Assistant Professor,
Departments of Computer Science and Physics,
660 McBryde (MC 0106), Virginia Tech
Telephone: 540-231-4237
E-mail @cs.vt.edu : alexey
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Publications
1. Goldfeld, M.G, Lobysheva, I., Mikoyan, M.D., Chernavskii, D.S., and Onuphriev A.V., ``ATP Synthesis By Free and Membrane-Bound H+ ATPase of the Chloroplasts in Conditions of a pH shift.", Biophysics 38, 1005 (1993). ABSTRACT
2. Alexey Onufriev and J.B. Marston, ``Memory Loss and Auger Processes in a Many-Body Theory of Charge Transfer", Phys. Rev. B. 53, 13340 (1996). PDF
3. Alexey Onufriev and J.B. Marston, ``Enlarged Symmetry and Coherence in Arrays of Quantum Dots", Phys. Rev. B., 59, 12573 (1999). PDF
4. Alexey Onufriev, D. Bashford and D.A. Case ``A Modification of the Generalized Born Model Suitable for Macromolecules", J. Phys. Chem., 104, 3712 (2000). PDF
5. Leduc SA, McAuley GA, Pentzell CB, Onufriev A, Lupton JH, Asllani I, Martin T. ``Physics passages and questions." In: MCAT in-class passage compendium. The Princeton Review: (2001). (textbook)
6. Alexey Onufriev, D.A. Case and G. M. Ullmann, `` A Novel View of pH Titration in Biomolecules", Biochemistry, (``New Concepts") 40, 3413 (2001). PDF
7. Alexey Onufriev, D. Bashford and D.A. Case, "Effective Born radii in the generalized Born approximation: The Importance of Being Perfect.", J. Comp. Chem. 23, 1297-1304 (2002). PDF
8. Alexey Onufriev, D.A. Case, and D. Bashford, "Structural details, pathways, and energetics of unfolding apomyoglobin.``, J. Mol. Biol. 325, 555-567 (2003). PDF
9. J. D. Hirst, S. Bhattacharjee, and Alexey Onufriev, Theoretical studies of time-resolved spectroscopy of protein folding", Faraday Discussions. 122, 253-267 (2003). PDF
10. H. T. Allawi, M. W. Kaiser, Alexey Onufriev, Wu-Po Ma, A. E. Brogaard, D. A. Case, B. P. Neri and V. I. Lyamichev, "Modeling of Flap Endonuclease Interactions with DNA Substrate", J. Mol. Biol. 328 , 537-554 (2003). PDF
11. Alexey Onufriev, A. Smondyrev, and D. Bashford, ``Proton Affinity Changes Driving Unidirectional Proton Transport in the Bacteriorhodopsin Photocycle", J. Mol. Biol. 232 , 1183-1193 (2003). PDF
12. Alexey Onufriev, D. Bashford and D.A. Case, "Exploring native states and large-scale conformational changes with a modified Generalized Born model.", Proteins, 55, 383-394 (2004). PDF
13. M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, C. L. Brooks, ``Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures", J. Comp. Chem , 468 , 96-111 (2004). PDF
14. A. Onufriev and G. M. Ullmann, "Decomposing Complex Ligand Binding into Simple Components: Connections between Microscopic and Macroscopic models", J. Phys. Chem. B., 108, 11157-11169 (2004). PDF
15. G. Sigalov, P. Scheffel, and A. Onufriev, "Incorporating variable dielectric environments into the generalized Born model", J. Chem. Phys., 122, (2005). PDF
16. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS and Onufriev A., "H++: a server for estimating pKas and adding missing hydrogens to macromolecules", Nucleic Acids Res. Jul 1;33:W368-71. (2005). PDF
17. David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods, "The Amber biomolecular simulation programs", J. Comp. Chem., 26, 1668-1688 (2005). PDF
18. G. Sigalov, A. Fenley, and A. Onufriev, "Analytical Linearized Poisson--Boltzmann Approach: Beyond the Generalized Born Approximation", J. Chem. Phys., 124, 124902 (2006) PDF
19. Myers J, Grothaus G, Narayanan S, Onufriev A, "A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules", Proteins, 63, 928-938 (2006). PDF
20. N. Saha, L. T. Watson, K. Kafadar, A. Onufriev, N. Ramakrishnan, C. Vasquez-Robinet, and J. Watkinson, ``A general probabilistic model of the PCR process'', Appl. Math. Comput., 182, 232--243, (2006)
21. J. Z. Ruscio and Alexey Onufriev, "A Computational Study of Nucleosomal DNA Flexibility", Biophys. J., 91, 4121-4132 (2006). PDF
22. N. Saha, L. T. Watson, K. Kafadar, N. Ramakrishnan, A. Onufriev, S. P. Mane, and C. Vasquez-Robinet, "Validation and estimation of parameters for a general probabilistic model of the PCR process'', J. Comput. Biology, 14, 102--117 (2007)
23. J. Mongan, C Simmerling, J.A. McCammon, D.A. Case, and A. Onufriev, `` Generalized Born Model with a Simple, Robust Molecular Volume Correction ", J. Chem. Theory and Comput., 3, 156-169 (2007). PDF
24. J. Mongan, A. Svrcek-Seiler, and A. Onufriev, ``Analysis of integral expressions for effective Born radii", J. Chem. Phys. 127, 185101 (2007). PDF
25. Ramu Anandakrishnan and Alexey Onufriev, ``Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules", Journal of Computational Biology, 15, 165-184 (2008).
26. Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. Murali, and Alexey V. Onufriev, ``Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin", Proceedings of the National Academy of Sciences, (USA), 15, 9204-9209 (2008).
27. Andrew T. Fenley, John C. Gordon, and A. Onufriev, ``An Analytical Approach to Computing Biomolecular Electrostatic Potential, I: Derivation and Analysis", Journal of Chemical Physics, (in press) (2008).
28. John C. Gordon, Andrew T. Fenley, and A. Onufriev, ``An Analytical Approach to Computing Biomolecular Electrostatic Potential, II: Validation and Applications", Journal of Chemical Physics, (in press) (2008).
29. A. Onufriev, ``Implicit Solvent Models in Molecular Dynamics Simulations", Annual Review of Computational Chemistry, (in press) (2008).