PUBLICATIONS

  1. van Wynsberghe, A.*; Ivanov*, I.; Tainer, J.A.; McCammon J.A. Multi-scale modeling of  PCNA monoubiquitin interactions (in preparation)

  2. Ivanov, I.; Tainer, J. A.; McCammon, J. A. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading (submitted)

  3. Cheng, X.; Ivanov, I.; Hailong, W.; Sine, S. M.; McCammon, J. A. Molecular dynamics simulations of ELIC - a prokaryotic homologue of the nicotinic acetylcholine receptor Biophysical Journal 2009, 96, 4502–4513

  4. Amaro, R. E.; Cheng, X.; Ivanov, I.; Xu, D.; McCammon, J. A. Characterizing loop dynamics and
    ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular
    dynamics and end-point free energy calculations.     Journal of the American Chemical Society 2009,
    131, 4702-4709

  5. Som A.; Vemparala S.; Ivanov I.; Tew G. N. Synthetic mimics of antimicrobial peptides. Peptide
    Science (Biopolymers) 2008, 90, 83-93.

  6. Gorfe, A. A.; Chang, C. A.; Ivanov, I.; McCammon, J. A.Dynamics of the Acetylcholinesterase Tetramer Biophysical Journal 2007, 94, 1144-1154.

  7. Ivanov, I.; Cheng, X.; Sine, S. M.; McCammon, J. A. Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop Family Journal of the American Chemical Society 2007 129 8217-8224

  8. Cheng, X.; Ivanov, I.; Wang, H.; Sine, S. M.; McCammon, J. A. Nanosecond Time Scale Conformational Dynamics of the Human alpha7 Nicotinic Acetylcholine Receptor Biophysical Journal 2007 127doi:10.1529/biophysj.107.109843

  9. Ivanov, I.; Tainer, J. A.; McCammon, J. A. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV
    Proceedings of the National Academy of Sciences U.S.A. 2007 , 104,1465-70

  10. Ivanov, I.; Chapados B.; McCammon, J. A.;Tainer, J. A. Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications
    Nucleic Acids Research 2006 34, 6023-33.

  11. Ivanov, I; Vemparala, S.; Pophristic, V.; Kuroda, K.; DeGrado, W. F.; McCammon, J.A.; Klein, M. L. Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces Journal of the American Chemical Society 2006 128, 1778-1779.

  12. Vemparala, S.; Ivanov, I.; Pophristic, V.; Spiegel, K.; DeGrado, W. F.; Klein, M. L. Ab initio calculations of intra bond parameters for a class of arylamide polymers Journal of Computational Chemistry 2006 27, 693.

  13. Pophristic, V.; Vemparala, S.; Ivanov, I.; Liu, Z.; Klein, M. L.; DeGrado, W. F. Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics and classical molecular dynamics study Journal of Physical Chemistry B 2006 110, 3517-3526.

  14. Ivanov, I.; Raugei, S.; Chen, B.; Klein, M. L. Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation Journal of Physical Chemistry B 2006 110, 6365-

  15. Choi, S.; Clements, D. J.; Pophristic, V.; Ivanov, I.; Vemparala, S.; Bennett, J. S.; Klein, M. L.; Winkler, J. D.; and DeGrado, W. F. The Design and Evaluation of Heparin-Binding Foldamers Angewandte Chemie-International Edition 2005 

  16. Ivanov, I. and M. L. Klein Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics methods Journal of the American Chemical Society 2005 127, 4010-4020

  17. Nielsen, S. O. ; Lopez, C. F. ; Ivanov, I. ; Moore, P. B. ; Shelley, J. C. ; Klein, M. L. Transmembrane peptide induced lipid sorting and mechanism of L- alpha to inverted phase transition using coarse grain molecular dynamics Biophysical Journal 2004 87, 2107-2115

  18. Chen, B. ; Ivanov, I. ; Klein, M. L. ; Parrinello, M. Hydrogen bonding in water  Physical Review Letters 2003 91, 215503

  19. Ivanov, I.; Klein, M. L. First Principles Computational Study of the Active Site of Arginase Proteins: Structure, Function, and Bioinformatics 2004 54, 1-7

  20. Min, G. et al. Solution characterization of monodisperse atactic polystyrenes by static and dynamic light scattering International Journal Of Polymer Analysis And Characterization 2003 (accepted)

  21. Ivanov, I. ; Klein, M. L. Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics  Journal of the American Chemical Society 2002 124, 13380-13381

  22. Chen, B. ; Ivanov, I. ; Park, J. M. ; Parrinello, M. ; Klein, M. L.  Solvation structure and mobility mechanism of OH-: A Car- Parrinello molecular dynamics investigation of alkaline solution Journal of Physical Chemistry B  2002 106, 12006-12016

  23. Chen, B. ; Park, J. M. ; Ivanov, I. ; Parrinello, M. ; Klein, M. L. First-principles study of aqueous hydroxide solutions Journal of the American Chemical Society 2002 124, 8534-8535.

  24. Ivanov, I., Gherman, B. F. & Yaron, D. Comparison of the INDO band structures of polyacetylene, polythiophene, polyfuran, and polypyrrole Synthetic Metals 2001 116, 111-114.

Selected Presentations 

  1. Ivanov, I.; Cheng, X.; McCammon, J. A. A. Barriers to ion translocation in the human alpha 7 nicotinic acetylcholine receptor 51th Annual Meeting of the Biophysical Society, Baltimore, MD 2007.

  2. Ivanov, I.; Tainer, J. A.; McCammon, J. A. Ab initio molecular dynamics reveals striking reorganization of the trinuclear metal cluster of endonuclease IV during catalysis 232nd National Meeting of the American Chemical Society, San Francisco, CA 2006.

  3. Ivanov, I.; Tainer, J. A.; McCammon, J. A. Interactions and dynamics of sliding clamp proteins on DNA Annual Meeting of the Protein Society, San Diego, CA 2006

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