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| Dr. Nicolae-Viorel (Vio) Buchete is a College Lecturer of Theoretical & Computational Nano-Bio Physics in the UCD School of Physics. He has several postgraduate qualifications from universities in both the US (Boston University) and the EU (Al. I. Cuza University of Iasi, Romania, and University of Patras, Greece). Before moving to UCD, he was awarded his PhD from Boston University in 2003, and he held a postdoctoral research fellowship at the National Institutes of Health (Bethesda, MD) until 2008. His general research interests are in the areas of theoretical and computational nanoscience, biophysics and chemical physics. Ongoing research projects in his group at UCD are concerned with statistical mechanics and molecular dynamics of biomolecular systems, systems biology and structural bioinformatics, and with multiscale modeling of biomolecules and complex fluids.
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| Theoretical and computational nanoscience, biophysics and chemical physics Research WebpageNews:
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| Sponsor : University College Dublin (UCD) Title : Computational Nano-Bio Physics Start Date / End Date : 01-SEP-08 / 31-AUG-14 |
| Sponsor : University College Dublin (UCD) Title : Helix formation and helix-helix interactions in protein folding Start Date / End Date : 03-AUG-09 / 31-JAN-11 |
| Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : Theoretical and computational methods for studies of conformational transitions in biomolecules Start Date / End Date : 01-OCT-08 / 30-SEP-11 |
| Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : Multiscale Molecular Study of Protein Folding and Aggregation Processes Start Date / End Date : 01-OCT-08 / 30-SEP-11 |
| Sponsor : Irish Research Council for Science Engineering and Technology (IRCSET) Title : Computational Study of Structure, Dynamics and Activity of Amyloid Fibrils and Oligomers Start Date / End Date : 01-OCT-08 / 30-SEP-11 |
Buchete, N.V., Straub, J.E. and Thirumalai, D.; (2009) 'On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions' In: Gregory A. Voth (eds). Coarse-Graining of Condensed Phase and Biomolecular Systems. USA: CRC Press.  [Details] |
| Tofoleanu, F. and Buchete, N.V.; (2012) 'Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes'. Journal of Molecular Biology, 421 (4-5):572-586. [DOI] [Details] |
| Tofoleanu, F; Buchete, NV (2012) 'Alzheimer's Aβ peptide interactions with lipid membranes: Fibrils, oligomers and polymorphic amyloid channels'. Prion, 6 (4):339-345. [DOI] [Details] |
| Buchete, NV (2012) 'Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations'. Biophysical Journal, 103 :1411-1413. [DOI] [Details] |
| Murphy, R.D., Conlon, J., Mansoor, T., Luca, S., Vaiana, S.M. and Buchete, N.V. (2012) 'Conformational dynamics of human IAPP monomers'. Biophysical Chemistry, 167 :1-7. [DOI] [Details] |
| Berezhkovskii, A.M., Tofoleanu, F., and Buchete, N.V.; (2011) 'Are peptides good two-state folders?'. Journal Of Chemical Theory And Computation, 7 (8):2370-2375. [DOI] [Details] |
| Buchner, G.S., Murphy, R.D., et al.; (2011) 'Dynamics of protein folding: Probing the kinetic network of folding-unfolding transitions with experiment and theory'. Biochimica Et Biophysica Acta-Proteins and Proteomics, 1814 (8):1001-1020. [DOI] [Details] |
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| Rosta E., and Buchete, N.V. and Hummer, G.; (2009) 'Thermostat artifacts in replica exchange molecular dynamics simulations'. Journal Of Chemical Theory And Computation, 5 (5):1393-1399. [DOI] [Details] |
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| Buchete N.V., and G. Hummer.; (2008) 'Peptide folding kinetics from replica exchange molecular dynamics'. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), 77 (3). [DOI] [Details] |
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| Buchete N.V., and G. Hummer.; (2008) 'Coarse master equations for Peptide folding dynamics'. Journal of Physical Chemistry B, 112 (19):6057-6069. [DOI] [Details] |
