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 (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 (1999)
Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA

B.S. in Chemistry (1996)
Department of Chemistry, Sofia University, Sofia, Bulgaria

B. PROFESSIONAL APPOINTMENTS

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. RESEARCH

C.1 Publications (65 publications, cited >3417 times in Google Scholar, h-index 34)

  1. Bralić, A., Tehseen, M., Sobhy, M.A., Tsai, C-L., Alhudhali, L., Yi, G., Yu, J., Yan, C., Ivanov, I. , Tsutakawa, S.E., Tainer, J.A. & Hamdan, S.M. A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. (2022) Nucleic Acids Research,  doi:10.1093/nar/gkac1095 (chosen as breakthrough article)
  2. Yan, C., Dodd, T., Yu, J., Leung, B., Xu, J., Oh, J., Wang, D. & Ivanov, I.* Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. (2021) Nature Communications, 12, 7001, doi:10.1038/s41467-021-27295-4 (highlighted by the Oak Ridge Leadership Computing Facility)
  3. Dodd, T., Yao, X., Hamelberg, D. &Ivanov I.* Subsets of adjacent nodes (SOAN): A fast method for computing suboptimal paths in protein dynamic networks. (2021) Molecular Physics, 119, 19-20, doi:10.1080/00268976.2021.1893847 (Invited article for the Michael L. Klein special issue)
  4. 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) Nature Communications 11, 5379, doi:10.1038/s41467-020-19165-2 (highlighted by the Oak Ridge Leadership Computing Facility)
  5. Tsutakawa, S.E., Tsai, C-L., Yan, C., Bralić, A., Chazin, W.J., Hamdan, S.M., Schärer, O.D., Ivanov, I.&Tainer, J.A.Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. (2020) DNA Repair, 96, 102972, doi:10.1016/j.dnarep.2020.102972
  6. Qian, K., Yan, C., Su, H., Dang, T., Zhou, B., Wang, Z., Zhao, X., Ivanov, I.& Zheng, Y.G. Pharmacophore-based screening of diamidine small molecule inhibitors for protein arginine methyltransferases. RCS Medicinal Chemistry(2020),doi:10.1039/D0MD00259C
  7. 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),117, 17747-17756, doi:10.1073/pnas.2006231117
  8. 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, 2470–2483doi:10.1021/acs.jcim.0c00087
  9. 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)
  10. 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), 431, 2493-2510, doi:10.1016/j.jmb.2019.04.035
  11. Carter, E.K., Laughlin-Toth, S., Dodd, T., Wilson, D.W. & Ivanov, I.*Small molecule binders recognize DNA microstructural variations via an induced fit mechanism. Physical Chemistry Chemical Physics (2019) 21, 1841-1851, doi:10.1039/C8CP05537H
  12. 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) 115, 5974-5979, doi:10.1073/pnas.1803323115
  13. Li, J., Li, S., Guo, J., Li, Q., Long, J., Ma, C., Ding, Y., Yan, C., Li, L., Wu, Z., Zhu, H., Li, K., Wen, L., Zhang, Q., Xue, Q., Zhao, C., Liu, N., Ivanov, I., Luo, M., Xi, R., Long, H., Wang, P.W. & Chen, Y. Natural product Micheliolide (MCL) irreversibly activates pyruvate kinase M2 and suppresses leukemia.Journal of Medicinal Chemistry(2018)61, 4155–4164, doi:10.1021/acs.jmedchem.8b00241
  14. Han, Y., Yan, C., Fishbain, S., Ivanov, I.& He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018) 4, 40,doi:10.1038/s41421-018-0044-z
  15. 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
  16. 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 (recommended by Faculty of 1000 Prime)
  17. Zhang, J., Qian, K., Yan, C., He, M., Jassim, B., Ivanov, I.& Zheng, Y. Discovery of decamidine as a new and potent PRMT1 inhibitor. Medicinal Chemistry Communications(2017)8, 440-444, doi:10.1039/C6MD00573J
  18. 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
  19. 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 >200 times)
  20. 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
  21. 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
  22. 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)
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. Xu, X., Guardiani, C., Yan, C. & Ivanov, I.* Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1Nucleic Acids Research(2013) 41, 10020-10031, doi:10.1093/nar/gkt810
  31. 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
  32. 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
  33. Ivanov, I.* Enzyme cofactors: Double-edged sword for catalysis. Nature Chemistry(2013) 5, 6-7, doi:10.1038/nchem.1529
  34. 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)
  35. 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
  36. 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)
  37. 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 Facilityat http://www.olcf.ornl.gov/2011/11/09)
  38. 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
  39. 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
  40. 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 (recommended byFaculty of 1000 Prime)
  41. 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)
  42. 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
  43. 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)
  44. 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)
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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 (Faculty of 1000 Prime recommended)
  52. 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
  53. 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
  54. 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
  55. 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)
  56. Ivanov, I.Terascale ab initio molecular dynamics simulations of proton transfer and dissociation processes in chemical and biological systems. (2004) ProQuestAAI3152059
  57. 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
  58. 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
  59. 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
  60. 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 >350 times)
  61. 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
  62. 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
  63. 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 (cited >100 times)
  64. 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 corresponding author

