IVAYLO IVANOV’S CV

CV in PDF format

CURRICULUM VITAE

Ivaylo Ivanov
Professor of Chemistry
College of Arts & Sciences
Georgia State University

A. EDUCATION

Ph.D. in Chemistry, December 2004
Department of Chemistry,
University of Pennsylvania, Philadelphia, PA
Dissertation: “Terascale Ab Initio Molecular Dynamics Simulations of Proton
Transfer and Dissociation Processes in Chemical and Biological Systems”

M.S. in Chemistry, May 1999
Carnegie Mellon University, Pittsburgh, PA

B.S. in Chemistry, June 1996
Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria

B. PROFESSIONAL CREDENTIALS

2020 – Present    Professor, Computational Biophysical Chemistry
Department of Chemistry, Georgia State University, Atlanta, Georgia

2015 – 2020     Associate Professor, Computational Biophysical Chemistry
Department of Chemistry, Georgia State University, Atlanta, Georgia

2009 – 2015     Assistant Professor, Computational Biophysical Chemistry
Department of Chemistry, Georgia State University, Atlanta, Georgia

2009 – Present      Faculty Member, joint appointment in Department of Biology
Georgia State University, Atlanta, Georgia

2009 – Present      Faculty Member, Molecular Basis of Disease Program
Georgia State University, Atlanta, Georgia

2009 – Present      Faculty Member, Center for Biotechnology and Drug Design
Georgia State University, Atlanta, Georgia

2012 – Present      Faculty Member, Center for Diagnostics & Therapeutics
Georgia State University, Atlanta, Georgia

2005 – 2009         Postdoctoral Research Associate
Department of Chemistry & Biochemistry
University of California-San Diego, La Jolla, California

1999 – 2004          Research & Teaching Assistant
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania

C. SCHOLARSHIP AND PROFESSIONAL DEVELOPMENT

C.1 Research support

C.1.1 Research Funding

  1. National Institutes of Health R01 GM110387 (09/01/15 – 08/31/20); Title: “Integrative Modeling of PCNA Assemblies Engaged in Genome Duplication and Repair”; Role: Principal Investigator; Total cost: $1,675,000
  2. Cleon C. Arrington Research Initiation Grant from GSU (07/01/18-6/30/19); Title: “Uncovering the Complex Interplay of DNA Repair and Epigenetic Regulation in Genome Maintenance”; Role: Principal Investigator; Total cost: $20,000
  3. National Institutes of Health R01 GM126154; (04/01/2018-12/31/2021) Title: “Mechanism and Inhibition of Protein Arginine Methylation”; Role: Co-Investigator; Total cost: $160,000 (to I.I.)
  4. National Science Foundation CAREER Award MCB-1149521 (05/01/12 – 04/30/18); Title: “Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Loaders”; Role: Principal Investigator; Total cost: $824,000
  5. National Institutes of Health R01 CA118113-06A1; (06/01/14-5/31/19) Title: “p68 and Ca-Calmodulin Interaction in Cell Migration”; Role: Co-Investigator; Direct cost: $40,000 (to I.I.)
  6. Cleon C. Arrington Research Initiation Grant from GSU (02/01/11-6/30/12); Title: “Modeling Assemblies and Interactions in Eukaryotic Clamp Loading”; Role: Principal Investigator; Total cost: $10,000

      C.1.2 Computational support at the national supercomputing facilities

  1. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award (01/01/2019 – 12/31/19); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation”; Role: Principal Investigator; Awarded 220,000 service units on OLCF Summit machine (equivalent to 198 million CPU hours)
  2. NSF/XSEDE program CHE110042 (10/01/17 – 9/30/18); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 2,240,000 CPU hours and 81,000 GPU node hours. The value of the awarded resources is $58,429.
  3. ERCAP DOE Production Award at NERSC (01/07/17 – 01/05/18); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 6,000,000 CPU hours
  4. NSF/XSEDE program CHE110042 (04/01/16 – 9/30/17); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 6,275,000 CPU hours. The value of the awarded resources is $215,334.
  5. ERCAP DOE Production Award at NERSC (01/07/16 – 12/31/17); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 3,600,000 CPU hours
  6. NSF/XSEDE program CHE110042 (10/01/14 – 9/30/15); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 6,703,000 CPU hours. The value of the awarded resources is $251,899.
  7. ERCAP DOE Production Award at NERSC (01/07/15 – 12/31/15); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 2,200,000 CPU hours
  8. 2013 ASCR Leadership Computing Challenge Award (07/01/2013-12/31/2014); Title: “Exploring the Chemical Landscape for Base Excision DNA Repair”; Role: Principal Investigator; Awarded 3,000,000 CPU hours
  9. ERCAP DOE Production Award at NERSC (01/07/14 – 01/05/15); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 4,000,000 CPU hours
  10. NSF/XSEDE program CHE110042 (10/01/12 – 12/31/13); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 4,726,000 CPU hours
  11. ERCAP DOE Production Award at NERSC (01/07/12 – 01/05/13); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 2,000,000 CPU hours
  12. NERSC Initiative for Scientific Exploration (NISE) Award (05/01/11 – 04/30/12); Title: “An Integrative Strategy to Model Complex Biological Assemblies”; Role: Principal Investigator; Awarded 960,000 CPU hours
  13. Computational time on the special purpose Anton machine at the National Resource for Biomedical Supercomputing (NRBSC) in Pittsburgh (09/01/11 – 06/30/12); Title: “Modeling connexin hemichannels important for intercellular communication”; Role: Principal Investigator; Awarded 50,000 CPU hours
  14. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award BIP007 (01/01/2009 – 12/31/10); Title: “Interplay of AAA+ Molecular Machines, DNA Repair Enzymes and Sliding Clamps at the Replication Fork: A Multiscale Approach to Modeling Replisome Assembly and Function”; Role: Principal Investigator; Awarded 6,500,000 CPU hours

