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Nicolae Buchete

Assoc. Prof., Theoretical & Computational Nano-Bio Physics

School of Physics
Room 111
University College Dublin
UCD Science Centre North
Belfield, Dublin 4
Ireland

Tel: +353-(0)1-716-2088 (Physics)
Email: buchete@ucd.ie

Biography

Nicolae-Viorel (Vio) Buchete is an Associate Professor of Theoretical & Computational Nano-Bio Physics in the UCD School of Physics. He has several postgraduate degrees from universities in both the US (Boston University) and the EU (Al. I. Cuza University of Iasi, Romania, and University of Patras, Greece). He was awarded his PhD from Boston University, and he held research fellowships at the National Institutes of Health (Bethesda, MD). His general research interests are in the areas of theoretical and computational biological physics, chemical physics, and nanoscience. Ongoing research projects in his group at UCD are concerned with statistical mechanics and molecular dynamics of biomolecular systems, systems biology, structural bioinformatics, and with multiscale modeling of biomolecules and complex fluids.


News:


Professional

Honours and Awards

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
Year: 2001.
Title: Feldman Award, http://www.bu.edu/chemistry/gradprograms/awards.html
Year: 2000.
Title: Sugata Ray Memorial Award, http://www.bu.edu/chemistry/gradprograms/awards.html
Year: 2000.
Title: Sigma Xi, Graduate Research Award at Science Day 2000, BU, http://sigmaxi.org
Year: 1998.
Title: Dean's Award for Research, Science Day, http://web.bu.edu/research/spotlight/scienceday
Year: 1998.
Title: Outstanding Teaching Fellow Award, http://www.bu.edu/chemistry/gradprograms/awards.html

Associations

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
     

Conference Contributions

Murphy, R. D., Leahy, C. T., Buchete, N-V.; (2009) 'Helix formation and helix-helix interactions in protein folding'. [Oral Presentation], 238th Meeting of the American Chemical Society, Washington D.C , 16-AUG-09 - 20-AUG-09.
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.
 

Employment

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

Education

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:
     

Journals Edited

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.
 

Publications

 

Book Chapters

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. , pp.141-156 Available Online [Details]
 