C.2 Grants and Awards

C.2.1 Research Funding

  1. National Institute of Environmental Health Sciences R01 ES032786 (3/24/22 – 3/31/27); Title: “Integrative Modeling of Biomolecular Machinery in Nucleotide Excision Repair”; Role: Principal Investigator; Total cost: $2,082,459
  2. National Institute of General Medical Sciences R35 GM139382 (3/1/21 – 2/28/26); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation and DNA Repair”; Role: Principal Investigator; Total cost: $2,261,126
  3. National Science Foundation MCB-2027902 (8/1/20 – 7/31/24); Title: “Advanced Computational Modeling of Pathways for Epigenetic Regulation and Genome Maintenance”; Role: Principal Investigator; Total cost: $765,882
  4. National Cancer Institute P01 CA092584 (9/27/21 – 8/31/26); Title: “Structural Cell Biology of DNA Repair Machines”; Role: Investigator; Total cost: $424,780
  5. National Cancer Institute P01CA092584 (4/30/20 – 8/31/21);Title: “Structural Cell Biology of DNA Repair Machines”; Role: Subcontract PI; Total cost: $85,000
  6. National Institute of General Medical Sciences R01 GM110387 (9/1/15 – 8/31/21); Title: “Integrative Modeling of PCNA Assemblies Engaged in Genome Duplication and Repair”; Role: Principal Investigator; Total cost: $1,675,000
  7. Cleon C. Arrington Research Initiation Grant (7/1/18 – 6/30/19); Title: “Uncovering the Complex Interplay of DNA Repair and Epigenetic Regulation in Genome Maintenance”; Role: Principal Investigator; Total cost: $20,000
  8. National Institutes of Health R01GM126154; (4/1/18 – 12/31/21) Title: “Mechanism and Inhibition of Protein Arginine Methylation”; Role: Co-Investigator; Total cost:$160,000(to I.I.)
  9. National Science Foundation CAREER Award MCB-1149521 (5/1/12 – 4/30/18); Title: “Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Loaders”; Role: Principal Investigator; Total cost: $824,000
  10. National Institutes of Health R01 CA118113-06A1; (6/1/14 – 5/31/19) Title: “p68 and Ca-Calmodulin Interaction in Cell Migration”; Role: Co-Investigator; Direct cost: $40,000(to I.I.)
  11. Cleon C. Arrington Research Initiation Grant (2/1/11 – 6/30/12); Title: “Modeling Assemblies and Interactions in Eukaryotic Clamp Loading”; Role: Principal Investigator; Total cost: $10,000