C.2 Publications (58 publications, cited >2500 times in Google Scholar, h-index 28)

  1. Dodd, T., Botto, M., Paul, F., Leiro, R.F, Lamers, M.H., & Ivanov, I.* Defined path for conformational switching from polymerization to editing in a high-fidelity DNA polymerase. (2020) (submitted)
  2. Yuan, Z., Schneider, S., Dodd, T., Riera, A., Bai, L., Yan, C., Ivanov, I.*, Stillman, B., Li, H., & Speck, C. Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6. Proceedings of the National Academy of Sciences USA (2020) (in press)
  3. Dodd, T., Yan, C., & Ivanov, I.* Simulation-based methods for model building and refinement in cryo-electron microscopy. Journal of Chemical Information and Modeling (2020) 60, 5, 2470–2483 doi:10.1021/acs.jcim.0c00087
  4. Yan, C., Dodd, T., Tainer, J.A., He, Y., Tsutakawa, S.E., & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nature Structural & Molecular Biology (2019), 26, 397-406, doi:10.1038/s41594-019-0220-3 (recommended by Faculty of 1000 Prime)
  5. Perumal, S.K.; Xu, X.; Yan, C.; Ivanov, I.* & Benkovic, S.J. Recognition of a key anchor residue by a conserved hydrophobic pocket ensures subunit interfaces integrity in DNA clamps. Journal of Molecular Biology (2019) doi:10.1016/j.jmb.2019.04.035
  6. Carter, E.K.; Laughlin, S.; Dodd, T.; Wilson, W.D. & Ivanov, I* Small molecule binders recognize DNA microstructural variations via an induced fit mechanism Physical Chemistry Chemical Physics (2019) doi:10.1039/C8CP05537H
  7. Han, Y.; Yan, C.; Fishbain, S.; Ivanov, I. & He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018) doi:10.1038/s41421-018-0044-z
  8. Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I.* Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018) doi:10.1073/pnas.1803323115
  9. Li, J. et al. Natural Product Micheliolide (MCL) Irreversibly Activates Pyruvate Kinase M2 and Suppresses Leukemia. (2018) Journal of Medicinal Chemistry doi: 10.1021/acs.jmedchem.8b00241
  10. Han, Y.; Yan, C.; Nguyen, K.; Jackobel, A.; Ivanov, I.; Knutson, B.A.; He, Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.  eLife (2017) 6, e27414, doi:10.7554/eLife.27414
  11. Rashid F. et al. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife (2017) 6, e21884, doi:10.7554/eLife.21884
  12. Zhang, J., Qian, K., Yan, C., He, M., Jassim, B., Ivanov, I. & Zheng, Y. Discovery of decamidine as a new and potent PRMT1 inhibitor. (2017) Medicinal Chemistry Communications (2017) 8, 440-444, doi:10.1039/C6MD00573J
  13. Laughlin S.; Carter E.K.; Ivanov, I* & Wilson, W.D. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Research (2017) 45, 1297-1306, doi:10.1093/nar/gkw1232
  14. He, Y., Yan, C., Inouye, C., Fang, J., Tjian, R., Ivanov, I. & Nogales E. Structural basis of transcription promoter opening using single particle cryo-EM. Nature (2016) 533, 359–365, doi:10.1038/nature17970 (cited >100 times)
  15. Turaga, R.C., Yin, L., Yang, J.J., Lee, H., Ivanov, I., Yan, C., Grossniklaus, H.E., Wang, S., Ma, C., Sun, L. & Liu, Z. Development of protein drug targeting integrin αvβ3 at a novel site by rational protein design. Nature Communications (2016) 7, 11675, doi:10.1038/ncomms11675
  16. Hudson, W.H., Kossmann, B., de Vera, I.M., Chuo, S.W., Weikum, E.A., Eick G., Thornton, J., Ivanov, I., Kojetin, D.J., & Ortlund, E.A Distal substitutions drive divergent DNA specificity among paralogous transcription factors through a subdivision of conformational space. Proceedings of the National Academy of Sciences USA (2016) 113, 326-331, doi:10.1073/pnas.1518960113
  17. Xu, X., Yan, C., Kossmann, B. & Ivanov, I.* Secondary interaction interfaces with PCNA control conformational switching of DNA polymerase PolB from polymerization to editing. Journal of Physical Chemistry B (2016) 120, 8379–8388, doi:10.1021/acs.jpcb.6b02082 (Invited article for the J. Andrew McCammon Festschrift special issue)
  18. Kossmann, B., Marchand C, Pommier Y* & Ivanov, I* Discovery of selective inhibitors of tyrosyl-DNA phosphodiesterase 2 by targeting the enzyme DNA-binding cleft. Bioorganic and Medicinal Chemistry Letters (2016) 26, 3232-3236, doi:10.1016/j.bmcl.2016.05.065
  19. Musille, P. M., Kossmann, B., Kohn, J. A., Ivanov, I., & Ortlund E. A. Unexpected allosteric network contributes to LRH-1 co-regulator selectivity. Journal of Biological Chemistry (2016) 291, 1411-1426, doi:10.1074/jbc.M115.662874
  20. Xu, X., Yan, C., Wohlhueter, R., & Ivanov I* Integrative modeling of macromolecular assemblies from low to near-atomic resolution. Computational and Structural Biotechnology Journal (2015) 13, 492–503, doi:10.1016/j.csbj.2015.08.005
  21. Brosey, C.A., Soss, S.E., Brooks, S., Yan, C., Ivanov, I., Dorai, K., & Chazin, W.J. Functional dynamics in RPA DNA binding and protein recruitment domains. Structure (2015) 23, 1028–1038, doi:10.1016/j.str.2015.04.008
  22. Tsutakawa, S.E., Yan, C., Xu, X., Weinacht, C., Frudental, B., Zhuang, Z., Washington, M.T., Tainer, J.A. & Ivanov, I.* Structurally distinct ubiquitin- and SUMO-modified PCNA: Implications for their distinct roles in the DNA Damage response. Structure (2015) 23, 724–733, doi:10.1016/j.str.2015.02.008
  23. Kossmann, B. & Ivanov, I.* Alkylpurine Glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases. PLOS Computational Biology (2014) 10, e1003704. doi:10.1371/journal.pcbi.1003704
  24. Yan, L., Yan, C., Su, H., Qian, K., Wofford, S., Zhao, X., Ivanov, I.* & Zheng Y.G.* Diamidine compounds as selective inhibitors of protein arginine methyltransferase 1. Journal of Medicinal Chemistry (2014) 57, 2611–2622, doi:10.1021/jm401884z
  25. Xu, X., Guardiani, C., Yan, C. & Ivanov, I.* Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1. Nucleic Acids Research (2013) 41, 10020-10031, doi:10.1093/nar/gkt810
  26. Wang, L., Xu, X., Kumar, R., Maiti, B., Liu, C. T., Ivanov, I.*, Lee, T.-H. & Benkovic, S. J. Probing DNA clamps with single-molecule force spectroscopy. Nucleic Acids Research (2013) 41, 7804-7814, doi:10.1093/nar/gkt487
  27. Tsutakawa, S. E., Shin, D. S., Mol, C. D., Izumi, T., Arvai, A. S., Mantha, A. K., Szczesny, B., Ivanov, I., Hosfield, D. J., Maiti, B., Pique, M. E., Frankel, K. A., Hitomi, K., Cunningham, R. P., Mitra, S. & Tainer, J. A. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. Journal of Biological Chemistry (2013) 288, 8445-8455, doi:10.1074/jbc.M112.422774