Peer Reviewed Journals

Leahy, CT; Kells, A; Hummer, G; Buchete*, NV; Rosta*, E (2017) 'Peptide dimerization-dissociation rates from replica exchange molecular dynamics'. Journal of Chemical Physics, 147 (15):152725. Available Online [DOI] [Details]
Martini, L; Kells, A; Covino, R; Hummer, G; Buchete, NV; Rosta, E (2017) 'Variational Identification of Markovian Transition States'. Physical Review X, . Available Online [DOI] [Details]
Ryan, K; Neumayer, SM; Maraka, HVR; Buchete, NV; Kholkin, AL; Rice, JH; Rodriguez, BJ (2017) 'Thermal and aqueous stability improvement of graphene oxide enhanced diphenylalanine nanocomposites'. Science and Technology of Advanced Materials, 18 (1):172-179. Available Online [DOI] Link to full text [Details]
McDermott, N; Meunier, A; Wong, S; Buchete, V; Marignol, L (2017) 'Profiling of a panel of radioresistant prostate cancer cells identifies deregulation of key miRNAs'. Clinical and Translational Radiation Oncology, 2 :63-68. Available Online [DOI] [Details]
Sanchez-Sanz, G; Tywoniuk, B; Matallanas, D; Romano, D; Nguyen, LK; Kholodenko, BN; Rosta, E; Kolch, W; Buchete, NV (2016) 'SARAH Domain-mediated MST2-RASSF Dimeric Interactions'. PLoS Computational Biology, 12 (10):e1005051. Available Online [DOI] [Details]
Leahy, CT; Murphy, RD; Hummer, G; Rosta, E; Buchete, NV; (2016) 'Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers'. Journal of Physical Chemistry Letters, 7 (14):2676-2682. Available Online [DOI] [Details]
Sanchez-Sanz, G; Matallanas, D; Nguyen, LK; Kholodenko, BN; Rosta, E; Kolch, W; Buchete, NV (2016) 'MST2-RASSF protein-protein interactions through SARAH domains'. Briefings in Bioinformatics, 17 (4):593-602. Available Online [DOI] [Details]
Jambrina, PG; Rauch, N; Pilkington, R; Rybakova, K; Nguyen, LK; Kholodenko, BN; Buchete, NV; Kolch, W; Rosta, E (2016) 'Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation'. Angewandte Chemie International Edition, 55 (3):983-986. Available Online [DOI] [Details]
Kelly, CM; Muzard, J; Brooks, BR; Lee, GU; Buchete, NV (2015) 'Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules'. Physical Chemistry Chemical Physics, 17 :9634-9643. Available Online [DOI] [Details]
Kelly, CM; Northey, T; Ryan. K; Brooks, BR; Kholkin, AL; Rodriguez, BJ; Buchete, NV; (2015) 'Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field'. Biophysical Chemistry, 196 :16-24. Available Online [DOI] [Details]
Gheorghescu, AK; Tywoniuk, B; Duess, J; Buchete, NV; Thompson, J (2015) 'Exposure of chick embryos to cadmium changes the extra-embryonic vascular branching pattern and alters expression of VEGF-A and VEGF-R2'. Toxicology and Applied Pharmacology, 289 (1):79-88. Available Online [DOI] [Details]
Nasica-Labouze, J; et al. (2015) 'Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies'. Chemical Reviews, 115 (9):3518-3563. Available Online [DOI] [Details]
Ryan, K., Beirne, J.G., Redmond, G., Kilpatrick, J.I., Guyonnet, J., Buchete, N-V., Kholkin, A.L., and Rodriguez, B.J. (2015) 'Nanoscale piezoelectric properties of self-assembled Fmoc-FF peptide fibrous networks'. ACS applied materials & interfaces, 7 (23):12702-12707. Available Online [DOI] [Details]
Cournia, Z; et al. (2015) 'Membrane protein structure, function and dynamics: A perspective from experiments and theory'. Journal of Membrane Biology, 248 (4):611-640. Available Online [DOI] [Details]
Tofoleanu, F; Brooks, BR; Buchete, NV (2015) 'Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups'. ACS Chemical Neuroscience, 6 (3):446-455. Available Online [DOI] [Details]
Jambrina, P.G. and Bohuszewicz, O. and Buchete, N.-V. and Kolch, W. and Rosta, E. (2014) 'Molecular mechanisms of asymmetric RAF dimer activation'. Biochemical Society Transactions, 42 (4):784-790. Available Online [DOI] [Details]
Berezhkovskii, AM; Murphy, RD; Buchete, NV (2013) 'Network random walk model of two-state protein folding: Test of the theory'. Journal of Chemical Physics, 138 (3):036101-2. Available Online [DOI] Link to full text [Details]
Murphy, RD,Conlon, J,Mansoor, T,Luca, S,Vaiana, SM,Buchete, NV (2012) 'Conformational dynamics of human IAPP monomers'. Biophysical Chemistry, 167 :1-7. Available Online [DOI] [Details]
Buchete, NV (2012) 'Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations'. Biophysical Journal, 103 :1411-1413. Available Online [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. Available Online [DOI] [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. Available Online [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. Available Online [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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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):030902. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
Best R.B., Buchete N.V., and G. Hummer.; (2008) 'Are Current Molecular Dynamics Force Fields too Helical?'. Biophysical Journal, 95 (1):L07-L09. Available Online [DOI] [Details]
Buchete N.V., and G. Hummer.; (2008) 'Coarse master equations for Peptide folding dynamics'. Journal of Physical Chemistry B, 112 (19):6057-6069. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
Buchete NV, Straub JE, and D. Thirumalai.; (2004) 'Orientational potentials extracted from protein structures improve native fold recognition'. Protein Science, 13 (4):862-874. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [DOI] [Details]
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. Available Online [Details]
 

