Scientific CV

Dr. Soroosh Pezeshki

Fields of Expertise

  • Theoretical Chemistry and Physics
  • Molecular Dynamics
  • Molecular and Quantum Mechanics
  • Biophysics
  • Computational Chemistry and Physics

Education and Work Experience

2000 High school diploma "Abitur" with award from the German Physical Society at Emilie-Wüstenfeld-Gymnasium in Hamburg
2000-2005 Physics student at Chemnitz University of Technology
2002-2005 Student assistant in the groups of Prof. Hietschold, Prof. Zahn, and Prof Schreiber and experimental physics lab assistant
2004-2005 Student in the group of Prof. M. Schreiber
Diplom (equi. M.Sc.); Research field: Computational and theoretical physics
2006 Research associate in the group of Prof. M. Schreiber at Chemnitz University of Technology
2006-2009 PhD student and research associate in the group of Prof. U. Kleinekathöfer at Jacobs University Bremen
Research field: Computational biophsiycs
2007 and 2008 Visiting stays at the group of Prof. Ruggerone and Prof. Ceccarelli / University of Cagliari, Italy
2010-2014 Assistant Research Professor in the group of Prof. H. Lin at University of Colorado Denver
Research field: Computational Chemistry

Peer Reviewed Publications

  1. Soroosh Pezeshki, Michael Schreiber, and Ulrich Kleinekathöfer, "Shaping femtosecond coherent anti-Stokes Raman spectra using optimal control theory", Phys. Chem. Chem. Phys., 2008, 10:2058 - 2066
  2. Catalin Chimerel, Liviu Movileanu, Soroosh Pezeshki, Mathias Winterhalter, and Ulrich Kleinekathöfer,"Transport at the nanoscale: temperature dependence of ion conductance", Eur. Biophys. J., 2008, 38:121-125
  3. Soroosh Pezeshki, Catalin Chimerel, Andrey N. Bessonov, Mathias Winterhalter, and Ulrich Kleinekathöfer, "Understanding ion conductance on a molecular level: An all-atom modeling of the bacterial porin OmpF", Biophys. J., 2009, 97:1898-1906
  4. Istvan Biro, Soroosh Pezeshki, Helge Weingart, Mathias Winterhalter, and Ulrich Kleinekathöfer, "Comparing the temperature-dependent conductance of the two structurally similar E. coli porins OmpC and OmpF", Biophys. J., 2010, 98:1830-1839
  5. Soroosh Pezeshki and Hai Lin, "Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds", JCTC, 2011, 7:3625-3634
  6. Xin Wu, Walter Thiel, Soroosh Pezeshki, and Hai Lin, "Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models", JCTC, 2013, 9:2672-2686
  7. Jonathan Church, Soroosh Pezeshki, Christal Davis, and Hai Lin, "Charge Transfer and Polarization for Chloride Ions Bound in ClC Transport Proteins: Natural Bond Orbital and Energy Decomposition Analyses", J. Phys. Chem. B, 2013, 117:16029-16043
  8. Soroosh Pezeshki and Hai Lin, “Recent Developments in QM/MM Methods towards Open-Boundary Multi-Scale Simulations”, Molecular Simulation, 2014, 41:168–189
  9. Soroosh Pezeshki and Hai Lin, “Molecular Dynamics Simulations of Ion Solvation by Flexible-Boundary QM/MM: On-the-fly Partial Charge Transfer between QM and MM Subsystems”, JCC, 2014, 35:1778–1788
  10. Soroosh Pezeshki, Christal Davis, Andreas Heyden, and Hai Lin, “Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Protein Binding Sites”, JCTC, 2014, 10:4765−4776
  11. Soroosh Pezeshki and Hai Lin, “Adaptive-Partitioning QM/MM Dynamics Simulations: 4. Proton Hopping in Bulk Water", JCTC, 2015, 11:2398–2411

Peer-Reviewed Book Chapters

  • Soroosh Pezeshki and Hai Lin, “Recent Progress in Adaptive-Partitioning QM/MM Methods for Born-Oppenheimer Molecular Dynamics”, 2015, in “Quantum Modeling of Complex Molecular Systems” edited by Jean-Louis Rivail, Manuel Ruiz-Lopez, and Xavier Assfeld; Published by Springer, Heidelberg; ISBN 978-3-319-21626-3