  28. Ivanov, I.* Enzyme cofactors: Double-edged sword for catalysis. Nature Chemistry (2013) 5, 6-7, doi:10.1038/nchem.1529
  29. Brosey, C. A., Yan, C., Tsutakawa, S. E., Heller, W. T., Rambo, R. P., Tainer, J. A., Ivanov, I.* & Chazin, W. J. A new structural framework for integrating replication protein A into DNA processing machinery. Nucleic Acids Research (2013) 41, 2313-2327, doi:10.1093/nar/gks1332 (selected as a featured paper in the top 5% of NAR submissions)
  30. Querol-Audi, J., Yan, C., Xu, X., Tsutakawa, S. E., Tsai, M.S., Tainer, J. A., Cooper, P. K., Nogales, E. & Ivanov, I.* Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proceedings of the National Academy of Sciences USA (2012) 109, 8528-8533, doi:10.1073/pnas.1121116109
  31. Cheng, X. & Ivanov, I. Molecular dynamics. Methods in Molecular Biology (Clifton, N.J.) (2012) 929, 243-285 (Springer Protocols Series; ISBN 978-1-62703-049-6)
  32. Tsutakawa, S. E., Van Wynsberghe, A. W., Freudenthal, B. D., Weinacht, C. P., Gakhar, L., Washington, M. T., Zhuang, Z., Tainer, J. A. & Ivanov, I.* Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA. Proceedings of the National Academy of Sciences USA (2011) 108, 17672-17677, doi:10.1073/pnas.1110480108 (Faculty of 1000 recommended Factor 8.0; highlighted by the Oak Ridge Leadership Computing Facility at http://www.olcf.ornl.gov/2011/11/09)
  33. Sander, T., Frolund, B., Bruun, A. T., Ivanov, I., McCammon, J. A. & Balle, T. New insights into the GABA(a) receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data. Proteins: Structure Function and Bioinformatics (2011) 79, 1458-1477, doi:10.1002/prot.22975
  34. Fritsch, S., Ivanov, I., Wang, H. & Cheng, X. Ion selectivity mechanism in a bacterial pentameric ligand-gated ion channel. Biophysical Journal (2011) 100, 390-398, doi:10.1016/j.bpj.2010.11.077
  35. Feng, Y., Wang, J., Asher, S., Hoang, L., Guardiani, C., Ivanov, I.* & Zheng, Y. G. Histone H4 acetylation differentially modulates arginine methylation by an in cis mechanism. Journal of Biological Chemistry (2011) 286, 20323-20334, doi:10.1074/jbc.M110.207258
  36. Tainer, J. A., McCammon, J. A. & Ivanov, I.* Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading. Journal of the American Chemical Society (2010) 132, 7372-7378, doi:10.1021/ja100365x (highlighted by the National Center for Computational Sciences (NCCS) at http://www.nccs.gov/2010/06/24)
  37. Cheng, X., Ivanov, I., Wang, H., 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, doi:10.1016/j.bpj.2009.03.018
  38. 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, doi:10.1021/ja8085643 (cited >100 times)
  39. Som, A., Vemparala, S., Ivanov, I. & Tew, G. N. Synthetic mimics of antimicrobial peptides. Biopolymers (2008) 90, 83-93, doi:10.1002/bip.20970 (cited >100 times)
  40. Gorfe, A. A., Chang, C. E. A., Ivanov, I. & McCammon, J. A. Dynamics of the acetylcholinesterase tetramer. Biophysical Journal (2008) 94, 1144-1154, doi:10.1529/biophysj.107.117879
  41. 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 USA (2007) 104, 1465-1470, doi:10.1073/pnas.0603468104
  42. 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, doi:10.1021/ja070778l
  43. Cheng, X., Ivanov, I.*, Wang, H., Sine, S. M. & McCammon, J. A. Nanosecond timescale conformational dynamics of the human alpha 7 nicotinic acetylcholine receptor. Biophysical Journal (2007) 93, 2622-2634, doi:10.1529/biophysj.107.109843
  44. Vemparala, S., Ivanov, I., Pophristic, V., Spiegel, K. & Klein, M. L. Ab initio calculations of intramolecular parameters for a class of arylamide polymers. Journal of Computational Chemistry (2006) 27, 693-700, doi:10.1002/jcc.20382
  45. Pophristic, V., Vemparala, S., Ivanov, I., Liu, Z. W., 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, doi:10.1021/jp054306
  46. 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 from all-atom molecular dynamics. Journal of the American Chemical Society (2006) 128, 1778-1779, doi:10.1021/ja0564665
  47. Ivanov, I.*, Chen, B., Raugei, S. & Klein, M. L. Relative pKa values from first-principles molecular dynamics: The case of histidine deprotonation. Journal of Physical Chemistry B (2006) 110, 6365-6371, doi:10.1021/jp056750i
  48. Ivanov, I.*, Chapados, B. R., 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, 6023-6033, doi:10.1093/nar/gkl744
  49. Ivanov, I.* & Klein, M. L. Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics. Journal of the American Chemical Society (2005) 127, 4010-4020, doi:10.1021/ja043693i
  50. Choi, S., Clements, D. J., Pophristic, V., Ivanov, I., Vemparala, S., Bennett, J. S., Klein, M. L., Winkler, J. D. & DeGrado, W. E. The design and evaluation of heparin-binding foldamers. Angewandte Chemie-International Edition (2005) 44, 6685-6689, doi:10.1002/anie.200501279 (featured on the cover of Angewandte Chemie)
  51. Ivanov, I. Terascale ab initio molecular dynamics simulations of proton transfer and dissociation processes in chemical and biological systems. (2004) ProQuest AAI3152059
  52. 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, doi:10.1529/biophysj.104.040311
  53. Ivanov, I.* & Klein, M. L. First principles computational study of the active site of arginase. Proteins: Structure Function and Genetics (2004) 54, 1-7, doi:10.1002/prot.10572
  54. Min, G., Savin, D., Gu, Z., Patterson, G. D., Kim, S. H., Ramsay, D. J., Fishman, D., Ivanov, I., Sheina, E., Slaby, E. & Oliver, J. Solution characterization of monodisperse atactic polystyrenes by static and dynamic light scattering. International Journal of Polymer Analysis and Characterization (2003) 8, 187-207, doi:10.1080/10236660304875
  55. Chen, B., Ivanov, I., Klein, M. L. & Parrinello, M. Hydrogen bonding in water. Physical Review Letters (2003) 91, doi:10.1103/PhysRevLett.91.215503 (cited >300 times)
  56. 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, doi:10.1021/ja027972m
  57. Chen, B., Park, J. M., Ivanov, I., Tabacchi, G., Klein, M. L. & Parrinello, M. First-principles study of aqueous hydroxide solutions. Journal of the American Chemical Society (2002) 124, 8534-8535, doi:10.1021/ja020350g
  58. 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 solutions. Journal of Physical Chemistry B (2002) 106, 12006-12016, doi:10.1021/jp026504w
  59. 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, doi:10.1016/s0379-6779(00)00526-9

