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Published or accepted for publication
  • 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.


  • Stochastic effects in a seasonally forced epidemic model
    Ganna Rozhnova & Ana Nunes, Phys. Rev. E 82, 041906 (2010)& Virtual Journal of Biological Physics Research 20 (8), October-15 (2010).
    Copyright (2010) American Physical Society. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Physical 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.


  • Population dynamics on random networks: simulations and analytical models
    Ganna Rozhnova & Ana Nunes, European Physical Journal B 74, 235-242 (2010).
    Copyright (2010) EDP Sciences, Societá Italiana di Fisica, Spriger Verlag. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the publishers.


  • 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.


  • Cluster approximations for infection dynamics on random networks
    Ganna Rozhnova & Ana Nunes, Phys. Rev. E 80, 051915 (2009)& Virtual Journal of Biological Physics Research 18 (11), December-1 (2009).
    Copyright (2009) American Physical Society. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Physical Society.


  • 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.


  • Stochastic fluctuations in the susceptible-infective-recovered model with distributed infectious periods
    Andrew J. Black, Alan J. McKane, Ana Nunes & Andrea Parisi, Phys. Rev. E 80, 021922 (2009) & Virtual Journal of Biological Physics Research 18 (5), September-1 (2009).
    Copyright (2009) 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.


  • SIRS Dynamics on Random Networks: Simulations and Analytical Models
    Ganna Rozhnova & Ana Nunes, in Complex Sciences: Complex 2009, Part I, LNICST 4 (ed. Jie Zhou), 792-797, Springer, 2009. preprint


  • Fluctuations and oscillations in a simple epidemic model
    Ganna Rozhnova & Ana Nunes, Phys. Rev. E 79, 041922 (2009) & Virtual Journal of Biological Physics Research 17 (9), May-1 (2009).
    Copyright (2009) American Physical Society. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Physical Society.


  • 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, Journal of Chemical 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.


  • Coherence thresholds in models of language change and evolution: The effects of noise, dynamics, and network of interactions
    J. M. Tavares, M. M. Telo da Gama & A. Nunes, Phys. Rev. E 77, 046108 (2008) & Virtual Journal of Biological Physics Research 15, (8) April-15 (2008).
    Copyright (2008) The American Physical Society.


  • Stochastic Fluctuations in Epidemics on Networks
    M. Simões, M. M. Telo da Gama & A. Nunes, J R Soc Interface 5, 555-566 (2008). preprint


  • Pathways to folding, nucleation events and native geometry
    Rui D.M. Travasso, Margarida M. Telo da Gama & Patrícia F.N. Faísca, Journal of Chemical Physics 127, 145106 (2007) & Virtual Journal of Biological Physics Research 14, (8) October-15 (2007).


  • Conformational states and protein stability in a proteomic perspective
    Vesna Prosinecki, Patrícia F.N. Faísca & Claudio M. Gomes, Current Proteomics 4, 44-52 (2007).


  • 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.


  • 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).


  • Epidemics in small world networks
    M. M. Telo da Gama & A. Nunes, European Physical Journal B - Condensed Matter 50, 205-208 (2006).
    Copyright (2006) Springer Verlag.


  • Pair approximation models for disease spread
    J. Benoit, A. Nunes & M. M. Telo da Gama, European Physical Journal B - Condensed Matter 50, 177-181 (2006).
    Copyright (2006) Springer Verlag.


  • Localized contacts between hosts reduce pathogen diversity
    A. Nunes, M.M. Telo da Gama & M.G.M. Gomes, Journal of Theoretical Biology 241, 477-487 (2006).
    Copyright (2006) Elsevier B.V. All rights reserved.


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


  • Recurrent epidemics in small world networks
    J. Verdasca, M.M. Telo da Gama, A. Nunes, N.R. Bernardino, J.M. Pacheco & M.C. Gomes, Journal of Theoretical Biology 233, 553-561 (2005).
    Copyright (2005) Elsevier B.V. All rights reserved.