Conference Publications

Crowe, A; Sanchez-Sanz, G; Tywoniuk, B; Shields, DC; Buchete, NV; (2016) Coarse Master Equation-Based Analysis of N-Methylation and Temperature Effects on the Dynamics of Cyclic Peptides Biophysical Society 60th Annual Meeting , pp.379A-379A [Details]
Yuan, Y; Tywoniuk, B; Buchete, NV (2015) Structural Stability of Diabetes-Related Amylin Protofilaments: Applications to Fibril Design Biophysical Society 59th Annual Meeting; Biophysical Journal , pp.387a-387a Available Online [DOI] [Details]
Kaskova-Gheorghescu, A; Buchete, NV; Thompson, J (2014) Fractal analysis of the chick extra-embryonic angiogenesis following cadmium exposure Irish Journal of Medicinal Science , pp.S25-S25 [Details]
Kelly, CM; Buchete, NV (2014) Conformational and Dynamic Properties of Extracellular Domains of Cell Adhesion Molecules Biophysical Society 58th Annual Meeting; Biophysical Journal , pp.51a-52a Available Online [DOI] [Details]
Tofoleanu, F; Buchete NV (2013) Molecular Interactions of Alzheimer's A beta Peptide Fibrils and Oligomers with Lipid Membranes Biophysical Society 57th Annual Meeting; Biophysical Journal Philadelphia, PA, , 02-FEB-13 - 06-FEB-13 , pp.592A-592A Available Online [DOI] [Details]
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 Available Online [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]
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 Available Online [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 Available Online [DOI] [Details]
Tofoleanu F, Buchete NV; (2009) Nanoscale structural and stability properties of amyloid fibrils 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]
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]
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 Available Online [Details]
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 Available Online [Details]
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 Available Online [Details]
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 Available Online [Details]
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 Available Online [Details]
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 Available Online [Details]
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 , pp.201 [Details]
                                                                                                                                       

Research

Research Interests

Theoretical and computational biological physics, chemical physics, and nanoscience
Statistical mechanics and molecular dynamics of biomolecular systems
Systems biology and structural bioinformatics
Multiscale modeling of biomolecules and complex fluids

Research Webpage

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Recent Postgraduates

PhD & Research Master Students:
  • Cathrine M. Kelly (PhD, 2015) - Next: University College Dublin, Ireland
  • Aoife Crowe (Research Master, 2015): Co-supervisor Prof. Denis Shields (UCD), Next:
  • Cathal T. Leahy   (PhD, 2013) - Next: Deloitte & Touche, Dublin, Ireland
  • Florentina Tofoleanu (PhD, 2012) - Next: Postdoctoral Fellow, National Institutes of Health, USA
  • Ronan D. Murphy (PhD, 2012) - Next: Financial Software Consultant, Murex, Ireland

Postdoctoral Fellows:

  • Goar Sanchez-Sanz (2013-16) - Next: UCD School of Chemistry
  • Durba Roy (2012-14) - Next: BITS Pilani, India

Current Postgraduate Students

Sarah McCartan, Doctor of Philosophy (PhD)   -   Thesis Supervisor

Collaborators

Internal Collaborators

Dr. Vio Buchete's Group @ UCD

Theoretical and Computational Nano-Bio Physics

Current Group Members:

Group Alumni:
(PhD Tree)

Interns:

 


External Collaborators

M Girtan [UA]
M Sanduloviciu [UAIC]
  ER Rosta [KCL]
  AM Berezhkovskii [NIH], RB Best [NIH], BR Brooks [NIH]
  J Mittal [Lehigh U.], J Kubelka[UWYO], SM Vaiana [ASU], S Luca [UNMC]