Thesis

  • Diplom thesis (eq. Master thesis): “Wellenpaket Rechnung zur Simulation von Femtosekunden Spektroskopie” (Wave-packet calculations for spectroscopy simulations), TU-Chemnitz, 2005
  • Ph.D thesis: “Simulation of Transport Through OmpF and OmpC Channels”, Jacobs University Bremen, 2009

Published Research Software

  • QMMM: Hai Lin, Yan Zhang, Soroosh Pezeshki, and Donald G. Truhlar

Contributions to Conferences and Summer Schools

  1. S. Pezeshki*, U. Kleinekathoefer and M. Schreiber, "Influence of chirp on the time-resolved CARS signal of molecular iodine", poster at "DPG-Springmeeting" in Berlin, Germany, March 2005
  2. S. Pezeshki*, U. Kleinekathoefer and M. Schreiber, "Influence of chirp on the time-resolved CARS signal of molecular iodine", poster at "Classical and Quantum Dynamical Simulations in Chemical and Biological Physics" in Dresden/ Germany June 2005
  3. S. Pezeshki*, J. Liebers, M. Schreiber and U. Kleinekathoefer, "Shaping of CARS spectra using optimal control theory", poster at "DPG-Springmeeting" in Frankfurt, Germany, March 2006
  4. S. Pezeshki*, M. Winterhalter and U. Kleinekathoefer, “Simulation of transport through OmpF channels”, poster at "DPG-Springmeeting" in Regensburg, Germany, March 2007
  5. S. Pezeshki*, M. Winterhalter and U. Kleinekathoefer, “Simulation of transport through OmpF channels”, poster at "Computer Simulation and Theory of Macromolecules” in Huenfeld, Germany, April 2007
  6. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, “Transport through OmpF channels simulated using molecular dynamics”, poster at "DPG-Springmeeting" in Berlin, Germany, March 2008
  7. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, “Transport through OmpF channels simulated using molecular dynamics”, poster at "Marie Curie Actions: Mid-Term Review Meeting (Translocation)" in Marseille, France, April 2008
  8. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, “Transport through OmpF channels simulated using molecular dynamics”, poster at "Computer Simulation, Theory of Macromolecules" in Huenfeld, Germany, April 2008
  9. S. Pezeshki*, “Simulation of Transport through OmpF Channels”, oral presentation at "Computer Simulation and Theory of Macromolecules" in Huenfeld, Germany, April 2008
  10. S. Pezeshki, C. Chimerel, M. Winterhalter and U. Kleinekathoefer*, ”Transport through OmpF channels simulated using molecular dynamics“, poster at "North German Biophysical Meeting" in Borstel, Germany, January 2009
  11. U. Kleinekathoefer*, S. Pezeshki, C. Chimerel, L. Movileanu and M. Winterhalter, ”Ion Transport through OmpF in Molecular Dynamics Simulations and Experiments“, poster at "Annual Meeting of the Biophysical Society" in Boston, USA, March 2009
  12. S. Pezeshki*, M. Winterhalter and U. Kleinekathoefer, "Transport through OmpF Channels Simulated using Molecular Dynamics", poster at "DPG-Springmeeting" in Dresden, Germany, March 2009
  13. M. M. Tomozeiu*, S. Pezeshki and U. Kleinekathoefer, ”Water Diffusion through OmpF protein using Molecular Dynmics Simulation“, oral presentation at "DPG-Springmeeting“ in Dresden, Germany, March 2009
  14. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, ”Ion Transport through OmpF in Molecular Dynamics Simulations and Experiments“, poster at "Computer Simulation and Theory of Macromolecules" in Huenfeld, Germany, April 2009
  15. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, ”Ion Transport through OmpF in Molecular Dynamics Simulations and Experiments“, poster at "Quantum and classical simulation of biological systems" in Bremen, Germany (Wilhelm und Else Heraeus Summer School), June 2009