C.2.2 Computational Support at the National Supercomputing Facilities 

  1. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award (1/1/22 – 12/31/22); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation”; Role: Principal Investigator; Awarded 190,000 service units at the Oak Ridge Leadership Computing Facility. The value of an INCITE award for a single project typically exceeds a million dollars.
  2. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award (1/1/21 – 12/31/21); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation”; Role: Principal Investigator; Awarded 260,000 service units (>25 million CPU hours and 3,000,000 GPU hours) at the Oak Ridge Leadership Computing Facility.
  3. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award (1/1/20 – 12/31/20); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation”; Role: Principal Investigator; Awarded 260,000 service units (>25 million CPU hours and 3,000,000 GPU hours) at the Oak Ridge Leadership Computing Facility.
  4. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award (1/1/2019 – 12/31/19); Title: “Advanced Computational Modeling of Molecular Machines in Gene Regulation”; Role: Principal Investigator; Awarded 220,000 service units (>25 million CPU hours) at the Oak Ridge Leadership Computing Facility. The INCITE Award provided access to Summit, rated at the time the most powerful supercomputer in the world.
  5. NSF/XSEDE program CHE110042 (4/1/19 – 3/31/20); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 2,154,00 CPU hours at the Texas Advanced Computing Center. The value of the awarded resources is $34,942.
  6. NSF/XSEDE program CHE110042 (10/1/17 – 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.
  7. ERCAP DOE Award (1/7/18 – 1/5/19); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 1,000,000 CPU hours at the National Energy Research Scientific Computing Center.
  8. ERCAP DOE Award (1/7/17 – 1/5/18); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 6,000,000 CPU hours at the National Energy Research Scientific Computing Center.
  9. NSF/XSEDE program CHE110042 (4/1/16 – 9/3/17); 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.
  10. ERCAP DOE Award (1/7/16 – 1/5/17); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 3,600,000 CPU hours at the National Energy Research Scientific Computing Center.
  11. NSF/XSEDE program CHE110042 (10/1/14 – 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.
  12. ERCAP DOE Award (1/7/15 – 12/31/15); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 2,200,000 CPU hours at the National Energy Research Scientific Computing Center.
  13. 2013 ASCR Leadership Computing Challenge Award (7/1/2013 – 12/31/2014); Title: “Exploring the Chemical Landscape for Base Excision DNA Repair”; Role: Principal Investigator; Awarded 3,000,000 CPU hours at the National Energy Research Scientific Computing Center.
  14. ERCAP DOE Award (1/7/14 – 1/5/15); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 4,000,000 CPU hours at the National Energy Research Scientific Computing Center.
  15. NSF/XSEDE program CHE110042 (10/1/12 – 12/31/13); Title: “Integrative Modeling of Complex Biological Assemblies”; Role: Principal Investigator; Awarded 4,726,000 CPU hours
  16. ERCAP DOE Award (1/7/12 – 1/5/13); Title: “Integrative Modeling of Protein/DNA Complexes at the Replication Fork”; Role: Principal Investigator; Awarded 2,000,000 CPU hours at the National Energy Research Scientific Computing Center.
  17. NERSC Initiative for Scientific Exploration (NISE) Award (5/1/11 – 4/30/12); Title: “An Integrative Strategy to Model Complex Biological Assemblies”; Role: Principal Investigator; Awarded 960,000 CPU hours at the National Energy Research Scientific Computing Center.
  18. Computational time on the special purpose Anton machine at the National Resource for Biomedical Supercomputing (NRBSC) in Pittsburgh (9/1/11 – 6/30/12); Title: “Modeling connexin hemichannels important for intercellular communication”; Role: Principal Investigator; Awarded 50,000 CPU hours
  19. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) Award BIP007 (1/1/09–12/31/10); 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 at the Oak Ridge Leadership Computing Facility.

