Scientific Publications

"[Academic] reading, after a certain age, diverts the mind too much from its creative pursuits.
Any man who reads too much and uses his own brain too little falls into lazy habits of thinking"
–A. Einstein.

Think before you print!

In preparation

• Contact order dependent kinetics at optimal cooperativity
• The hydrophobic effect and the molecular origins of protein folding cooperativity
• Knotted proteins: a challenging folding puzzle (Invited Review)
• ...
• and more!

Published and submitted for publication

• Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants
  Heinirch Krobath, Silvia G. Estácio, Patricia F. N. Faísca & E.I. Shakhnovich (submitted, 2011)
  



• Why do protein folding rates correlate with metrics of native topology?
  Patricia F. N. Faísca, Rui D.M. Travasso, Andrea Parisi & Antonio Rey (submitted, 2011)
  



• Non-native interactions play an effective role in protein folding dynamics
  Patricia F. N. Faísca, Ana Nunes, Rui D.M. Travasso & E.I. Shakhnovich
  Protein Sci. 19, 2196-2209 (2010). (see the Editor's Highlight)
  Copyright (2010) The Protein Society.



• The protein folding transition state: Insights from kinetics and thermodynamics
  Rui D. M. Travasso, Patricia F. N. Faísca & Antonio Rey
  J. Chem. Physics 133, 125102 (2010) & Virtual Journal of Biological Physics Research 20 (7), October-1 (2010). Copyright (2010) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.



• Folding of knotted proteins: Insights from lattice simulations
  Patricia F. N. Faísca, Rui D. M. Travasso, Tiago Charters, Ana Nunes & Marek Cieplak, Physical Biology 7, 016009 (2010).
  Copyright (2010) IOP Publishing Ltd.



• The nucleation mechanism of protein folding: a survey of computer simulation studies
  P. F. N. Faísca, J. Phys. Cond. Matt. 21, 373102 (2009).
  Copyright (2009) IOP Publishing Ltd.



• On the relation between conformational plasticity and native geometry
  P. F. N. Faísca & C. M. Gomes, Biophysical Chemistry 138, 99-106 (2008).
  Copyright (2008) Elsevier B.V. All rights reserved.



• Critical residues in protein folding: Insights from phi-value and Pfold analysis
  P.F.N. Faísca, R.D.M. Travasso, R.C. Ball & E.I. Shakhnovich, J. Chem. Physics 129, 095108 (2008) & Virtual Journal of Biological Physics Research 16 (6), September-15 (2008).
  Copyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.



• Pathways to folding, nucleation events and native geometry
  Rui D.M. Travasso, Margarida M. Telo da Gama & Patrícia F.N. Faísca, J. Chem. Physics 127, 145106 (2007) & Virtual Journal of Biological Physics Research 14, (8) October-15 (2007).
  Copyright (2007) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.



• Conformational states and protein stability in a proteomic perspective
  Vesna Prosinecki, Patrícia F.N. Faísca & Claudio M. Gomes, Current Proteomics 4, 44-52 (2007).
  Copyright (2008) Elsevier B.V. All rights reserved.



• Nucleation phenomena in protein folding: The modulating role of protein sequence
  Rui D.M. Travasso, Patrícia F.N. Faísca & Margarida M. Telo da Gama, J. Phys.: Cond. Matt. 19, 15 pp. (2007) 285212. Copyright (2007) IOP Publishing Ltd



• Shaping protein folding dynamics with native state's geometry
  P.F.N. Faísca, Soft Condensed Matter: New Research, K.L. Dillon (Ed.), Nova Science Publishers (2007).



• Cooperativity and the origins of rapid, single-exponential kinetics in protein folding
  P.F.N. Faísca & K.W. Plaxco, Protein Sci. 15, 1608-1618 (2006).
  Copyright (2006) The Protein Society.



• Folding of small proteins: A matter of geometry?
  P.F.N. Faísca & M.M. Telo da Gama, Molec. Phys. 103, 2903-2910(2005).



• The Go model revisited: Native structure and the geometric coupling between local and long-range contacts
  P.F.N. Faísca, M.M. Telo da Gama & A. Nunes, Proteins: Structure, Function and Bioinformatics 60, 712-722 (2005).
  This is a preprint of an article accepted for publication in Proteins: Structure, Function and Bioinformatics. Copyright © (1999-2005) John Wiley & Sons. All rights reserved.



• Native geometry and the dynamics of protein folding
  P.F.N. Faisca & M.M. Telo da Gama, Biophysical Chemistry 115, 169-175 (2005).
  Copyright (2005) Elsevier B.V. All rights reserved.



• Folding and form: Insights from lattice simulations
  P.F.N. Faísca, M.M. Telo da Gama & R.C. Ball, Phys. Rev. E 69, 051917, 8 pp. (2004) & and Virtual Journal of Biological Physics Research 7 (11), June-1 (2004).
  Copyright (2004) The American Physical Society.



• Protein folding kinetics: Insights from lattice simulations
  P.F.N. Faísca, M.M. Telo da Gama & R.C. Ball, Proceedings of the International School of Physics Enrico Fermi, Course CLV, 'The Physics of Complex Systems (New advances and perspectives)' 155, 515-520 (2004), F. Mallamace (Ed.) & H.E. Stanley(Ed.), IOS press.



• Melnikov method for parabolic orbits
  J. Casasayas, P. Faísca & A. Nunes, Nonlinear Differential Equations and Applications 10, 119-131 (2003).



• Topological complexity, contact order and protein folding rates
  P.F.N. Faísca & R.C. Ball, J. Chem. Physics117, 8587-8592 (2002) & Virtual Journal of Biological Physics Research 4 (9), November-1 (2002).
  Copyright (2002) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.



• Thermodynamic control and dynamical regimes in protein folding
  P.F.N. Faísca & R.C. Ball, J. Chem. Physics116, 7231-7238 (2002) & Virtual Journal of Biological Physics Research 3 (8), April-15 (2002).
  Copyright (2002) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.



• Protein folding physics: in virtuo experiments
  P.F.N. Faísca, Ph.D. dissertation, University of Warwick (June 2002).

Other Publications

'Nobel' Interviews (in english and portuguese)

• Entrevista com Claude Cohen-Tannoudji
  P.F.N. Faísca, Gazeta de Física, 30 (Fasc. 2), 25-29 (2007).


• An interview with Harold Kroto
  P.F.N. Faísca & S. Estácio, Europhysics News 38 (Number 3), 28-31 (2007).


• Entrevista a Harold Kroto
  P.F.N. Faísca e S. Estácio, Gazeta de Física 29 (Fasc. 3), 46-50 (2006).


• An interview with Anthony Leggett
  P.F.N. Faísca & P. Patrício, Europhysics News 37 (Number 2), 30-32 (2006).


• Entrevista a Anthony Leggett
  P.F.N. Faísca e P. Patrício, Gazeta de Física 28 (Fasc. 3), 18-22 (2005).


• Entrevista a Pierre-Gilles de Gennes
  P.F.N. Faísca e P. Patrício, Gazeta de Física 27 (Fasc. 3), 12-19 (2004).

Public awarness of science (in portuguese)

• O mistério da forma das proteínas
  P.F.N. Faísca, O Código secreto: À descoberta dos padrões da natureza, pp. 301-326, Gradiva (2005).


• O mistério da forma das proteínas
  P.F.N. Faísca, Gazeta de Física, 29 (Fasc. 3), 34-39 (2006).


• Folding de proteínas: da biologia para a física na rota da complexidade, Anuário da revista Fórum Estudante (ano III), pp. 58-59 (2005).