(* denotes papers for which I am corresponding author)

C.3 Selected Awards

  1. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) award from the Department of Energy Office of Science (2018)
  2. Cleon C. Arrington Research Initiation Grant from Georgia State University (2018)
  3. ASCR Leadership Computing Challenge Award (2013) “Exploring the Chemical Landscape for Base Excision DNA Repair”
  4. Dean’s Early Career Award (2013), Georgia State University
  5. NSF CAREER Award MCB-1149521 (2012) “Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Loaders”
  6. NSF/XSEDE program CHE110042 (2012) “Integrative Modeling of Complex Biological Assemblies”
  7. NERSC Initiative for Scientific Exploration (NISE) Award from the Department of Energy Office of Science (2011) “An Integrative Strategy to Model Complex Biological Assemblies”
  8. Cleon C. Arrington Research Initiation Grant (2011) from Georgia State University
  9. NSF/Teragrid program CHE110042 (2011) “Exploring the Chemical Landscape for Base Excision DNA Repair”
  10. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) award from the Department of Energy Office of Science (2010) “Interplay of AAA+ Molecular Machines, DNA Repair Enzymes and Sliding Clamps at the Replication Fork: A Multiscale Approach to Modeling Replisome Assembly and Function”
  11. Principal Investigator on a NSF LRAC (Large Resource Allocation Committee) award “Large Scale Classical and Ab Initio Molecular Dynamics Simulations of Enzymes and Supramolecular Assemblies Involved in DNA Repair”
  12. Burroughs Wellcome Fund (La Jolla Interfaces in Science) Postdoctoral Fellowship 2005-07
  13. Chemical Computing Group Excellence Award, American Chemical Society (2003)
  14. Chemistry Department Chairman’s Award, University of Pennsylvania (2000)
  15. Chemistry Department Teaching Award, Carnegie Mellon University (1999)

