Research Interests:

  • Car-Parrinello molecular dynamics of chemical and biological systems 

  • New algorithms. Hierarchical and multi-scale techniques in molecular dynamics simulation. Mixed quantum-classical systems. Algorithms for efficient sampling on complex free energy surfaces

  • Parallel computation. Development of scaleable parallel algorithms for molecular dynamics.

  • Optimization on free energy landscapes - theory, algorithms, models of protein folding.

  • Photophysics of conjugated polymers as related to the fabrication of advanced electronic materials and the relevant theoretical methods to describe it; e.g. semi-empirical methods, time dependent density functional theory. 

  • Coarse-grain methods in molecular dynamics and their applications to the study of self-assembly processes in chemistry and biology.

Image Gallery

Progress Report

Antimicrobial Polymers Movie ( MPEG format; download only if FAST internet connection is available! )

Arginase Active Site Movie ( AVI format; download only if FAST internet connection is available! )

Refereed Publications:

Gorfe, A. A.; Chang, C. A.; Ivanov, I.; McCammon, J. A. Dynamics of the acetylcholinesterase tetramer Biophysical Journal 2007 doi:10.1529/biophysj.107.117879

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

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

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

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.

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.

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.

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.

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-

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 

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

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

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

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

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)

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.

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.

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.

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:  

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.

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.


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

Ivanov, I. ; Raugei, S. ; Klein, M. L. Effect of ions on the dipole moment and electronic properties of water: an ab initio molecular dynamics study Gordon Research Conference on Computational Chemistry , Plymouth, NH 2004.

Ivanov, I. and M. L. Klein Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics methods Biochemistry 2003 42 (28), 143. (Meeting abstract)

Ivanov, I. ; Klein, M. L. Weak acid deprotonation in aqueous solution Gordon Research Conference on the Chemistry and Physics of Liquids, Plymouth, NH 2003.

Ivanov, I. ; Klein, M. L. Large-scale  density functional study of the binuclear manganese center of arginase Abstracts of Papers of the American Chemical Society 2003, PHYS.

Ivanov, I. ; Klein, M. L. Relative pKas from first principles molecular dynamics: the case of histidine deprotonation Abstracts of Papers of the American Chemical Society 2003, COMP.

Ivanov, I. ; Klein, M. L. Analysis of the deprotonation of a histidine residue in aqueous solution from constrained ab initio molecular dynamics American Conference on Theoretical Chemistry (ACTC 2002), Champion, PA 2002.

Ivanov I. ; Yaron, D. Band structures of the conjugated polymers polythiophene polyfuran and polypyrrole International Workshop on Methods for Macromolecular Modeling (M3), New York, NY 2000.