Nicolae-Viorel (Vio) Buchete, Ph.D.

Vio BucheteCollege Lecturer:
Theoretical & Computational Nano-Bio Physics
Homepage 

Research Webpage @ UCD

 Contact info

Office: +353-(0)1-716-2088 (Physics)
             +353-(0)1-716-5310 (CASL/ACAM)
E-mail: buchete@ucd.ie
URL: http://buchete.googlepages.com

News

June 3 - 6, 2014: Applications are invited to attend our 2014 CECAM-IE Tutorial "Advances in Biomolecular Modelling and Simulations using CHARMM" to be held at the University College Dublin!!! [more info]

June 5 - 8, 2012: Applications are invited to attend our CECAM Tutorial "Advances in Biomolecular Modelling and Simulations using CHARMM" to be held at the University College Dublin!!! [more info]

January 2012: Certificate of Appreciation from the Publications Division of the American Chemical Society (ACS).
                                        

June 2011: Scholarships may become available during June/July 2011 for (post)graduate students in Nano-Bio Physics and  Simulation Science in  the UCD School of Physics. Candidates are strongly encouraged to submit via e-mail their CV and a brief statement of research interests, as soon as possible! Particular attention will be given to applicants with a Physics background interested in computational/theoretical research projects in systems biology, structural bioinformatics and/or atomistic and coarse-grained modeling of proteins and nucleic acids.

March 2011: American Institute of Physics: listed in the Top 20 J. Chem. Phys. Reviewers - 2010

January 2011: Our group joins the UCD Complex & Adaptive Systems Laboratory. Vio's lab is relocated to the 3rd floor of the CASL Building. Come and visit us there!

April 30 - May 2, 2009: Applications are invited to attend our ACAM-CECAM workshop "Frontiers in Biomolecular Aggregation: Experiments, Applications and Simulations" to be held at the Univ. College Dublin Conway Institute of Biomolecular and Biomedical Research!!! [more info

Research Interests

    Theoretical and computational nanoscience, biophysics and chemical physics

    Statistical mechanics and molecular dynamics of biomolecular systems

    Systems biology and structural bioinformatics

    Multi-scale modeling of biomolecules and complex fluids

Education

Publications: Research Articles 

  1. Berezhkovskii, A.M., Murphy, R.D., and Buchete, N.V., " Network random walk model of two-state protein folding: Test of the theory", J. Chem. Phys., 138, 036101 (2013). [DOI Link, PDF]
  2. Tofoleanu, F., and Buchete, N.V., "Molecular interactions of Alzheimer's Aβ protofilaments with lipid membranes", J. Mol. Biol., 421:572-586 (2012). [DOI Link, PDF]
  3. Tofoleanu, F., and Buchete, N.V., "Alzheimer's Aβ peptide interactions with lipid membranes: Fibrils, oligomers and polymorphic amyloid channels", Prion, 6:1-7 (2012). [DOI Link, Free PDF]
  4. Buchete, N.V., "Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations", Biophys. J., 103:1411-1413 (2012). [DOI Link, PDF]
  5. Murphy, R.D., Conlon, J., Mansoor, T., Luca, S., Vaiana, S.M. and Buchete, N.V., “Conformational dynamics of human IAPP monomers”, Biophys. Chem., 167:1-7 (2012). [DOI Link, PDF]
  6. Berezhkovskii, A.M., Tofoleanu, F., and Buchete, N.V., "Are peptides good two-state folders?", J. Chem. Theory Comput., 7:2370-2375 (2011). [DOI Link, PDF]
  7. Buchner, G.S., Murphy, R.D., et al., "Dynamics of protein folding: Probing the kinetic network of folding-unfolding transitions with experiment and theory", Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, 1814:1001-1020 (2011). [DOI Link, PDF]
  8. E. Rosta, N.V. Buchete and G. Hummer, “Thermostat artifacts in replica exchange molecular dynamics simulations”, J. Chem. Theory Comput., 5:1393-1399 (2009). [DOI Link, Request PDF]
  9. N.V. Buchete and G. Hummer, "Coarse master equations for peptide folding dynamics, J. Phys. Chem. B, 122:6057-6069 (2008). [Full Text/Abstract, Request PDF]
  10. R.B. Best, N.V. Buchete and G. Hummer, "Are current molecular dynamics force fields too helical?," Biophys. J., 95:L07-L09 (2008); [Full Text/Abstract, Request PDF]
  11. N.V. Buchete and G. Hummer, "Peptide folding kinetics from replica exchange molecular dynamics," Phys. Rev. E, 77:030902 (2008). [DOI Link, Request PDF]
  12. N.V. Buchete, J.E. Straub and D. Thirumalai, "Dissecting contact potentials for proteins: Relative contributions of individual amino acids," Proteins: Structure, Function and Bioinformatics 70:119-130 (2008). [Full Text/Abstract, PubMed, PDF]
  13. N.V. Buchete and G. Hummer, "Structure and dynamics of parallel β-sheets, hydrophobic core, and loops in Alzheimer's Aβ fibrils," Biophys. J. 92:3032-3039 (2007). [Free Full Text] 
  14. A.L. Milac, N.V. Buchete, T.A. Fritz, G. Hummer and L.A. Tabak, "Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2," J. Mol. Biol. 373:439-451 (2007). [Free Full Text]
  15. N.V. Buchete, R. Tycko and G. Hummer, "Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments," J. Mol. Biol. 353:804-821, (2005). [Full Text/Abstract, Request PDF]
  16. N.V. Buchete, J.E. Straub and D. Thirumalai, "Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis," J. Mol. Graph. Model.22:441-450, (2004). [Full Text/Abstract, Download PDF]
  17. N.V. Buchete, J.E. Straub and D. Thirumalai, "Development of novel statistical potentials for protein fold recognition", Curr. Opin. Struct. Biol. 14:225-232, (2004). [Full Text/Abstract, Download PDF]
  18. N.V. Buchete, J.E. Straub and D. Thirumalai, "Orientational potentials extracted from protein structures improve native fold recognition", Protein Sci. 13:862-874, (2004). [Free Full Text, Download PDF]
  19. N.V. Buchete, J. E. Straub, and D. Thirumalai, "Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases," Polymer 45:597-608 (2004). [Download PDF]
  20. N.V. Buchete, J. E. Straub and D. Thirumalai, "Aniostropic coarse-grained statistical potentials improve the abilitiy to identify nativelike protein structures," J. Chem. Phys. 118:7658-7671 (2003). [arXiv:physics/0302009, Download PDF]
  21. N.V. Buchete and J. E. Straub, "Mean first-passage time calculations for the coil-to-helix transition: The active helix Ising model," J. Phys. Chem. B 105:6684-6697 (2001). [Download PDF]
  22. V. Melnig, D. Romanescu, N.V. Buchete and P.T. Frangopol, "Dynamic analysis possibilities of an electrochemical interface. The Ni/H2SO4 system," Revue Roumaine de Chimie 42:659-668 (1997). [Download PDF]
  23. C. Cotrutz, N.V. Buchete, G. Abusan and P.T. Frangopol, "A new method for the analysis of ECG signals using nonlinear dynamic systems theory," Medizinische Physik, 416-417 (1995). [Download PDF]
  24. N.V. Buchete, A. Dasu, I. Andricioaei and P.T. Frangopol, "A nonlinear dynamic systems theory approach to biological potential oscillations," Biophysics of Membrane Transport - School Proceedings, pt. II, 201-202 (1994). [Request PDF]

