UCD School of Physics

Scoil na Fisice UCD

Dr Nicolae Buchete MA MPhysics PhD

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.

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Peer Reviewed Journals:

Tofoleanu, F. and Buchete, N.V. (2012) 'Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes'. Journal of Molecular Biology, .

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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. 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.

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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.

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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).

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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.

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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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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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Conference Publications:

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]

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

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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]
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]
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]
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]
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]
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]
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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Book Reviews

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]