C.4 Invited Presentations

  1. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling Southeast Regional Meeting of the American Chemical Society (SERMACS), Augusta, GA 2018
  2. DNA sculpting as a strategy for base extrusion and damage selection by DNA repair glycosylases Southeast Regional Meeting of the American Chemical Society (SERMACS), Augusta, GA 2018
  3. DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG Third Fusion Conference: Dynamic Structures in DNA Damage Responses and Cancer, Cancun, Mexico 2018
  4. DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG Lawrence Berkeley National Laboratory, Berkeley, CA 2018
  5. Modeling biological assemblies from low to near atomic resolution Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands 2016
  6. Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing Second Fusion Conference: Dynamic Structures in DNA Damage Responses and Cancer, Cancun, Mexico 2016
  7. DNA sculpting as a strategy for base extrusion and damage selection by DNA repair glycosylases Southeast Regional Meeting of the American Chemical Society (SERMACS), Nashville, TN 2014
  8. Structurally distinct complexes of ubiquitin and SUMO-modified PCNA lead to distinct DNA damage response pathways, Department of Chemistry, Vanderbilt University, Nashville, TN, GA 2014
  9. Structurally distinct complexes of ubiquitin and SUMO-modified PCNA lead to distinct DNA damage response pathways Lawrence Berkeley National Laboratory, Berkeley, CA 2014
  10. Integrative modeling of complex biological assemblies in DNA replication and transcription coupled repair Fusion Conference: Dynamic Structures in DNA Damage Responses and Cancer, Cancun, Mexico 2014
  11. Integrative modeling of complex biological assemblies in DNA replication and transcription coupled repair Southeast Regional Meeting of the American Chemical Society (SERMACS), Atlanta, GA 2013
  12. Structurally distinct complexes of Ubiquitin and SUMO-modified PCNA lead to distinct functional outcomes in DNA damage response Department of Biochemistry, Emory University, Atlanta, GA 2013
  13. Proliferating cell nuclear antigen and its protein partners in DNA repair, Department of Biomolecular Sciences, University of Mississippi, Oxford, MS 2012
  14. Integrative modeling of protein/DNA complexes at the replication fork Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 2012
  15. Integrative modeling of FEN1 complexes with the sliding clamps PCNA and Rad9-Hus1-Rad1 Mutagenesis Gordon Research Conference, Newport, RI 2012
  16. Solution phase X-ray scattering and multiscale computational modeling reveal the structural dynamics of ubiqutinated PCNA Symposium in Honor of J. Andrew McCammon, 243rd National Meeting of the American Chemical Society, San Diego, CA 2012
  17. Integrative modeling of protein/DNA complexes at the replication fork Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 2012
  18. Integrative Modeling of Protein/DNA Complexes at the Replication Fork Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 2011
  19. Integrative Modeling of Protein/DNA Complexes at the Replication Fork Conference on Computational Physics (CCP2011) 2011
  20. Integrative Modeling of Protein/DNA Complexes at the Replication Fork Lawrence Berkeley National Laboratory, Berkeley, CA 2011
  21. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 2009
  22. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading Frontiers in Macromolecular Simulations Symposium, Georgia Institute of Technology, Atlanta, GA 2009
  23. The Interplay of AAA+ Molecular Machines and Sliding Clamps at the DNA Replication Fork Colorado Initiative in Molecular Biotechnology, University of Colorado, Boulder, CO 2009
  24. The Interplay of AAA+ Molecular Machines and Sliding Clamps at the DNA Replication Fork Department of Chemistry, University of California Los Angeles, Los Angeles, CA 2009
  25. The three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV Protein Dynamics and Catalysis Conference, Tarrytown, NY 2008
  26. High Performance Computing in Molecular Simulation and Computational Structural Biology13th Annual San Diego Supercomputer Center Summer Institute, La Jolla, CA 2007
  27. Insight into DNA repair systems from classical and ab initio molecular dynamics Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 2007
  28. Insight into DNA repair systems from classical and ab initio molecular dynamics Department of Chemistry, Columbia University, New York, NY 2007
  29. DNA repair systems and ligand-gated ion channels: Insights from classical and ab initio molecular dynamics Department of Biochemistry, Washington University School of Medicine, St. Louis 2007
  30. Workshop on Petascale Computing in the Biosciences, National Science Foundation, Arlington, VA 2006 (Invited participant, contributor to the final report)

