Statistical Physics of Complex Systems and nanobiotechnology

Group leader: Francesco PIAZZA

Quantum Biology

We participate to the EU-funded STREP project "Phonon-assisted Processes for Energy Transfer and Sensing" (PAPETS). This project pioneers the emerging field of Quantum Biology in Europe and will focus on two problems. On the one side, we will investigate the functioning of light-harvesting complexes and try to elucidate how and why such complicated molecular machines appear to employ quantum coherence to achieve their stunning efficiency in harvesting sun light. PAPETS will also test a revolutionary model of olfaction, introduced in the 1990s by Luca Turin ( see his original paper), and holding great promise to unveil a formidable biological mechanism that still resists tenaciously to all theoretical explanations. The new mechanism posits that olfaction relies on inelastic electron tunneling. The main idea is that odorants would be recognized not through their shapes (lock-and-key recognition), but through their vibrational spectrum. The nose would thus act as a sort of nano-spectrometer.

To investigate the role of protein vibrations in exciton transfer, we have introduced the Quantum Network Model, where a coarse-grained description of protein dynamics is coupled to a tight-binding Hamiltonian, whose elements are explicitly modulated by the classical dynamics of the underlying protein. This mean-field model realizes the so-called Ehrenfest dynamics. Despite surface-hopping is prevented by construction in this theoretical framework, we find that our model allows one to get considerable insight into how specific vibrational modes affect exciton transport.

Allosteric communication in proteins

What are the structural and dynamical determinants of the astonishing ability of protein scaffolds to propagate mechanical perturbations from a given site to another precise, distant location? We employ different coarse-grained models of protein dynamics to study this problem, coupled with concepts and methods from statistical physics such as complex networks tools and linear response theory.

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We have discovered that proteins typically display normal modes that are strongly localized at multiple locations in the protein. We termed normal modes that possess two localization peaks bi-localized modes. We found that such modes express fold-rooted spatial correlations that effectively mediate long-range energy transfer. Interestingly, a study of several structures of G-protein-coupled receptors (GPCRs) shows that bi-localized modes typically exist in these structures, connecting pairs of residues at either end of the trans-membrane portions of the scaffolds.

Diffusion-controlled reactions in complex environments
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A special kind of many-body interaction emerges when one considers diffusive flux to multiple sinks. This theoretical framework arises for example

when one wants to model diffusion-limited reactions among complex macromolecules or within complex environments. The origin of these interaction is simple: sinks tend to screen flux away from each other and therefore the overall flux (i.e. the overall rate) is reduced with respect to additivity. One thus usually speaks of anti-cooperative interactions. In order to solve such problems, we apply several advanced methods for the solution of the time-dependent and stationary diffusion equation in complex, multi-connected domains. These include, re-expansion theorems and dual-series relations methods.
Recent applications of these methods include the calculation of the reaction rate constant of complex core-shell nanoreactors (collaboration with Helmholtz zentrum, Berlin), new insight into the role of receptor configuration on the cell surface in ligand-receptor binding and the study of how large-scale conformational rearrangements in antibodies modulate the binding rate of small antigens.

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Macromolecular crowding

Diffusive transport is well understood in dilute environments with simple geometry. However, naturally occurring milieux where this kind of transport is important are usually rather crowded and characterized by complex and strongly confining landscapes. The first striking example of this is the cell, the primary reactor for all biochemical processes at the core of life itself. Between 30 % and 40 % of the available volume in a cell is occupied by all sort of biomolecules, cytoskeletal fibers and a wealth of subcellular organelles. Order-of-magnitude and greater changes are observed in binding rates in vivo, often featuring subtle modulations that are hard to explain. Remarkably, an interesting picture is emerging lately whereby the interior of the cell would share many properties with the liquid state of matter. We are tackling these problems from various angles, essentially studying modified diffusion equations both derived from microscopic stochastic exclusion processes and from basic concepts of the physics of liquids.

Recently, we have tackled the problem of how enzyme kinetics depend on the physico-chemical properties of the environment. To investigate this problem, we are performing enzyme kinetics experiments in the presence of artificial crowding agents, such as Ficoll (a highly branched polysaccharide), polymers such as PEG, small crowding molecules, such as glucose and mesoporous gels such as agarose. Furthermore, we are measuring the diffusion coefficient of reactants immersed in such complex media, using pulsed-field gradient NMR and Fluorescence recovery after photobleaching (FRAP). In parallel, we are running Brownian dynamics simulations with ultra-coarse grained models.

