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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Soroosh Pezeshki and Hai Lin, “Recent Developments in QM/MM Methods towards Open-Boundary Multi-Scale Simulations”, Molecular Simulation, 2014, 41:168–189
- 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
- Soroosh Pezeshki, Christal Davis, Andreas Heyden, and Hai Lin, “Adaptive-Partitioning QM/MM Dynamics Simulations: 3. Protein Binding Sites”, JCTC, 2014, 10:4765−4776
- Soroosh Pezeshki and Hai Lin, “Adaptive-Partitioning QM/MM Dynamics Simulations: 4. Proton Hopping in Bulk Water", JCTC, 2015, 11:2398–2411
- Hai Lin, Yan Zhang, Soroosh Pezeshki, Adam W. Duster, Bo Wang, Xin-Ping Wu, Shi-Wen Zheng, Laura Gagliardi, and Donald G. Truhlar, "QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations", Computer Physics Communications, 2024, 295:108987
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
- 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
- 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
- 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
- S. Pezeshki*, M. Winterhalter and U. Kleinekathoefer, “Simulation of transport through OmpF channels”, poster at "DPG-Springmeeting" in Regensburg, Germany, March 2007
- 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
- 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
- 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
- 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
- S. Pezeshki*, “Simulation of Transport through OmpF Channels”, oral presentation at "Computer Simulation and Theory of Macromolecules" in Huenfeld, Germany, April 2008
- 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
- 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
- S. Pezeshki*, M. Winterhalter and U. Kleinekathoefer, "Transport through OmpF Channels Simulated using Molecular Dynamics", poster at "DPG-Springmeeting" in Dresden, Germany, March 2009
- 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
- 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
- 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
- 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
- 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
- S. Pezeshki*, "Simulation of Transport through OmpF and OmpC Channels", oral presentation at "North German Biophysical Meeting" in Borstel, Germany, January 2010
- 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
- S. Pezeshki and H. Lin*, “Open-boundary QM/MM for enzyme simulations”, oral presentation at "PR IUPAC 2011”, San Juan, Puerto Rico, August 2011
- S. Pezeshki* and H. Lin, “Steered molecular dynamics with adaptive partitioning QM/MM”, poster at “ACS 242nd National Meeting” in Denver, Colorado, August 2011
- 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
- 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
- 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
- J. Church*, S. Pezeshki, and H. Lin, “Interactions between Chloride Ion and Amino Acids”, poster at “ACS RMRM 2012” in Westminster, Colorado, October 2012
- 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
- 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"
- 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
- 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
- S. Pezeshki*, “Adaptive Partitioning QM/MM”, invited Seminar talk at Freie Universität Berlin, Germany, November 2014
- 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
- S. Pezeshki*, “Adaptive Partitioning QM/MM-MD Simulations”, invited Seminar talk at European Molecular Biology Laboratory, Hamburg, Germany, April 2015
- 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