People » Alexander Balaeff


Dr. Alexander Balaeff received his Ph.D. in Physics from theUniversity of Illinois at Urbana-Champaign in 2002. He spent nine years as a postdoctoral associate in three different instutions [I.B.M. Thomas J. Watson Research Center, Yorktown Heights, NY (2003-2004), University of Illinois at Urbana-Champaign, Beckman Institute (2004-2005) and Duke University, Department of Chemistry (2005-2012)] before joining UCF in 2012, where he is an Assistant Professor since 2012.

DNA Origami etc.

Multiscale Modeling of Biomolecular Assemblies

Molecular Electronics

Biomolecular Structure and Dynamics under Applied Forces

1. Yuqi Zhang, Chaoren Liu, Alexander Balaeff, Spiros S. Skourtis, and David N. Beratan, “A Flickering Resonance Mechanism for Biological Charge Transfer”, Proceedings of the National Academy of Sciences, U.S.A.,111(28):10049-10054, 2014.

2. E. Wierzbinski, A. de Leon, X. Yin, A. Balaeff, K. Davis, S. Reppireddy, R. Venkatramani, S. Keinan, D. Ly, M. Madrid, D. Beratan, C. Achim, and D. Waldeck, Effect of Backbone Flexibility on charge Transfer Rates in Peptide Nucleic Acid Duplexes. Journal of the American Chemical Society, 134(22):9335–9342, 2012.

3. M. Wolack, A. Balaeff, S. Gutmann, H. Helmrich, R. Vosloo, M. Beerbom, E. Wierzbinski, D. Waldeck, S. Bezer, C. Achim, D. Beratan, and R. Schlaf, “Electronic structure of self-assembled peptide nucleic acid thin films”. Journal of Physical Chemistry C, 115(34):17123-17135, 2011.

4. A. Balaeff, S. Craig, and D. Beratan, “B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics”. Journal of Physical Chemistry A,Special Issue: David W. Pratt Festschrift, 115(34):9377-9391, 2011.

5. R. Venkatramani, S. Keinan, A. Balaeff, and D. Beratan, “Nucleic Acid Charge Transfer: Black, White, and Gray”. Coordination Chemistry Reviews, 255(7-8):635-648, 2011.

6. R. Venkatramani, K. Davis, E. Wierzbinski, S. Bezer, A. Balaeff, S. Keinan, A. Paul, L. Kocsis, D. Beratan, C. Achim, and D. Waldeck, “Evidence for a near-resonant charge transfer mechanism for double-stranded peptide nucleic acid”. Journal of the American Chemical Society, 133(1): 62-72, 2011.

7. S. Keinan, R. Venkatramani, A. Balaeff, and D. Beratan, “Is MD geometry sampling sufficient for nucleobase electronic structure analysis of ET reactions? Comparing classical MD and QM/MM methods”. Journal of Physical Chemistry C, 114(48):20496–20502, 2010.

8. D. Beratan, S. Skourtis, I. Balabin, A. Balaeff, S. Keinan, R. Venkatramani, and D. Xiao, “Steering electrons on moving pathways”. Accounts of Chemical Research, 42(10):1669-1678, 2009.

9. A. Paul, S. Bezer, R. Venkatramani, L. Kocsis, E. Wierzbinski, A. Balaeff, S. Keinan, D. Beratan, C. Achim, D. Waldeck, “Role of nucleobase energetics and nucleobase interactions in single stranded Peptide Nucleic Acid charge transfer”. Journal of the American Chemical Society, 131(18):6498-6507, 2009.

10. W. He, E. Hatcher, A. Balaeff, D. Beratan, M. Madrid, R. Gil, and C. Achim, “Solution structure of a Peptide Nucleic Acid from NMR data: Features and limitations”. Journal of the American Chemical Society, 130(40): 13264-13273, 2008.

11. E. Hatcher, A. Balaeff, S. Keinan, R. Venkatramani, D. Beratan, “PNA versus DNA: Effect of structural fluctuations on electronic structure and hole transport mechanisms”. Journal of the American Chemical Society, 130(35):11752-11761, 2008.

12. A. Balaeff, L. Mahadevan, and K. Schulten, “Modeling DNA loops using the theory of elasticity”. Physical Review E, 73:031919, 2006.

13. E. Villa, A. Balaeff, and K. Schulten, “Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation”. Proceedings of the National Academy of Sciences, USA, 102:6783-6788, 2005.

14. E. Villa, A. Balaeff, L. Mahadevan, and K. Schulten, “Multiscale method for simulating protein-DNA complexes”. Multiscale Modeling and Simulation, 2:527-553, 2004.

15. A. Balaeff, C. Koudella, L. Mahadevan, and K. Schulten, “Modeling DNA loops using continuum and statistical mechanics”, Philosophical Transactions of the Royal Society of London, Series A, “Mechanics of DNA” (theme issue), pp. 1355-1371, 2004.

16. A. Balaeff, L. Mahadevan, and K. Schulten, “Structural basis for cooperative DNA binding by CAP and lac repressor”. Structure, 12(1):123-132, 2004.

17. A. Balaeff, L. Mahadevan, and K. Schulten, “Elastic rod model of a DNA loop in the lac operon”, Physical Review Letters, 83(23):4900-4903, 1999.

18. A. Balaeff, M. Churchill, and K. Schulten, “Structure prediction of a complex between the chromosomal protein HMG-D and DNA”, PROTEINS, 30(1):113-135, 1998.

19. Y. Lysov, A. Chernyi, A. Balaev, F. Gnuchev, K. Beattie, and A. Mirzabekov, “DNA sequencing by contiguous stacking hybridization on modified oligonucleotide matrices”, Molecular Biology (Moscow), 29(1):62-66, 1995.

20. Y. Lysov, A. Chernyi, A. Balaeff, K. Beattie, and A. Mirzabekov, “DNA sequencing by hybridization to oligonucleotide matrix. Calculation of continuous stacking hybridization efficiency”, Journal of Biomolecular Structure and Dynamics, 11(4):797-812, 1994.

21. Y. Lysov, A. Chernyi, A. Balaev, F. Gnuchev, K. Beattie, and A. Mirzabekov, ”Sequencing efficacy of contiguous stacking hybridization on oligonucleotide matrices of variable tuple length”, Molecular Biology (Moscow), 28(4):544-548, 1994.

22. Y. Lysov, A. Chernyi, A. Balaev, K. Beattie, V. Florentiev, and A. Mirzabekov, “DNA sequence reconstruction from the data of contiguous stacking hybridization with oligonucleotide matrix”, Molecular Biology (Moscow), 27(5):698-704, 1993.

• UCF in-house research grant (2013)
• Conceptual and writing contributions to successful proposals for multi-million dollar collaborative
research grants:
• U. S. Department of Defense Multidisciplinary University Research Initiative (MURI) (2011) 2
• U. S. National Science Foundation Renewal Grant (2011)
• Co-PI on a Development Allocation from the NSF Teragrid Resource (2007)
• Participation in writing and editing of successful proposals for multi-million dollar research grants and large-scale awards of supercomputer time from the NSF, NIH, and private funding agencies (1995-2002)
• The Intl. Union of Biochemistry and Molecular Biology Young Scientist Travel Fellowship, 2000
• University of Illinois Student Travel Grant, 2000

Oversees the following Graduate Students