 



30 documents

Article dans une revue

  • Annise Rivière, Stefano Lepri, Daniele Colognesi, Francesco Piazza. Wavelet imaging of transient energy localization in nonlinear systems at thermal equilibrium: The case study of NaI crystals at high temperature. Physical Review B : Condensed matter and materials physics, American Physical Society, 2019, 99 (2), ⟨10.1103/PhysRevB.99.024307⟩. ⟨hal-02067449⟩
  • A. Sozza, Francesco Piazza, M. Cencini, F. de Lillo, G. Boffetta. Point-particle method to compute diffusion-limited cellular uptake. Physical Review E , American Physical Society (APS), 2018, 97 (2), pp.023301. ⟨hal-01966405⟩
  • Rafael Roa, Stefano Angioletti-Uberti, Yan Lu, Joachim Dzubiella, Francesco Piazza, et al.. Catalysis by Metallic Nanoparticles in Solution: Thermosensitive Microgels as Nanoreactors. Zeitschrift für Physikalische Chemie, Oldenbourg Verlag, 2018, 232 (5-6), pp.773-803. ⟨hal-01966375⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Nonlinear macroscopic transport equations in many-body systems from microscopic exclusion processes. Frontiers in Physics, Frontiers, 2016, 18 (30), pp.20758-20767. ⟨hal-01408558⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Macroscopic Transport Equations in Many-Body Systems from Microscopic Exclusion Processes in Disordered Media: A Review. Frontiers in Physics, Frontiers, 2016, 4, ⟨10.3389/fphy.2016.00033⟩. ⟨hal-02071749⟩
  • Cristiano de Michele, Paolo de Los Rios, Giuseppe Foffi, Francesco Piazza, Yanay Ofran. Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces. PLoS Computational Biology, Public Library of Science, 2016, 12 (3), ⟨10.1371/journal.pcbi.1004752⟩. ⟨hal-01406916⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Conformation-controlled binding kinetics of antibodies. Scientific Reports, Nature Publishing Group, 2016, 6, ⟨10.1038/srep18976⟩. ⟨hal-01406993⟩
  • Marta Galanti, Duccio Fanelli, Stefano Angioletti-Uberti, Matthias Ballauff, Joachim Dzubiella, et al.. Reaction rate of a composite core–shell nanoreactor with multiple nanocatalysts. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (30), pp.20758 - 20767. ⟨10.1039/C6CP01179A⟩. ⟨hal-01407893⟩
  • Marta Galanti, Duccio Fanelli, Sergey D. Traytak, Francesco Piazza. Correction: Theory of diffusion-influenced reactions in complex geometries. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (26), pp.17757 - 17757. ⟨10.1039/C6CP90149B⟩. ⟨hal-01408564⟩
  • Marta Galanti, Duccio Fanelli, Sergey D. Traytak, Francesco Piazza. Theory of diffusion-influenced reactions in complex geometries. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2016, 18 (23), pp.15950 - 15954. ⟨10.1039/c6cp01147k⟩. ⟨hal-01406998⟩
  • Jean-Yves Dewavrin, Muhammed Abdurrahiem, Anna Blocki, Mrinal Musib, Francesco Piazza, et al.. Synergistic Rate Boosting of Collagen Fibrillogenesis in Heterogeneous Mixtures of Crowding Agents. Journal of Physical Chemistry B, American Chemical Society, 2015, 119 (12), pp.4350-4358. ⟨10.1021/jp5077559⟩. ⟨hal-02072238⟩
  • Simon Aubailly, Francesco Piazza. Cutoff lensing: predicting catalytic sites in enzymes. Scientific Reports, Nature Publishing Group, 2015, 5 (1), ⟨10.1038/srep14874⟩. ⟨hal-02072226⟩
  • Francesca Di Patti, Duccio Fanelli, Francesco Piazza. Optimal search strategies on complex multi-linked networks. Scientific Reports, Nature Publishing Group, 2015, 5 (1), ⟨10.1038/srep09869⟩. ⟨hal-02072243⟩
  • Stefano Iubini, Octavi Boada, Yasser Omar, Francesco Piazza. Transport of quantum excitations coupled to spatially extended nonlinear many-body systems. New Journal of Physics, Institute of Physics: Open Access Journals, 2015, 17 (11), pp.113030. ⟨10.1088/1367-2630/17/11/113030⟩. ⟨hal-02072269⟩
  • Francesco Piazza, Sergey Traytak. Diffusion-influenced reactions in a hollow nano-reactor with a circular hole. Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2015, 17 (16), pp.10417-10425. ⟨10.1039/c4cp05605a⟩. ⟨hal-02072294⟩