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| Best R.B., Buchete N.V., and G. Hummer.; (2008) 'Are Current Molecular Dynamics Force Fields too Helical?'. Biophysical Journal, 95 (1):L07-L09. [DOI] [Details] |
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| Buchete N.V., and Straub J.E., and Thirumalai., D.; (2008) 'Dissecting contact potentials for proteins: relative contributions of individual amino acids'. Proteins, 70 (1):119-130. [DOI] [Details] |
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| Milac AL, Buchete NV, Fritz TA, Hummer G, and LA Tabak.; (2007) 'Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2'. Journal of Molecular Biology, 373 (2):439-451. [DOI] [Details] |
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| Buchete NV, and G Hummer.; (2007) 'Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils'. Biophysical Journal, 92 (9):3032-3039. [DOI] [Details] |
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| Buchete NV, Tycko R, and G Hummer.; (2005) 'Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments'. Journal of Molecular Biology, 353 (4):804-821. [DOI] [Details] |
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| Buchete NV, Straub JE, and D. Thirumalai.; (2004) 'Development of novel statistical potentials for protein fold recognition'. Current opinion in structural biology, 14 (2):225-232. [DOI] [Details] |
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| Buchete NV, Straub JE, and D. Thirumalai; (2004) 'Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis'. Journal of Molecular Graphics &Amp; Modelling, 22 (5):441-450. [DOI] [Details] |
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| Buchete NV, Straub JE, and D. Thirumalai.; (2004) 'Orientational potentials extracted from protein structures improve native fold recognition'. Protein Science, 13 (4):862-874. [DOI] [Details] |
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| Buchete NV, Straub JE, and D Thirumalai.; (2004) 'Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases'. Polymer, 45 (2):597-608. [DOI] [Details] |
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| Buchete NV, Straub JE, and D Thirumalai.; (2003) 'Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures'. The Journal of Chemical Physics, 118 (16):7658-7671. [DOI] [Details] |
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| Buchete NV, and JE Straub.; (2001) 'Mean First-Passage Time Calculations for the Coil-to-Helix Transition: The Active Helix Ising Model'. J. Phys. Chem. B, 105 (28):6684-6697. [DOI] [Details] |
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| Melnig V, Romanescu D, Buchete NV, and Frangopol PT.; (1997) 'Dynamic analysis possibilities of an electrochemical interface. The Ni/H2SO4 system'. Revue Roumaine De Chimie, 42 (8):659-668. [Details] |
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| Murphy, RD; Buchete, NV (2011) Probing the Kinetic Network of Folding-Unfolding Transitions in Proteins Biophysical Society 55th Annual Meeting; Biophysical Journal Baltimore, MD, , 05-MAR-11 - 09-MAR-11 , pp.536a-537a [DOI] [Details] |
| Buchete NV, Tofoleanu F; (2009) Comparative study of molecular structures and stability properties of amyloid fibrils Abstracts of Papers of the American Chemical Society [Details] |
| Leahy CT, Murphy RD, Buchete NV ; (2009) Theoretical and computational study of conformational transitions in helix-forming peptides Abstracts of Papers of the American Chemical Society [Details] |
| Murphy RD, Leahy CT, Buchete NV ; (2009) Helix formation and helix-helix interactions in protein folding Abstracts of Papers of the American Chemical Society [Details] |
| Tofoleanu F, Buchete NV; (2009) Nanoscale structural and stability properties of amyloid fibrils Abstracts of Papers of the American Chemical Society [Details] |
| Murphy, R.D. and Leahy, C.T. and Buchete, N.V.; (2009) Dynamics of Intra- and Inter-Helix Contact Formation Biophysical Society 53rd Annual Meeting; Biophysical Journal Boston, MA, , 28-FEB-09 - 04-MAR-09 , pp.427A-427A [DOI] [Details] |
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| C.A. Andrei, B. Vohnsen, and N.V. Buchete; (2009) Multiscale molecular modeling of collagen fibrils Nanotech2009, Houston, USA Houston, USA, , 03-MAY-09 - 07-OCT-09 [Details] |