  • 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 (2004) 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, Physical Review 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.


  • Topological complexity, contact order and protein folding rates
    P.F.N. Faísca & R.C. Ball, Journal of Chemical 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, Journal of Chemical 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.

Other Publications by team members
  • Defects and Multistability in eutectic solidification patterns
    Andrea Parisi & Mathis Plapp, Europhysics Letters 90, 26010 (2010).


  • Role of transverse temperature gradients in the generation of lamellar eutectic solidification patterns
    Mikaël Perrut, Andrea Parisi, Silvère Akamatsu, Sabine Bottin-Rousseau, Gabriel Faivre & Mathis Plapp, Acta Materialia 58, 1761 (2010).


  • A numerical study of the orbits of second species of the planar circular RTBP
    Joaquim Font, Ana Nunes and Carles Simó, Celestial Mechanics and Dynamical Astronomy 103, 143-162 (2009).


  • Adhesion of membranes via receptor–ligand complexes: Domain formation, binding cooperativity, and active processes
    Thomas R. Weikl, Mesfin Asfaw, Heinrich Krobath, Bartosz Rózycki and Reinhard Lipowsky, Soft Matter 5, 3213-3224 (2009).


  • Binding cooperativity of membrane adhesion receptors
    Heinrich Krobath, Bartosz Rózycki, Reinhard Lipowsky and T.R. Weikl Soft Matter 5, 3354-3361 (2009).


  • Reheating induced by competing decay modes
    T. Charters, A. Nunes, J. P. Mimoso, Phys. Rev. D 78, 083539 (2008).


  • Stability of lamellar eutectic growth
    Andrea Parisi and Mathis Plapp, Acta Materialia 56, 1348 (2008).


  • Lateral diffusion of receptor-ligand bonds in membrane adhesion zones: Effect of thermal membrane roughness
    Heinrich Krobath, G. J. Schütz, Reinhard Lipowsky and T.R. Weikl Europhysics Letters 5, 78:38003 (2007).


  • Asymptotic behavior of the warm inflation scenario with viscous pressure
    J. P. Mimoso, A. Nunes and D. Pavón, Phys. Rev. D 73, 023502 (2006).


  • Impact of bistability in the synchronization of chaotic maps with delayed coupling
    P.G. Lind, A. Nunes and J.A.C. Gallas, Physica A 371, 100-103 (2006).


  • Phase dynamics and particle production in preheating
    T. Charters, A. Nunes, J. P. Mimoso, Phys. Rev. D 71, 083515 (2005).


  • Relation between driving energy, crack shape and speed in brittle dynamic fracture
    Andrea Parisi and Robin C Ball, Physical Review B 72, 054101 (2005).


  • A Note on the Reducibility of Linear Differential Equations with Quasi periodic Coefficients
    X. Yuan and A. Nunes, International Journal of Mathematics and Mathematical Sciences 2003, 4071-4083 (2003).


  • A Qualitative Analysis of the Attractor Mechanism of General relativity
    J. P. Mimoso and A. Nunes, Astrophysics and Space Science 283, 661-666 (2003).


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


  • Consecutive quasi-collisions in the planar circular RTBP
    J. Font, A. Nunes and C. Simó, Nonlinearity 15, 115-142 (2002).


  • Role of surface waves on the relation between crack speed and the work of fracture
    Andrea Parisi and Robin C Ball, Physical Review B 66, 165432 (2002).


Public awarness of science (in portuguese)
  • Caos no sistema solar
    A. Nunes, O Código secreto: À descoberta dos padrões da natureza, pp. 109-134, Gradiva (2005).


  • Fractais e a geometria da natureza
    A. Nunes, O Código secreto: À descoberta dos padrões da natureza, pp. 169-191, Gradiva (2005).


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


  • De que tamanho e o mundo?
    A. Nunes, O Código secreto: À descoberta dos padrões da natureza, pp. 329-354, Gradiva (2005).


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


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