  • Francesco Piazza. Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk.. Physical Biology, Institute of Physics: Hybrid Open Access, 2014, 11 (3), pp.036003. ⟨hal-01180839⟩
  • I.V. Dubinko, Francesco Piazza. On the role of disorder in catalysis driven by discrete breathers. Letters on materials, Elsevier, 2014, 4 (4), pp.273-278. ⟨hal-01178866⟩
  • Enrico Spiga, Luciano A Abriata, Francesco Piazza, Matteo Dal Peraro. Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics.. Journal of Physical Chemistry B, American Chemical Society, 2014, 118 (20), pp.5310-5321. ⟨hal-01180892⟩
  • Marta Galanti, Duccio Fanelli, Amos Maritan, Francesco Piazza. Diffusion of tagged particles in a crowded medium. EPL - Europhysics Letters, European Physical Society/EDP Sciences/Società Italiana di Fisica/IOP Publishing, 2014, 107 (2), pp.20006. ⟨10.1209/0295-5075/107/20006⟩. ⟨hal-01178998⟩
  • Pierre de Buyl, Giovanni de Ninno, Duccio Fanelli, Cesare Nardini, Aurelio Patelli, et al.. Absence of thermalization for systems with long-range interactions coupled to a thermal bath. Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, American Physical Society, 2013, 87 (4), ⟨10.1103/PhysRevE.87.042110⟩. ⟨hal-02070760⟩
  • Mohamed Naji, Francesco Piazza, Guillaume Guimbretiere, Aurélien Canizares, Yann Vaills. Structural Relaxation Dynamics and Annealing Effects of Sodium Silicate Glass. Journal of Physical Chemistry B, American Chemical Society, 2013, 117 (18), pp.5757-5764. ⟨10.1021/jp401112s⟩. ⟨hal-02070892⟩
  • Marta Galanti, Duccio Fanelli, Francesco Piazza. Persistent random walk with exclusion. European Physical Journal B: Condensed Matter and Complex Systems, Springer-Verlag, 2013, 86 (11), ⟨10.1140/epjb/e2013-40838-y⟩. ⟨hal-02070835⟩
  • G Foffi, A. Pastore, Francesco Piazza, A Temussi. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10–14 June 2012). Physical Biology, Institute of Physics: Hybrid Open Access, 2013, 10 (4), pp.040301. ⟨10.1088/1478-3975/10/4/040301⟩. ⟨hal-02071788⟩
  • F. Piazza, N Dorsaz, C. de Michele, P de Los Rios, F Foffi. Diffusion-limited reactions in crowded environments: a local density approximation. Journal of Physics: Condensed Matter, IOP Publishing, 2013, 25 (37), pp.375104. ⟨10.1088/0953-8984/25/37/375104⟩. ⟨hal-02071799⟩
  • Francesco Piazza, Giuseppe Foffi, Cristiano de Michele. Irreversible bimolecular reactions with inertia: from the trapping to the target setting at finite densities. Journal of Physics: Condensed Matter, IOP Publishing, 2013, 25 (24), pp.245101. ⟨10.1088/0953-8984/25/24/245101⟩. ⟨hal-02070906⟩
  • Peter Csermely, Kuljeet Singh Sandhu, Eszter Hazai, Zsolt Hoksza, Huba J M Kiss, et al.. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.. Current Protein and Peptide Science, Bentham Science Publishers, 2012, 13 (1), pp.19-33. ⟨hal-00721841⟩
  • Carlo Maffi, Marco Baiesi, Lapo Casetti, Francesco Piazza, Paolo de Los Rios. First-order coil-globule transition driven by vibrational entropy.. Nature Communications, Nature Publishing Group, 2012, 3, pp.1065. ⟨10.1038/ncomms2055⟩. ⟨hal-00748173⟩
  • Stefano Luccioli, Alberto Imparato, Stefano Lepri, Francesco Piazza, Alessandro Torcini. Discrete breathers in a realistic coarse-grained model of proteins.. Physical Biology, Institute of Physics: Hybrid Open Access, 2011, 8 (4), pp.046008. ⟨10.1088/1478-3975/8/4/046008⟩. ⟨hal-00720642⟩
  • Alessio Zaccone, Nicolas Dorsaz, Francesco Piazza, Cristiano de Michele, Massimo Morbidelli, et al.. Crowding, intermolecular interactions, and shear flow effects in the diffusion model of chemical reactions.. Journal of Physical Chemistry B, American Chemical Society, 2011, 115 (22), pp.7383-96. ⟨10.1021/jp200439a⟩. ⟨hal-00720723⟩
  • Francesco Piazza, Yves-Henri Sanejouand. Breather-mediated energy transfer in proteins. Discrete and Continuous Dynamical Systems - Series S, American Institute of Mathematical Sciences, 2011, 4 (5), pp.1247-1266. ⟨hal-00720691⟩