C.2.3 Honors and Awards (selected) 

  1. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) award from the Department of Energy Office of Science(2019 – 2022)
  2. Cleon C. Arrington Research Initiation Grant from Georgia State University (2018)
  3. ASCR Leadership Computing Challenge Award from the Department of Energy Office of Science (2013)
  4. Dean’s Early Career Award from Georgia State University (2013)
  5. CAREER Award from the National Science Foundation (2012)
  6. NERSC Initiative for Scientific Exploration (NISE) Award from the Department of Energy Office of Science (2011)
  7. Cleon C. Arrington Research Initiation Grant from Georgia State University (2011)
  8. Innovative and Novel Computational Impact on Theory and Experiment (INCITE) award from the Department of Energy Office of Science(2010)
  9. La Jolla Interfaces in Science Postdoctoral Fellowship, Burroughs Wellcome Fund (2005– 2007)
  10. Chemical Computing Group Excellence Award from the American Chemical Society (2003)
  11. Chemistry Department Chairman’s Award from the University of Pennsylvania (2000)
  12. Chemistry Department Teaching Award from Carnegie Mellon University (1999)

C.3 Recognition and Media Coverage

  1. Coverage of a publication in Nature Communications (2021), doi:10.1038/s41467-021-27295-4; Featured on the website of the Oak Ridge Leadership Computing Facility in a news story “Decoding the Role of CSB Protein in DNA Repair”.
  2. Coverage of a publication in Nature Communications(2020), doi:10.1038/s41467-020-19165-2; Altmetric score 16. Featured on the website of the Oak Ridge Leadership Computing Facility in a news story “Simulations Reveal Nature’s Design for Error Correction During DNA Replication”.
  3. Coverage of a publication in Nature Structural & Molecular Biology(2019), doi:10.1038/s41594-019-0220-3; Altmetric score 63. The article is in the 96thpercentile(ranked 4,371st) of the 118,590 tracked articles of a similar age in all journals and in the 85thpercentile(ranked 2nd) of the 14 tracked articles of a similar age in Nature Structural & Molecular Biology. Featured on the website of the Oak Ridge Leadership Computing Facility in a news story “Summit Charts a Course to Uncover the Origins of Genetic Diseases”.
  4. Coverage of a publication in 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, Primeur Magazine, HealthNewsDigest.com, Newswise and Publicnow.
  5. Coverage of a publication in Nature(2016), doi:10.1038/nature17970; Altmetric score 135. The article is in the 98thpercentile(ranked 3,654th) of the 227,366 tracked articles of a similar age in all journals and in the 60thpercentile(ranked 388th) of the 975 tracked articles of a similar age in Nature. Highlighted by the Science360site and the MCB Division of the National Science Foundation, Phys.org, Technology.org, e!Science News, Nanowerk, Bioportfolio, EurekAlert!, NewswiseandScience Dailyamong other media sources. Highlighted by the Texas Advanced Computing Center in a news story “How to See Living Machines”.
  6. Coverage of a publication in Nature Communications(2016), doi:10.1038/ncomms11675; Altmetric score 201. The article is in the 99thpercentile(ranked 1,781st) of the 190,421 tracked articles of a similar age in all journals and in the 94thpercentile(ranked 37th) of the 713 tracked articles of a similar age in Nature Communications.
  7. Coverage of a publication in Proceedings of the National Academy of Sciences (2016), doi:10.1073/pnas.1518960113; Altmetric score 51. The article is in the 96thpercentileof the 252241 tracked articles of a similar age in all journals and in the 76thpercentile(ranked 238) of the 1024 tracked articles of a similar age in PNAS. Highlighted by ScienceDaily, Health Medicine Network, PhysOrg.comand EurekAlert!among other media sources.
  8. Coverage of a publication in Proceedings of the National Academy of Sciences(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).
  9. Coverage of a publication in Nucleic Acids Research(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).
  10. Coverage of a publication in the Journal of the American Chemical Society(2010), doi:10.1021/ja100365x; Featured in a science highlight entitled “Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA” by the Oak Ridge Leadership Computing Facility (OLCF) of Oak Ridge National Laboratory (https://www.olcf.ornl.gov/2010/06/24/supercomputers-simulate-the-molecular-machines-that-replicate-and-repair-dna/).