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| Hummer G, Buchete NV, Best RB, et al.; (2008) Spatial and temporal coarse-graining in simulations of protein dynamics and complex formation Abstracts of Papers of the American Chemical Society [Details] | |||||||||
| Buchete NV, and G Hummer.; (2007) Exploring the structural stability and the mechanism of dissociation of Alzheimer's amyloid fibrils Biophysical Society Annual Meeting; Biophysical Journal Baltimore, MD, , pp.194A-194A [Details] |
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| Buchete NV, Tycko R, and G Hummer.; (2005) Molecular dynamics simulations of amyloid fibrils Abstracts of Papers of the American Chemical Society , pp.U742-U742 [Details] |
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| Buchete NV, Tycko R, and G Hummer.; (2004) Exploring the sequence space of beta-amyloid fibril forming peptides using threading and molecular dynamics Biophysical Society Annual Meeting; Biophysical Journal , pp.507A-507A [Details] |
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| Buchete NV, Straub JE, and D Thirumalai.; (2003) Effect of relative side chain orientations on the ability of statistical potentials to identify native-like structures of proteins Abstracts of Papers of the American Chemical Society , pp.U754-U755 [Details] |
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| Straub JE, Buchete NV, and D Thirumalai.; (2001) Protein threading using novel inter-residue contact potentials Biophysical Society Annual Meeting; Biophysical Journal , pp.557A-557A [Details] |
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| Cotrutz C, Buchete NV, Abusan G, and PT Frangopol.; (1995) A new method for the analysis of ECG signals using nonlinear dynamic systems theory . In: Jurgen Richter eds. Roentgen Gedachtnis Kongress, Deutschen Gesselschat fur Med. Physik Wurzburg, Germany, , 20-SEP-05 - 23-SEP-05 , pp.416-417 [Details] |
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| Buchete, N.V. et al.,; (1994) A nonlinear dynamic systems theory approach to biological potential oscillations Biophysics of Membrane Transport - School Proceedings, pt. I, 12th School on Biophysics of Membrane Transport [Details] | |||||||||
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| Buchete NV; (2007) Chemical Kinetics and Reaction Dynamics (by S.K. Upadhyay). Journal of Statistical Physics: Book Reviews [DOI] [Details] |
| Buchete NV; (2005) The art of molecular dynamics simulation (by D.C. Rapaport). Journal of Statistical Physics: Book Reviews [DOI] [Details] |
| Year: 2012. Title: Certificate of Appreciation from the Publications Division of the American Chemical Society (ACS) |
| Year: 2011. Title: Top 20 JCP Reviewer for 2010, AIP, http://jcp.aip.org/top_20_reviewers_for_2010 |
| Year: 2008. Title: Univ. College Dublin Seed Funding Award - Dissemination & Outputs, http://www.ucd.ie/research/schemes/seedfunding08/2008_R2_DisOut.htm |
| Year: 2007. Title: NIH Fellows Award for Research Excellence (FARE2007) |
| Year: 2006. Title: NIH Fellows Award for Research Excellence (FARE2006), http://felcom.nih.gov/FARE |
| Year: 2003. Title: ACS Chemical Computing Group Excellence Award, http://www.acscomp.org/Awards/CCG/ccg.html |
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| Year: 2001. Title: Feldman Award, http://www.bu.edu/chemistry/gradprograms/awards.html |
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| Year: 2000. Title: Sugata Ray Memorial Award, http://www.bu.edu/chemistry/gradprograms/awards.html |
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| Year: 2000. Title: Sigma Xi, Graduate Research Award at Science Day 2000, BU, http://sigmaxi.org |
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| Year: 1998. Title: Dean's Award for Research, Science Day, http://web.bu.edu/research/spotlight/scienceday |
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| Year: 1998. Title: Outstanding Teaching Fellow Award, http://www.bu.edu/chemistry/gradprograms/awards.html |