  16. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, ”Ion Transport through OmpF in Molecular Dynamics Simulations and Experiments“, poster at "Biosensing with channels: faster, smaller, smarter" in Bremen, Germany (Wilhelm und Else Heraeus Seminar), June 2009
  17. S. Pezeshki*, C. Chimerel, M. Winterhalter and U. Kleinekathoefer, ”Ion Transport through OmpF in Molecular Dynamics Simulations and Experiments“, poster at "North German Biophysical Meeting“ in Borstel, Germany, January 2010
  18. S. Pezeshki*, "Simulation of Transport through OmpF and OmpC Channels", oral presentation at "North German Biophysical Meeting" in Borstel, Germany, January 2010
  19. S. Pezeshki and H. Lin*, “Multi-scale simulations by open-boundary QM/MM”, oral presentation at “42nd ACS 2011 Central Region Meeting” Indianapolis, Indiana, June 2011
  20. S. Pezeshki and H. Lin*, “Open-boundary QM/MM for enzyme simulations”, oral presentation at "PR IUPAC 2011”, San Juan, Puerto Rico, August 2011
  21. S. Pezeshki* and H. Lin, “Steered molecular dynamics with adaptive partitioning QM/MM”, poster at “ACS 242nd National Meeting” in Denver, Colorado, August 2011
  22. S. Pezeshki* and H. Lin, “Sodium Ion Translocation through the Gramicidin A Channel by QM/MM Simulations”, oral presentation at “ACS RMRM 2012” in Westminster, Colorado, October 2012
  23. S. Pezeshki* and H. Lin, “Adaptive-Partitioning QM/MM Simulations of Proton Hopping between Hydronium Ion and Water Molecules”, oral presentation at “ACS RMRM 2012” in Westminster, Colorado, October 2012
  24. C. R. Davis*, S. Pezeshki, and H. Lin, “Molecular dynamics simulations of Escherichia coli ClC chloride ion transporters with different protonation states of critical residues”, poster at “ACS RMRM 2012” in Westminster, Colorado, October 2012
  25. J. Church*, S. Pezeshki, and H. Lin, “Interactions between Chloride Ion and Amino Acids”, poster at “ACS RMRM 2012” in Westminster, Colorado, October 2012
  26. N. L. Chon*, E. Kim*, S. Pezeshki, S. Reed, and H. Lin, “Interactions between the human C-Reactive Protein and lipid-coated nanoparticles”, poster at “ACS RMRM 2012” in Westminster, Colorado, October 2012
  27. N. L. Chon*, E. Kim*, S. Pezeshki, S. Reed, and H. Lin, “Molecular Dynamics Simulation of the Human C-Reactive Protein”, poster at "RaCAS”, Denver, Colorado, April 2013; Winner of the "Chancellor's Award of Excellence"
  28. C. R. Davis*, S. Pezeshki, and H. Lin, "Steered Molecular Dynamics Simulations of Escherichia coli ClC Chloride Ion Transporter", poster at "Gamma Sigma Epsilon Biennial Convention" in Frostburg, Maryland, October 2013
  29. C. R. Davis*, S. Pezeshki, and H. Lin, “Will charge delocalization of chloride ions offset the need for large-scale conformational changes of the ClC protein in ion translocation?”, poster at “Research and Creative Activities Symposium”, Denver, Colorado, April 2014
  30. S. Pezeshki*, “Adaptive Partitioning QM/MM”, invited Seminar talk at Freie Universität Berlin, Germany, November 2014
  31. C. R. Davis*, S. Pezeshki, C. Garza, H. Lin, “Combined QM/MM Study of the Translocation of Chloride Ions through Escherichia Coli Chloride Ion Transporters”, poster at Annual Meeting of the Biophysical Society, Baltimore, USA, March 2015
  32. S. Pezeshki*, “Adaptive Partitioning QM/MM-MD Simulations”, invited Seminar talk at European Molecular Biology Laboratory, Hamburg, Germany, April 2015
  33. S. Pezeshki and H. Lin*, “Proton transfer in water by adaptive QM/MM dynamics simulations”, poster at 15th International Congress of Quantum Chemistry, Beijing, China, June 2015