C.5 Selected Contributed Presentations

  1. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling 256th National Meeting of the American Chemical Society, Boston, MA 2018
  2. Electron microscopy and integrative modeling shed light on the structures of transcription pre-initiation complexes and the mechanisms of transcription initiation National Meeting of the Biophysical Society, San Francisco, CA 2018
  3. Electron microscopy and integrative modeling shed light on the structures of transcription pre-initiation complexes and the mechanisms of transcription initiation Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems, Keystone Symposium, Tahoe City, CA 2018
  4. Electron microscopy and integrative modeling shed light on the structures of transcription pre-initiation complexes and the mechanisms of transcription initiation Nucleic Acids Gordon Research Conference, Biddeford, ME 2017
  5. Integrative Modeling of Macromolecular Assemblies in Gene Regulation Molecular Machines: Integrative Structural and Molecular Biology EMBO Conference, EMBL Heidelberg, Germany 2016
  6. Integrative Modeling of Macromolecular Assemblies in Gene Regulation 5th Zing Nucleic Acids Conference, Tampa, FL 2016
  7. Damage recognition and base extrusion strategies of DNA repair glycosylase enzymes 251st National Meeting of the American Chemical Society, San Diego, CA 2016
  8. Hybrid modeling of ubiquitin- and SUMO-modified PCNA complexes: Implications for DNA damage responses 251st National Meeting of the American Chemical Society, San Diego, CA 2016
  9. Structurally Distinct Ubiquitin- and SUMO-Modified PCNA: Implications for their Distinct Roles in the DNA Damage Response Albany 2015 Conference, Albany, NY 2015
  10. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes 4th Zing Nucleic Acids Conference Cancun, Mexico 2014
  11. Integrative modeling of protein assemblies involved in transcription Biopolymers Gordon Research Conference, Newport, RI 2014
  12. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes Annual Meeting of the Biophysical Society, San Francisco, CA 2014
  13. Integrative modeling of complex biological assemblies in DNA replication and transcription coupled repair 246th National Meeting of the American Chemical Society, Indianapolis, IN 2013
  14. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes Nucleic Acids Gordon Research Conference, Biddeford, ME 2013
  15. Hybrid modeling of the ternary complexes of flap endonuclease-1 with sliding clamps and DNA Keystone Meeting on Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Tahoe City, CA 2013
  16. Electron microscopy and computational modeling reveal key structural aspects of the ternary assemblies of flap endonuclease 1 with sliding clamps and DNA 243rd National Meeting of the American Chemical Society, San Diego, CA 2012
  17. Integrative modeling of protein/DNA complexes at the replication fork 243rd National Meeting of the American Chemical Society, San Diego, CA 2012
  18. Structure and dynamics of the ternary complexes of FEN1/PCNA/DNA and FEN1/Rad9-Rad1-Hus1/DNA Eukaryotic DNA Replication & Genome Maintenance meeting, Cold Spring Harbor Laboratory, NY 2011
  19. Solution X-ray scattering reveals multiple modes of association for covalently-bound ubiquitin on PCNA Eukaryotic DNA Replication & Genome Maintenance meeting, Cold Spring Harbor Laboratory, NY 2011
  20. Multiple states of covalently bound ubiquitin on PCNA Keystone meeting on DNA Replication and Recombination, Keystone, CO 2011
  21. Multiple states of covalently bound ubiquitin on PCNA Gordon Research Conference DNA Damage, Mutation & Cancer, Ventura, CA 2010
  22. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading Biology department seminar, Georgia State University, Atlanta, GA 2010
  23. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading 24th Annual Symposium of the Protein Society, San Diego, CA 2010
  24. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading 240th National Meeting of the American Chemical Society, Boston, MA 2010
  25. Phosphoryl Transfer in Solution and in Enzymatic Active Sites: Insights from Ab Initio molecular dynamics Algorithms in Macromolecular Modeling (AM3) meeting, Austin, TX 2009
  26. The Interplay of AAA+ Molecular Machines and Sliding Clamps at the DNA Replication Fork Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, MN 2009

C.6 Ad hoc reviewer for the following journals

Science, Proceedings of the National Academy of Science USA, Journal of the American Chemical Society, Nucleic Acids Research, Journal of Physical Chemistry, ChemPhysChem, Journal of Chemical Theory and Computation, Biophysical Journal, Biochemistry, Chemical Communications, Journal of Chemical Physics, PLOS Computational Biology, PLOS One, Medicinal Research Reviews, Journal of Molecular Graphics and Modelling, Chemical Biology & Drug Design, Journal of Structural Biology, Journal of Chemical Information and Modeling, Journal of Physical Chemistry Letters

C.7 Collaborators in the past 5 years

Eva Nogales (UC-Berkeley)
Stephen J. Benkovic (Pennsylvania State University)
Walter Chazin (Vanderbilt University)
Y. George Zheng (University of Georgia)
Eric Ortlund (Emory University)
Samir Hamdan (KAUST)
Susan Tsutakawa (Lawrence Berkeley National Laboratory)
John A. Tainer (MD Anderson Cancer Center)
Zhihao Zhuang (University of Delaware)
M. Todd Washington (University of Iowa)
Xiaolin Cheng (Oak Ridge National Laboratory)
Yuan He (Northwestern University)
Zhi-ren Liu (Georgia State University)
Yves Pommier (NIH)
David Wilson (Georgia State University)

C.8 Society Memberships:

American Chemical Society (since 1999)
Biophysical Society (since 2004)
Protein Society (since 2004)
Sigma Xi (Full membership since 2004)

C.9 Media Coverage

1. Coverage of article Proceedings of the National Academy of Sciences (2018) doi:10.1073/pnas.1803323115

Featured on the website of the San Diego Supercomputer Center in a news story “How an Enzyme Repairs DNA via a Pinch-Push-Pull Mechanism”. Highlighted by the following news outlets: Scientific Computing Online, HealthNewsDigest.com, Newswise & Publicnow.

