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

 Contact info

University College Dublin
School of Physics, Room 111
Belfield, Dublin 4, IRELAND

Fax: +353-(0)1-283-7275

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 5 - 8, 2012: Applications are invited to attend our ACAM-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

Postdoctoral Research Fellow, Lab. of Chemical Physics, NIDDK, NIH, Bethesda, MD, 2003-8


Ph.D., Theoretical Chemistry and Biophysics, Boston University, Boston, MA, 2003 (M.A., 1998)


M.Sc., Physics, Al.I. Cuza University, Iasi, Romania, 1996 (B.Sc., Physics, 1995)


Postgraduate Certificate in Medical Physics, TEMPUS European Programme, Univ. of Patras, Greece, 1995-6

Publications: Research Articles 

1. Tofoleanu, F., and Buchete, N.V., "Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes", J. Mol. Biol., (2012, in press). [DOI Link, Request PDF]
2. 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, Request PDF]
3. Buchner, G.S., 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, Request PDF]
4. 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]
5. 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]
6. 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]
7. N.V. Buchete and G. Hummer, "Peptide folding kinetics from replica exchange molecular dynamics," Phys. Rev. E, 77:030902 (2008). [DOI Link, Request PDF]
8. 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, Request PDF]
9. 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] 
10. 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]
11. 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]
12. 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]
13. 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]
14. 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]
15. 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]
16. 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]
17. 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]
18. 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]
19. 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]
20. 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

• 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