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Francesco Piazza

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Related publications (29)

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Simple Monte Carlo model for crowd dynamics

Francesco Piazza

In this paper, we introduce a simple Monte Carlo method for simulating the dynamics of a crowd. Within our model a collection of hard-disk agents is subjected to a series of two-stage steps, implying (i) the displacement of one specific agent followed by ( ...

2010

Diffusion-Limited Reactions in Crowded Environments

Paolo De Los Rios, Nicolas Dorsaz, Giuseppe Foffi, Francesco Piazza

Diffusion-limited reactions are usually described within the Smoluchowski theory, which neglects interparticle interactions. We propose a simple way to incorporate excluded-volume effects building on simulations of hard sphere in the presence of a sink. Fo ...

American Physical Society2010

On inconsistent entities. A reply to Colyvan

Francesco Piazza

In a recent article M. Colyvan has argued that Quinean forms of scientific realism are faced with an unexpected upshot. Realism concerning a given class of entities, along with this route to realism, can be vindicated by running an indispensability argumen ...

2010

Heat wave propagation in a nonlinear chain

Francesco Piazza

We investigate the propagation of temperature perturbations in an array of coupled nonlinear oscillators at finite temperature. We evaluate the response function at equilibrium and show how the memory effects affect the diffusion properties. A comparison w ...

2009

Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics

Paolo De Los Rios, Francesco Piazza

Normal mode (NM) analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent NMs capture the salient features of the dynamics over a range ...

American Physical Society2009

Energy transfer in nonlinear network models of proteins

Francesco Piazza

We investigate how nonlinearity and topological disorder affect the energy relaxation of local kicks in coarse-grained network models of proteins. We find that nonlinearity promotes long-range, coherent transfer of substantial energy to specific functional ...

EDP Sciences2009

Long-range energy transfer in proteins

Francesco Piazza

Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e. g. either in the form of a photon, as in the case of the visual pigment rhodopsin, or through the breaking of a chemical bond, as in the pre ...

2009

Discrete breathers in protein structures

Francesco Piazza

Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, w ...

2008

A dynamical study of antibody-antigen encounter reactions

Paolo De Los Rios, Francesco Piazza

The effects of internal dynamics in diffusion-driven encounters between macro-molecules represent a problem of broad relevance in molecular biology. In this view, we investigate a typical antigen-antibody reaction chain, based on a coarse-grained mechanica ...

2007

Diffusion-limited unbinding of small peptides from PDZ domains

Paolo De Los Rios, Francesco Piazza

PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry, and dynamics with the PDZ function repres ...

2007