C.4 Invited Presentations

  1. Molecular simulation sheds light on the mechanisms of transcription-coupled DNA repair. Biophysical and Biochemical Dynamics and Diffusion Symposium in Honor of J. Andrew McCammon, National Meeting of the American Chemical Society, San Diego, CA 2022
  2. Advanced computational modeling of molecular machines in transcription initiation. Department of Medicinal Chemistry, Ohio State University, Columbus, OH 2022
  3. Advanced computational modeling of molecular machines in transcription initiation. Department of Biochemistry & Molecular Biology, McGovern Medical School, University of Texas Health, Houston, TX 2021
  4. Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. 3rd Conference on Bio-motors, Virus Assembly, and RNA Nanobiotechnology, Ohio State University, Columbus, OH 2021
  5. Advanced computational modeling of molecular machines in transcription initiation. Chemistry Department Seminar Program, Georgia State University, Atlanta, GA 2021
  6. Advanced computational modeling of the molecular machines responsible for transcription initiation and nucleotide excision repair. Cellular and Molecular Biophysics (CMB) cluster of the Gulf Coast Consortium (GCC), 2021
  7. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling. Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy 2021
  8. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling. Fourth Fusion Conference: Dynamic Structures in DNA Damage Responses and Cancer, Nassau, Bahamas 2020
  9. 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
  10. 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
  11. DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG.Lawrence Berkeley National Laboratory, Berkeley, CA 2018
  12. Lesion search and base extrusion strategy of thymine DNA glycosylase.Third Fusion Conference: Dynamic Structures in DNA Damage Responses and Cancer, Cancun, Mexico 2018
  13. Modeling biological assemblies from low to near atomic resolution.Van’t Hoff Institute for Molecular Sciences, University of Amsterdam,Amsterdam, The Netherlands 2016
  14. 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
  15. 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
  16. 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
  17. Structurally distinct complexes of ubiquitin and SUMO-modified PCNA lead to distinct DNA damage response pathways. Lawrence Berkeley National Laboratory, Berkeley, CA 2014
  18. 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
  19. 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
  20. 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
  21. Proliferating cell nuclear antigen and its protein partners in DNA repair. Department of Biomolecular Sciences, University of Mississippi, Oxford, MS 2012
  22. Integrative modeling of protein/DNA complexes at the replication fork. Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN2012
  23. Integrative modeling of FEN1 complexes with the sliding clamps PCNA and Rad9-Hus1-Rad1. Mutagenesis Gordon Research Conference, Newport, RI 2012
  24. Solution phase X-ray scattering and multiscale computational modeling reveal the structural dynamics of ubiqutinated PCNA. Symposium in Honor of J. Andrew McCammon,243rdNational Meeting of the American Chemical Society, San Diego, CA 2012
  25. Integrative modeling of protein/DNA complexes at the replication fork. Center for Diagnostics and Therapeutics (CDT), Georgia State University, Atlanta, GA 2012
  26. Integrative modeling of protein/DNA complexes at the replication fork. Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 2011
  27. Integrative modeling of protein/DNA complexes at the replication fork. Conference on Computational Physics (CCP2011)2011
  28. Integrative modeling of protein/DNA complexes at the replication fork. Lawrence Berkeley National Laboratory, Berkeley, CA 2011
  29. 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
  30. 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
  31. 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
  32. 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
  33. The three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV.Protein Dynamics and Catalysis Conference, Tarrytown, NY 2008
  34. High performance computing in molecular simulation and computational structural biology.13thAnnual San Diego Supercomputer Center Summer Institute, La Jolla, CA 2007
  35. 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
  36. Insight into DNA repair systems from classical and ab initio molecular dynamics. Department of Chemistry,Columbia University, New York, NY 2007
  37. 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

C.5 Contributed Presentations (selected out of >70 presentations)