2. Coverage of article Nature 533, 359–365 (2016) doi:10.1038/nature17970

Altmetric score 135. The article is in the 98 percentile (ranked 3,654th) of the 227,366 tracked articles of a similar age in all journals and in the 60 percentile (ranked 388th) of the 975 tracked articles of a similar age in Nature. Highlighted by the Science360 site and the MCB Division of the National Science Foundation, Phys.org, Technology.org, e! Science News, Nanowerk, Bioportfolio, EurekAlert!, Newswise, Science Daily among other media sources.

3. Coverage of article Nature Communications 7, 11675 (2016) doi:10.1038/ncomms11675

Altmetric score 201. The article is in the 99th percentile (ranked 1,781st) of the 190,421 tracked articles of a similar age in all journals and in the 94th percentile (ranked 37th) of the 713 tracked articles of a similar age in Nature Communications.

4. Coverage of article Proceedings of the National Academy of Sciences 113, 326–331 (2016) doi:10.1073/pnas.1518960113

Altmetric score 51. The article is in the 96 percentile of the 252241 tracked articles of a similar age in all journals and in the 76 percentile (ranked 238) of the 1024 tracked articles of a similar age in PNAS. Highlighted by ScienceDaily, Health Medicine Network, PhysOrg.com and EurekAlert! among other media sources.

5. Coverage of article Proceedings of the National Academy of Sciences 108, 17672-17677 (2011) doi:10.1073/pnas.1110480108.

Featured science highlight “Researchers Show How Proteins Help DNA Replicate Past a Damaged Site” by the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory (https://www.olcf.ornl.gov/2011/11/09/researchers-show-how-proteins-help-dna-replicate-past-a-damaged-site).

6. Coverage of article Nucleic Acids Research 41, (2013) doi:10.1093/nar/gks1332.

Featured science highlight “Neutrons help shed light on critical protein activity that protects our DNA” by the ORNL’s Neutron Sciences Directorate, Oak Ridge National Laboratory (http://neutrons2.ornl.gov/research/highlights/BioSANS/protein-activity-dna.html).

7. Coverage of article Journal of the American Chemical Society 132, (2010) 7372-7378, doi:10.1021/ja100365x

Featured science highlight “Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA” by the Oak Ridge Leadership Computing Facility (OLCF) at Oak Ridge National Laboratory (https://www.olcf.ornl.gov/2010/06/24/supercomputers-simulate-the-molecular-machines-that-replicate-and-repair-dna/).

D. TEACHING, INCLUDING ADVISING

D.1 Courses Taught

  1. Physical Chemistry II (Level: Advanced Undergraduate/Graduate): spring semester 2010, spring semester 2011, spring semester 2013, spring semester 2014, spring semester 2016, fall semester 2016, spring semester 2017
  2. Physical chemistry I (Level: Advanced Undergraduate/Graduate): fall semester 2010, spring semester 2012, spring semester 2015
  3. Instrumental methods III (Level: Advanced Undergraduate/Graduate), Spectroscopy lab: fall semester 2010, fall semester 2011, fall semester 2012, fall semester 2013, fall semester 2014, fall semester 2015
  4. Biophysical Chemistry (Level: Graduate): fall semester 2012, fall semester 2014, fall semester 2016
  5. Dissertation Research in Chemistry: spring semester 2011, summer semester 2011, fall semester 2011, spring semester 2012, summer semester 2012, fall semester 2012, spring semester 2013, summer semester 2013, fall semester 2013, spring semester 2014, summer semester 2014, fall semester 2014, spring semester 2015, summer semester 2015, fall semester 2015, spring semester 2016, summer semester 2016, fall semester 2016, spring semester 2017
  6. Chemistry Laboratory I (Undergraduate Research): summer semester 2011, fall semester 2011, summer semester 2012, fall semester 2013, summer semester 2014, fall semester 2014, summer semester 2015, fall semester 2015, spring semester 2016, summer semester 2016, fall semester 2016, spring semester 2017
  7. Chemistry Laboratory II (Undergraduate Research): fall semester 2011, spring semester 2012, fall semester 2012, fall semester 2014
  8. Seminars in Chemistry (Level: Advanced Undergraduate/Graduate): fall semester 2011, spring semester 2012, fall semester 2012, spring semester 2013, fall semester 2013, spring semester 2014, fall semester 2014, spring semester 2015, fall semester 2015, spring semester 2016
  9. Directed Research in Chemistry: summer semester 2010, fall semester 2010, spring semester 2011, spring semester 2012, summer semester 2012, fall semester 2012, spring semester 2013, summer semester 2013, fall semester 2013, spring semester 2014, summer semester 2014, fall semester 2014, spring semester 2015, summer semester 2015, fall semester 2015, summer semester 2016, fall semester 2016, spring semester 2017

D.2 Training and Mentoring

Postdoctoral Scholars

Dr. Chunli Yan (current)
Dr. Ashutosh Shandilya (current)
Dr. Kathleen Carter (current)
Dr. Buddhadev Maiti (subsequently postdoc at Carnegie Mellon Univ.)
Dr. Carlo Guardiani (subsequently at the Univ. of Warwick, UK)