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| Association: American Physical Society, Function/Role: Member |
| Association: Amercian Chemical Society, Function/Role: Member |
| Association: Biophysical Society, Function/Role: Member |
| Association: Sigma Xi, The Scientific Research Society, Function/Role: Member |
| Buchete NV; (2008) co-chair of platform session on Protein Dynamics. [Chaired Session], \i 52nd Biophysical Society Annual Meeting, Long Beach, CA000, Long Beach, CA , 02-FEB-08 - 06-FEB-08. |
| Buchete NV, and G Hummer.; (2008) Peptide folding dynamics from REMD. [Poster Presentation (Refereed)], Gordon Research Conference on Protein Folding Dynamics, Ventura, CA, Ventura, CA , 06-JAN-08 - 11-JAN-08. |
| Buchete NV, and G Hummer.; (2007) Coarse-grained master equations for peptide folding kinetics. [Oral Presentation], 229thACS National Meeting , Boston, MA, Boston, MA , 20-AUG-07 - 24-AUG-07. |
| Buchete NV, and G Hummer.; (2007) Exploring the structural stability of Alzheimer's amyloid fibrils. [Oral Presentation], \i 51st Biophysical Society Annual Meeting0 , Baltimore, MD, Baltimore, MD , 04-MAR-07 - 07-MAR-07. |
| Buchete NV and G Hummer; (2006) Contributions of parallel beta-sheets, hydrophobic core, and hydrophilic loops to the stability of Alzheimer's beta-amyloid fibrils. [Poster Presentation (Refereed)], \i Gordon Research Conference on Biopolymers0 , Newport, RI, Newport, RI , 11-JUN-06 - 16-JUN-06. |
| Buchete NV and G Hummer; (2006) Structural stability and conformational dynamics of Alzheimer's beta-amyloid protofilaments. [Invited Oral Presentation], \i NIH Structural Biology Interest Group (SBIG), 2nd annual Postdoctoral SBIG Symposium,0 NIH, Bethesda, MD, NIH, Bethesda, MD , 10-JAN-06 - 10-JAN-06. | |||||||||
| Buchete NV and G Hummer; (2006) Structural stability and conformational dynamics of Alzheimer's beta-amyloid protofilaments. [Poster Presentation (Refereed)], \i Gordon Research Conference on Protein Folding Dynamics0 , Ventura, CA, Ventura, CA , 08-JAN-06 - 13-JAN-06. | |||||||||
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| Employer: University College Dublin, School of Physics, Belfield, Dublin 4, Ireland Position: Lecturer, Computational Nano-Bio Physics |
| Employer: Boston University Position: Visiting Assistant Professor |
| Employer: National Institutes of Health, NIDDK Lab. of Chemical Physics, Bethesda, MD, USA Position: Research Fellow |
| Employer: Boston University, Graduate School of Arts and Sciences, Boston, MA, USA Position: Graduate Teaching and Research Assistant |
| Employer: Al I Cuza University of Iasi, Dept. of Physics, Iasi, Romania Position: Research Assistant |
| Year 1995 Institution: Al. I. Cuza University of Iasi, Iasi, Romania Qualification: BSc Subject: Physics |
| Year 1996 Institution: University of Patras, Greece Qualification: Post Graduate Certificate Subject: Medical Physics |
| Year 1996 Institution: Qualification: MSc Subject: |
| Year 1998 Institution: Boston University, MA Qualification: MA Subject: |
| Year 2003 Institution: Boston University, MA Qualification: PhD Subject: |
| The Journal Of Chemical Physics: Reviewer. |
| Biophysical Chemistry: Reviewer. |
| Proceedings Of The National Academy Of Sciences Usa: Reviewer. |
| Journal Of American Chemical Society: Reviewer. |
| Journal Of Chemical Theory And Computation: Reviewer. |
| Physical Review Letters: Reviewer. | |||||||||
| Journal Of Physical Chemistry B: Reviewer. | |||||||||
| Biochemistry: Reviewer. | |||||||||
| Journal Of Molecular Biology: Reviewer. | |||||||||
| Journal Of The Mechanical Behavior Of Biomedical Materials: Reviewer. | |||||||||
| Cell Biochemistry And Biophysics: Reviewer. | |||||||||
| Biophysical Journal: Reviewer. | |||||||||
| Proteins: Reviewer. | |||||||||
| Journal Of Statistical Physics: Reviewer. | |||||||||
| Journal Of Molecular Graphics &Amp; Modelling: Reviewer. | |||||||||
| Journal Of Structural Biology: Reviewer. | |||||||||
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| Dr. Vio Buchete's Group @ UCD Theoretical and Computational Nano-Bio Physics
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