  1. Structural and dynamic determinants of Rad26-mediated DNA damage discrimination by RNA Polymerase II. Pacifichem 2021 – International Chemical Congress of the Pacific Basin Societies, Honolulu, Hawaii (delivered online), 2021
  2. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling, Pacifichem 2021 – International Chemical Congress of the Pacific Basin Societies, Honolulu, Hawaii (delivered online), 2021
  3. Advanced computational modeling of molecular machines involved in transcription initiation. National Meeting of the American Chemical Society, Atlanta, GA 2021
  4. Transcription initiation machinery functional dynamics and genetic disease. 257thNational Meeting of the American Chemical Society, Orlando, FL2018
  5. Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling. 256thNational Meeting of the American Chemical Society, Boston, MA 2018
  6. 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
  7. 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
  8. Electron microscopy and integrative modeling shed light on the structures of transcription pre-initiation complexes and the mechanisms of transcription initiation.Southeast Regional Meeting of the American Chemical Society (SERMACS), Charlotte, NC 2017
  9. 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
  10. Integrative modeling of macromolecular assemblies in gene regulation. Molecular Machines: Integrative Structural and Molecular Biology EMBO Conference,EMBL Heidelberg, Germany 2016
  11. Integrative modeling of macromolecular assemblies in gene regulation.5thZing Nucleic Acids Conference, Tampa, FL 2016
  12. Damage recognition and base extrusion strategies of DNA repair glycosylase enzymes. 251stNational Meeting of the American Chemical Society, San Diego, CA 2016
  13. Hybrid modeling of ubiquitin- and SUMO-modified PCNA complexes: Implications for DNA damage responses. 251stNational Meeting of the American Chemical Society, San Diego, CA 2016
  14. Structurally distinct ubiquitin- and SUMO-modified PCNA: Implications for their distinct roles in the DNA damage response. Albany 2015 Conference, Albany, NY 2015
  15. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes.4thZing Nucleic Acids ConferenceCancun, Mexico 2014
  16. Integrative modeling of protein assemblies involved in transcription. Biopolymers Gordon Research Conference, Newport, RI 2014
  17. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes. Annual Meeting of the Biophysical Society, San Francisco, CA 2014
  18. Integrative modeling of complex biological assemblies in DNA replication and transcription coupled repair. 246thNational Meeting of the American Chemical Society, Indianapolis, IN 2013
  19. Integrative modeling of ubiquitinated and SUMOylated PCNA complexes. Nucleic Acids Gordon Research Conference, Biddeford, ME 2013
  20. 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
  21. Electron microscopy and computational modeling reveal key structural aspects of the ternary assemblies of flap endonuclease 1 with sliding clamps and DNA. 243rdNational Meeting of the American Chemical Society, San Diego, CA 2012
  22. Integrative modeling of protein/DNA complexes at the replication fork. 243rdNational Meeting of the American Chemical Society, San Diego, CA 2012
  23. 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
  24. 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
  25. Multiple states of covalently bound ubiquitin on PCNA. Keystone meeting on DNA Replication and Recombination, Keystone, CO2011
  26. Multiple states of covalently bound ubiquitin on PCNA. Gordon Research Conference DNA Damage, Mutation & Cancer, Ventura, CA 2010
  27. 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
  28. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.24thAnnual Symposium of the Protein Society, San Diego, CA 2010
  29. Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.240thNational Meeting of the American Chemical Society, Boston, MA 2010
  30. Phosphoryl transfer in solution and in enzymatic active sites: Insights from ab initio molecular dynamics. Algorithms in Macromolecular Modeling (AM3) meeting, Austin, TX 2009
  31. 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

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, Frontiers in Molecular Biosciences

C.7 Recent Collaborations  

  1. Eva Nogales (UC-Berkeley)
  2. Yuan He (Northwestern University)
  3. Stephen J. Benkovic (Pennsylvania State University)
  4. Walter Chazin (Vanderbilt University)
  5. George Zheng (University of Georgia)
  6. Eric Ortlund (Emory University)
  7. Samir Hamdan (KAUST)
  8. Susan Tsutakawa (Lawrence Berkeley National Laboratory)
  9. John A. Tainer (University of Texas M.D. Anderson Cancer Center)
  10. Dong Wang (University of California, San Diego)
  11. David Wilson (Georgia State University)

C.8 SocietyMemberships

  1. American Chemical Society (since 1999)
  2. Biophysical Society (since 2004)
  3. Protein Society (since 2004)
  4. Sigma Xi (Full membership since 2004)

