Publications by Francesco Piazza

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Francesco Piazza, Shiling Liang, Daniel Maria Busiello

The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...

Nature Research2021

Dissipation-driven selection of states in non-equilibrium chemical networks

Paolo De Los Rios, Francesco Piazza, Shiling Liang, Daniel Maria Busiello

Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present ...

2021

Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces

Paolo De Los Rios, Francesco Piazza, Giuseppe Foffi

In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, ...

Public Library Science2016

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Francesco Piazza, Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012) PREFACE

Francesco Piazza, Giuseppe Foffi

Iop Publishing Ltd2013

First-order coil-globule transition driven by vibrational entropy

Paolo De Los Rios, Francesco Piazza, Carlo Maffi

By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switc ...

Nature Publishing Group2012

Inertial effects in diffusion-limited reactions

Nicolas Dorsaz, Francesco Piazza, Giuseppe Foffi

Diffusion-limited reactions are commonly found in biochemical processes such as enzyme catalysis, colloid and protein aggregation and binding between different macromolecules in cells. Usually, such reactions are modeled within the Smoluchowski framework b ...

Institute of Physics2010

Vibrational entropy and the structural organization of proteins

Paolo De Los Rios, Francesco Piazza

In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...

2010

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

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

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

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

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 ...

IOP Publishing - EPL Association2009

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

Bottleneck genes and community structure in the cell cycle network of S-pombe

Paolo De Los Rios, Francesco Piazza, Cécile Caretta Cartozo

The identification of cell cycle-related genes is still a difficult task, even for organisms with relatively few genes such as the fission yeast. Several gene expression studies have been published on S. pombe showing similarities but also discrepancies in ...

Public Library of Science2007

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

Resolving the geometry of biomolecules imaged by cryo electron tomography

Francesco Piazza

In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics ...

2007

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

On the origin of the boson peak in globular proteins

Paolo De Los Rios, Francesco Piazza

We study the boson peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean random matrix theory, whose predictions can be numerica ...

Taylor & Francis2007