Graduate students

Thomas Dodd (current)
Jina Yu (current)
Kurt Martin (current)
Zhenyu Wang (current)

Dr. Kathleen Carter, completed a Ph.D. dissertation “Insights into the Association of Proteins and Small Molecules with the Minor Groove of DNA”
Bernard Scott, completed a M.S. thesis entitled “Computational Studies of Liver Receptor Homolog 1 in the Presence of Small Molecule Agonists: Allosteric Communication and Virtual Screening for New Potential Drug Candidates” (subsequently at the University of Utah)
Dr. Bradley R. Kossmann, completed a Ph.D. dissertation “Computational Investigations of Biomolecular Motions and Interactions in Genomic Maintenance and Regulation” (subsequently employed as a Senior Data Scientist at 360i company in Atlanta, GA)
Dr. Xiaojun Xu, completed a Ph.D. dissertation “Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Interacting Enzymes” (subsequently ORISE Fellow at the CDC and fellow at the La Jolla Institute of Allergy and Immunology)
Shih-Wei Chuo, completed a M.S. thesis entitled “Discovery of Potent Tyrosyl-DNA Phosphodiesterase 1 Inhibitors Using in silico Virtual Screening & Network Analysis for Evolution of Allosteric Communication in 3-ketosteroid Receptors” (subsequently at the University of California, Davis)
Stephanie Kofsky, graduated with a M.S. degree and accepted position at Kemira, Atlanta, GA
Patrick Chepaitis, graduated with a M.S. degree
Yang Zhen, graduated with a M.S. degree

Undergraduate student researchers

Fernando Cortez (spring/summer of 2010; hosted as McNair Scholar)
Amanuel Gebremariam (summer 2011; fall 2011; spring 2012)
Oladayo Agboola (fall 2011; spring 2012)
Bao-Khanh Ho (fall 2011)
Syiedah Korre (fall 2011)
Yosef Mekuria (summer and fall 2012)
Evan Sinyard (fall 2013)
Albertha Sabree (summer 2014; NSF REU program trainee)
Eric Zientowski (summer, fall 2014)
Zachary Ferris (fall, 2014)
Annie Yoon (fall, 2015)
Zacharia Robow (summer, fall 2015)
Thomas Dodd (fall 2015, spring 2016)
Lily Vassileva (fall 2016, spring 2017, summer 2017)
Nicole Ogbomoh (summer 2016, fall 2016)
Sam Delmerico (spring 2017, summer 2017)
Maia Wells (summer 2017)

Student Awards

Molecular Basis of Disease Doctoral Fellowship to Xiaojun Xu
Dean’s Doctoral Fellowship to Kathleen Carter
National XSEDE (Extreme Science and Engineering Discovery Environment) Scholarship to Bernard Scott)
Molecular Basis of Disease Doctoral Fellowship to Tom Dodd
Molecular Basis of Disease Doctoral Fellowship to Bradley R. Kossmann
Molecular Basis of Disease Travel Fellowship to Bradley R. Kossmann
Award for Outstanding Research at the Ph.D. level to Bradley R. Kossmann
Molecular Basis of Disease Outstanding Fellow Award to Bradley R. Kossmann
Hopkins Endowed Fellowship in Biophysical Chemistry to Tom Dodd
Molecular Basis of Disease Outstanding Fellow Award to Tom Dodd

E. SERVICE

2018              Panelist at the 2018 Scientific Computing Day at GSU
2017-2020    XSEDE Resource Allocation Committee (XRAC)
2017 Committee on Proposal Evaluation for Allocation of Supercomputing Time on the Special Purpose Anton Machine by D.E. Shaw Research
2017-2020 European Science Foundation (ESF) College of Expert Reviewers
2016 Ad hoc reviewer for NIH/CSR
2016-Present Reviewing Editor, Frontiers Journals in Physics, Physiology and Molecular Biosciences
2015-2017 Member of the University Senate, Georgia State University, Atlanta, GA
2015-2017 Member, Senate Admissions & Standards Committee, Georgia State University, Atlanta, GA
2015-2017 Member, Senate Planning & Development Committee, Georgia State University, Atlanta, GA
2014-Present Member, Computer Support Committee, Department of Chemistry, Georgia State University, Atlanta, GA
2014 Reviewer on the Genetics, Genomics, Proteomics panel of the NSF Graduate Research Fellowship Program (GRFP)
2013-Present Reviewer for regular NSF and NSF-CAREER proposals submitted to the MCB division of the National Science Foundation (Genetic Mechanisms Cluster)
2013 Assisted with the organization of the “Third International Conference on Chemical and Structural Biology of Nucleic Acids and Proteins for Novel Drug Discovery” (Sep. 13-15, 2013, Atlanta, USA).
2013 Panelist at an NSF-CAREER award workshop organized by University Research Services and Administration (URSA)
2011-2016 Coordinator for the Chemistry Department seminar series
2010-Present Library Liaison, Department of Chemistry, Georgia State University, Atlanta, GA
2009-Present Member, Petitions/Awards Committee, Department of Chemistry, Georgia State University, Atlanta, GA
2009-Present Member, Biophysical Chemistry Doctoral Preliminary Exam Committee, Department of Chemistry, Georgia State University, Atlanta, GA