D. TEACHING AND MENTORING

 D.1 Courses Taught

  1. Physical Chemistry II (2010 – 2018; advanced undergraduate/graduate level)
  2. Quantum Chemistry (2019 – 2021; advanced undergraduate/graduate level; developed an online version of this course and taught it in 2020 and 2021)
  3. Physical chemistry I (2010 – 2019; advanced undergraduate/graduate level)
  4. Thermodynamics and Chemical Kinetics (2019 – 2020; advanced undergraduate/graduate level)
  5. Instrumental methods in Spectroscopy (2010 – 2015; advanced undergraduate laboratory)
  6. Biophysical Chemistry (2012 – 2020; graduate level; team taught with other biophysical division faculty)
  7. Seminars in Chemistry (2011 – 2016; advanced undergraduate/graduate level; formal course based on the Chemistry Department seminar program)
  8. Directed Research in Chemistry (2010-2020)
  9. Undergraduate Research in Chemistry (2010 – 2021)

D.2 Training and Mentoring

Postdoctoral Scholars

  1. Dr. Chunli Yan (current)
  2. Dr. Ashutosh Shandilya (current)
  3. Dr. Kathleen Carter (subsequently postdoc at Emory University)
  4. Dr. Buddhadev Maiti (subsequently postdoc at Carnegie Mellon University)
  5. Dr. Carlo Guardiani (subsequently at the University of Warwick, UK)

Graduate students

  1. Jina Yu (current)
  2. Thomas Dodd (Ph.D. awarded)
  3. Zhenyu Wang (M.S. awarded, subsequently obtained industry position in China)
  4. Dr. Kathleen Carter (Ph.D. awarded, subsequently Research Scientist at Emory University)
  5. Bernard Scott (M.S. awarded, subsequently Ph.D. at the University of Utah)
  6. Dr. Bradley Kossmann (Ph.D. awarded, subsequently Director of Data Science at Softcrylic Co.)
  7. Dr. Xiaojun Xu (Ph.D awarded, subsequently ORISE Fellow at the CDC and Research Scientist at UCSD)
  8. Shih-Wei Chuo (M.S. awarded, subsequently completed Ph.D. at the University of California, Davis)
  9. Stephanie Kofsky (M.S. awarded, subsequently at Kemira Co.)
  10. Patrick Chepaitis (M.S. awarded, subsequently scientist at GBI)
  11. Yang Zhen (M.S. awarded)

Undergraduates research advisees

Fernando Cortez (2010), Amanuel Gebremariam (2011­–2012), Oladayo Agboola (2011–2012), Bao-Khanh Ho (2011), Syiedah Korre (2011), Yosef Mekuria (2012), Evan Sinyard (2013), Albertha Sabree (2014), Eric Zientowski (2014), Zachary Ferris (2014), Annie Yoon (2015), Zacharia Robow (2015), Thomas Dodd (2015–2016), Lily Vassileva (2016–2017), Nicole Ogbomoh (2016), Sam Delmerico (2017), Maia Wells (2017-2018)

Student Awards

  1. Molecular Basis of Disease Doctoral Fellowship: Xiaojun Xu, Kurt Martin, Tom Dodd, Bradley Kossmann
  2. Molecular Basis of Disease Travel Fellowship: Bradley Kossmann
  3. Dean’s Doctoral Fellowship: Kathleen Carter
  4. National Extreme Science and Engineering Discovery Environment Scholarship: Bernard Scott
  5. Award for Outstanding Research at the Ph.D. level: Bradley Kossmann
  6. Molecular Basis of Disease Outstanding Fellow Award: Bradley Kossmann, Tom Dodd
  7. Hopkins Endowed Fellowship in Biophysical Chemistry: Tom Dodd

E. UNIVERSITY AND PROFESSIONAL SERVICE

  • 2020 – Present    Member, College of Arts & Sciences Promotion & Tenure Committee
  • 2018                    Panelist at the 2018 Scientific Computing Day at GSU
  • 2017 – Present    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 – Present     European Science Foundation (ESF) College of Expert Reviewers
  • 2016                      Ad hoc reviewer for the National Institutes of Health/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