structure, dynamics, and hydrophobicity. Study of chemical reactions in solution. Conformation and dynamics of peptides and proteins. Dynamics of protein folding and binding. Molecular recognition and self-assembly. Mechanics of bio-inspired polymers. Development of two-dimensional vibrational spectroscopies. Development of methods for generating, characterizing and femtosecond infrared electric fields. Theory and simulation of molecular dynamics for interpreting nonlinear spectroscopies. Quantum mechanics, statistical mechanics, and spectroscopy of disordered systems and collective excitations.

 
PROFESSIONAL ACTIVITIES AND SOCIETIES
Faculty advisor to 21 graduate students and 8 postdoctoral scholars
MIT Core Faculty Member: G.R. Harrison Spectroscopy Lab (1999-2012), Laser Biomedical Research Facility (2010-2012)
MIT Biophysics Program Committee (2009-2012)
Member: Amer. Chem. Society, Biophysical Society, Optical Society of America (OSA), Protein Society
Ad Hoc Reviewer: DOE Site Review Panel, Argonne (1999), NIH Special Emphasis Panel/SRG (2008, 2010).
Visiting Member: NIH MSFB Study Section (2011)
Frontiers in Science Symposium, National Academy of Sciences, Irvine, CA, November 1998
Workshops: DOE, Electron Initiated Processes and Radical Chemistry in Water, Richland, WA Sept. 2002
Symposium Organizer/Co-Organizer: OSA Frontiers in Optics/Laser Science Meeting, October 2004; APS National Meeting, March 2005; ACS National Meeting, March 2008.
Conference Committees: Int'l. Conf on Ultrafast Phenomena, 2004-2008; Int'l Conf on Coherent Multidimensional Spectroscopy, 2004-; Int'l Conf on Time?Resolved Vibrational Spectroscopy, 2005-pres.
Conference Chair: 14th International Conference on Time?Resolved Vibrational Spectroscopy, 2009.
Editorial Committees: Advances in Chemical Physics; Annual Reviews of Physical Chemistry (2007-2012); Journal of Chemical Physics (2008-2010), Chemical Science (2012-2013), Journal of Physical Chemistry (2013-2015).
Advisory Committee: Munich-Centre for Advanced Photonics (2008-2011).
Scientific Advisory Board: Max-Born-Institute, Berlin, Germany (2011-2015).

 
PUBLICATIONS SINCE 2008

  • “Amide I two-dimensional infrared spectroscopy of proteins,” Z. Ganim, H. S. Chung, A. W. Smith, L. P. DeFlores, K. C. Jones, and A. Tokmakoff, Acc. Chem. Res., 41, 432 (2008).

  • “Ultrafast N-H vibrational dynamics of cyclic doubly hydrogen-bonded homo- and heterodimers,” P. B. Petersen, S. T. Roberts, K. Ramasesha, D. G. Nocera, and A. Tokmakoff, J. Phys. Chem. B, 112 13167-13171 (2008).

  • “Probing the folding transition state of ubiquitin mutants by temperature-jump induced downhill unfolding,” H.-S. Chung, A. Shandiz, T. R. Sosnick, and A. Tokmakoff, Biochem., 47 13870-7 (2008).

  • “Amide I′-II′ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity,” L. P. DeFlores, Z. Ganim, R. A. Nicodemus, and A. Tokmakoff, J. Am. Chem. Soc., 131, 3385 (2009).

  • “Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions,” S. T. Roberts, P. B. Petersen, K. Ramasesha, A. Tokmakoff, I. S. Ufimtsev, and T. J. Martinez, Proc. Nat. Acad. Sci., 106(36) 15154 (2009).

  • “Structural Rearrangements in Water Viewed Through Two-Dimensional Infrared Spectroscopy,” S. T. Roberts, K. Ramasesha and A. Tokmakoff, Acc. Chem. Res., 42(9), 1239 (2009).

  • “Heterodyne-detected dispersed vibrational echo spectroscopy,” K. C. Jones, Z. Ganim, and A. Tokmakoff, J. Phys. Chem. B, 113 14060-14066 (2009).

  • “Insulin Dimer Dissociation and Unfolding Revealed by Amide I Two-Dimensional Infrared Spectroscopy,” Z. Ganim, K. C. Jones, and A. Tokmakoff, Phys. Chem. Chem. Phys., 12, 3579-3588 (2010).

  • “Hydrogen Bond Rearrangements in Water Probed with Temperature-Dependent 2D IR,” R.A. Nicodemus, K. Ramasesha, S.T. Roberts, and A. Tokmakoff, J. Phys. Chem. Lett. 1, 1068-1072 (2010).