Publications: Book Chapters and Book Reviews

  1. N.V. Buchete, J.E. Straub and D. Thirumalai, "On the development of coarse-grained protein models: Importance of relative side chain orientations and backbone interactions," chapter 10 in "Coarse-Graining of Condensed Phase and Biomolecular Systems". USA: CRC Press. (2009). [Request PDF]
  2. N.V. Buchete, "Chemical kinetics and reaction dynamics (by S.K. Upadhyay): Book Review," J. Stat. Phys. 129:407-408 (2007). [Full Text/Abstract, Request PDF] 
  3. N.V. Buchete, "The art of molecular dynamics simulation (by D.C. Rapaport): Book Review," J. Stat. Phys. 118:365-367 (2005). [Full Text/Abstract, Request PDF]

Recent Talks & Poster Presentations

  • Jun. 5-8, 2012, ACAM-CECAM Tutorial "Advances in Biomolecular Modelling and Simulations using CHARMM" , UCD, Ireland, co-organizer
  • May 7-10, 2012, NIH CHARMM Tutorial, Bethesda, MD, oral presentation, co-organizer
  • Apr. 26, 2012, LCB Seminar, NHLBI, NIH, Rockville, MD, oral presentation
  • Mar. 25-29, 2012, 238th ACS National Meeting, San Diego, CA, oral presentation
  • Mar. 8, 2012, KCL Physics Seminar, King’s College London, invited oral presentation
  • August 16-20, 2009, oral presentation, 238th ACS National Meeting , Washington, DC
  • February 28 - March 4, 2009, 53rd Biophysical Society Annual Meeting, Boston, MA, co-chair of platform session on Protein Dynamics 
  • February 2-6, 2008, 52nd Biophysical Society Annual Meeting, Long Beach, CA, co-chair of platform session on Protein Dynamics 
  • January 6-11, 2008, Gordon Research Conference on Protein Folding Dynamics, Ventura, CA 
  • August 2007, "Coarse-grained master equations for peptide folding kinetics", oral presentation, 229th ACS National Meeting , Boston, MA
  • March 2007, "Exploring the structural stability and the mechanism of dissociation of Alzheimer's amyloid fibrils", oral presentation, 51st Biophysical Society Annual Meeting, Baltimore, MD
  • June 2006, "Contributions of parallel beta-sheets, hydrophobic core, and hydrophilic loops to the stability of Alzheimer's beta-amyloid fibrils", Gordon Research Conference on Biopolymers, Newport, RI
  • January 2006, "Structural stability and conformational dynamics of Alzheimer's beta-amyloid protofilaments", invited oral presentation, NIH Structural Biology Interest Group (SBIG), 2nd annual Postdoctoral SBIG Symposium, NIH, Bethesda, MD
  • January 2006, "Structural stability and conformational dynamics of Alzheimer's beta-amyloid protofilaments", Gordon Research Conference on Protein Folding Dynamics, Ventura, CA
  • October 2005, "Structure and stability of  Alzheimer's amyloid beta-peptide protofilaments", NIH Research Festival, Bethesda, MD
  • April 2005, "Molecular structures of Alzheimer's beta-amyloid protofilaments", NIH  symposium "Frontiers in Computational Biophysics" in honor of the 75th anniversary of Prof. Martin Karplus, Bethesda, MD 
  • March 2005, "Molecular dynamics simulations of amyloid fibrils", oral presentation, Computational Biophysics Section, Laboratory of Biophysical Chemistry, NIH, NHLBI, Bethesda, MD 
  • March 2005, "Molecular dynamics simulations of amyloid fibrils", oral presentation, 229th ACS National Meeting, San Diego, CA

Professional and Teaching Experience

Awards