  • “Orientational Dynamics of Water Probed with 2D-IR Anisotropy Measurements,” by Krupa Ramasesha, Rebecca A. Nicodemus, Aritra Mandal and Andrei Tokmakoff, in Ultrafast Phenomena XVII, Ed. by E. Riedle, R.W. Schoenlein, M. Chergui, and A. Taylor, (Springer Verlag, Berlin, in press).

  • “Source for ultrafast continuum infrared and terahertz radiation,” P. Petersen and A. Tokmakoff, Optics Letters, 35(12), 1962 (2010).

  • “Melting of a β-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations,“ A. W. Smith, J. Lessing, Z. Ganim, C. Sam Peng, A. Tokmakoff, S. Roy, T. L. C. Jansen, and J. Knoester, J. Phys. Chem. B, 114 10913-10924 (2010).

  • “A Fast-Scanning Fourier Transform 2D IR Interferometer,” S. T. Roberts, J. J. Loparo, K. Ramasesha, and A. Tokmakoff, Opt. Comm., 284 1062-1066 (2011).

  • “Proton Transfer in Concentrated Aqueous Hydroxide Visualized using Ultrafast Infrared Spectroscopy,” S.T. Roberts, K. Ramasesha, P.B. Petersen, A. Mandal, and A. Tokmakoff, J Phys Chem A, 115 3957-3972 (2011).

  • “Collective Hydrogen Bond Reorganization in Water Studied with Temperature-Dependent Ultrafast Infrared Spectroscopy,” R. A. Nicodemus, S. A. Corcelli, J. L. Skinner, and A. Tokmakoff, J. Phys. Chem. B, 115 5604-5616 (2011).

  • “Ultrafast 2D IR Anisotropy of Water Reveals Reorientation during Hydrogen-Bond Switching,” K. Ramasesha, S. T. Roberts, R. A. Nicodemus, A. Mandal and A. Tokmakoff, J. Chem. Phys., 135, 054509 (2011).

  • “Anharmonic Vibrational Modes of Nucleic Acids Bases Revealed by 2D IR Spectroscopy,” C. S. Peng, K. C. Jones, and A. Tokmakoff, J. Am. Chem. Soc., 133, 1565 (2011).

  • “Vibrational excitons in ionophores: Experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels,” Z. Ganim, A. Tokmakoff, and A.a Vaziri, New J. Phys., 13 113030 (2011).

  • “Solvent and Conformation Dependence of Amide I Vibrations in Peptides and Proteins Containing Proline,” S. Roy, J. Lessing, G. Meisl, Z. Ganim, A. Tokmakoff, J. Knoester, and T. L. C. Jansen, J. Chem. Phys., 135, 234507 (2011).

  • “Transient Two-Dimensional Spectroscopy with Linear Absorption Corrections Applied to Temperature Jump 2D IR,” K.C. Jones, Z. Ganim, C. Sam Peng, and A. Tokmakoff, J. Opt. Soc. Am. B, 29 118-129 (2012).

  • “Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution,” C. Baiz, C. Sam Peng, M. E. Reppert, K. C. Jones, and A. Tokmakoff, Analyst, 137 1793-1799 (2012).

  • “Identifying residual structure in intrinsically disordered systems: A 2D IR spectroscopic study of the GVGXPGVG peptide,” J. Lessing, S. Roy, M. Reppert, M. Baer, D. Marx, T. La Cour Jansen, J. Knoester, and A. Tokmakoff, J. Am. Chem. Soc., 134 5032-5035 (2012).

  • “A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy,” K. Ramasesha, L. De Marco, A. D. Horning, A. Mandal and A. Tokmakoff, J. Chem. Phys., 136 134507-1-11 (2012).

  • “An Introduction to Protein 2D IR Spectroscopy,” C. Baiz, M. Reppert, and A. Tokmakoff, in Ultrafast Infrared Vibrational Spectroscopy, ed. by M. D. Fayer (Taylor & Francis, New York, 2013).

  • “Heterogeneous folding of a β-hairpin peptide revealed through temperature-jump 2D IR spectroscopy,” K. C. Jones, C. Sam Peng and A. Tokmakoff, Proc. Nat'l. Acad. Sci. USA.

  • “Identification of lactam-lactim tautomers of aromatic heterocycles in aqueous solution using 2D IR spectroscopy,” C. Sam Peng and A. Tokmakoff, J. Phys. Chem. Lett., 3 3302-3306 (2012).