arXiv subjects

Francesco Piazza

Publications and source records attributed to Francesco Piazza.

At least 91 records · Page 5Linked to original sources

arXiv2014

Optimal search strategies on complex networks

Complex networks are ubiquitous in nature and play a role of paramount importance in many contexts. Internet and the cyberworld, which permeate our everyday life, are self-organized hierarchical graphs. Urban traffic flows on intricate road networks, which impact both transportation design and epidemic control. In the brain, neurons are cabled through heterogeneous connections, which support the propagation of electric signals. In all these cases, the true challenge is to unveil the mechanisms through which specific dynamical features are modulated by the underlying topology of the network. Here, we consider agents randomly hopping along the links of a graph, with the additional possibility of performing long-range hops to randomly chosen disconnected nodes with a given probability. We show that an optimal combination of the two jump rules exists that maximises the efficiency of target search, the optimum reflecting the topology of the network.

physics.soc-ph↗

arXiv2014

Quantum kinetics of ultracold fermions coupled to an optical resonator

We study the far-from-equilibrium statistical mechanics of periodically driven fermionic atoms in a lossy optical resonator. We show that the interplay of the Fermi surface with cavity losses leads to sub-natural cavity linewidth narrowing, squeezed light, and out-of-equilibrium quantum statistics of the atoms. Adapting the Keldysh approach, we set-up and solve a quantum kinetic Boltzmann equation in a systematic $1/N$ expansion with $N$ the number of atoms. In the strict thermodynamic limit $N,V\rightarrow \infty$, $N/V=\text{const.}$ we find the atoms (fermions or bosons) remain immune against cavity-induced heating or cooling. At next-to-leading order in $1/N$, we find a "one-way thermalization" of the atoms determined by cavity decay. We argue that, in absence of an equilibrium fluctuation-dissipation relation, the long-time limit $Δt \rightarrow \infty$ does not commute with the thermodynamic limit $N\rightarrow \infty$, such that for the physically relevant case of large but finite $N$, the dynamics ultimately becomes strongly coupled, especially close to the superradiance phase transition.

cond-mat.quant-gas↗

arXiv2014

Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk

In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins may be reconstructed as large-scale, collective modes sustained by long-lived nonlinear vibrations known as discrete breathers (DB) localized at key, hot-spot sites. DBs are spatially localized modes, whose nonlinear nature hinders resonant coupling with the normal modes, thus conferring them long lifetimes as compared to normal modes. DBs have been predicted to exist in proteins, localized at few $hotspot$ residues typically within the stiffest portions of the structure. We compute DB modes analytically in the framework of the nonlinear network model, showing that the displacement patterns of many DBs localized at key sites match to a remarkable extent the experimentally uncovered correlation blueprint. The computed dispersion relations prove that it is physically possible for some of these DBs to be excited out of thermal fluctuations at room temperature. Based on our calculations, we speculate that transient energy redistribution among the vibrational modes in a protein might favor the emergence of DB-like bursts of long-lived energy at hot-spot sites with lifetimes in the ns range, able to sustain critical, function-encoding correlated motions. More generally, our calculations provide a novel quantitative tool to predict fold-spanning dynamical pathways of correlated residues that may be central to allosteric cross-talk in proteins.

q-bio.BM↗

arXiv2014

Diffusion of tagged particles in a crowded medium

The influence of crowding on the diffusion of tagged particles in a dense medium is investigated in the framework of a mean-field model, derived in the continuum limit from a microscopic stochastic process with exclusion. The probability distribution function of the tagged particles obeys to a nonlinear Fokker-Planck equation, where the drift and diffusion terms are determined self-consistently by the concentration of crowders in the medium. Transient sub-diffusive or super-diffusive behaviours are observed, depending on the selected initial conditions, that bridge normal diffusion regimes characterized by different diffusion coefficients. These anomalous crossovers originate from the microscopic competition for space and reflect the peculiar form of the non-homogeneous advection term in the governing Fokker-Planck equation. Our results strongly warn against the overly simplistic identification of crowding with anomalous transport {\em tout court}.

cond-mat.stat-mech↗

arXiv2014

Umklapp Superradiance from a Collisionless Quantum Degenerate Fermi Gas

The quantum dynamics of the electromagnetic light mode of an optical cavity filled with a coherently driven Fermi gas of ultracold atoms strongly depends on geometry of the Fermi surface. Superradiant light generation and self-organization of the atoms can be achieved at low pumping threshold due to resonant atom-photon Umklapp processes, where the fermions are scattered from one side of the Fermi surface to the other by exchanging photon momenta. The cavity spectrum exhibits sidebands, that, despite strong atom-light coupling and cavity decay, retain narrow linewidth, due to absorptionless transparency windows outside the atomic particle-hole continuum and the suppression of inhomogeneous broadening and thermal fluctuations in the collisionless Fermi gas.

cond-mat.quant-gas↗

arXiv2013

Persistent random walk with exclusion

Modelling the propagation of a pulse in a dense {\em milieu} poses fundamental challenges at the theoretical and applied levels. To this aim, in this paper we generalize the telegraph equation to non-ideal conditions by extending the concept of persistent random walk to account for spatial exclusion effects. This is achieved by introducing an explicit constraint in the hopping rates, that weights the occupancy of the target sites. We derive the mean-field equations, which display nonlinear terms that are important at high density. We compute the evolution of the mean square displacement (MSD) for pulses belonging to a specific class of spatially symmetric initial conditions. The MSD still displays a transition from ballistic to diffusive behaviour. We derive an analytical formula for the effective velocity of the ballistic stage, which is shown to depend in a nontrivial fashion upon both the density (area) and the shape of the initial pulse. After a density-dependent crossover time, nonlinear terms become negligible and normal diffusive behaviour is recovered at long times.

cond-mat.stat-mech↗

arXiv2013

Nonlinear macroscopic transport equations in many-body systems from microscopic exclusion processes

Describing particle transport at the macroscopic or mesoscopic level in non-ideal environments poses fundamental theoretical challenges in domains ranging from inter and intra-cellular transport in biology to diffusion in porous media. Yet, often the nature of the constraints coming from many-body interactions or reflecting a complex and confining environment are better understood and modeled at the microscopic level. In this paper we investigate the subtle link between microscopic exclusion processes and the mean-field equations that ensue from them in the continuum limit. We derive a generalized nonlinear advection diffusion equation suitable for describing transport in a inhomogeneous medium in the presence of an external field. Furthermore, taking inspiration from a recently introduced exclusion process involving agents with non-zero size, we introduce a modified diffusion equation appropriate for describing transport in a non-ideal fluid of $d$-dimensional hard spheres. We consider applications of our equations to the problem of diffusion to an absorbing sphere in a non-ideal self-crowded fluid and to the problem of gravitational sedimentation. We show that our formalism allows one to recover known results. Moreover, we introduce the notions of point-like and extended crowding, which specify distinct routes for obtaining macroscopic transport equations from microscopic exclusion processes.

cond-mat.stat-mech↗

arXiv2013

Bose-Einstein Condensation versus Dicke-Hepp-Lieb Transition in an Optical Cavity

We provide an exact solution for the interplay between Bose-Einstein condensation and the Dicke-Hepp-Lieb self-organization transition of an ideal Bose gas trapped inside a single-mode optical cavity and subject to a transverse laser drive. Based on an effective action approach, we determine the full phase diagram at arbitrary temperature, which features a bi-critical point where the transitions cross. We calculate the dynamically generated band structure of the atoms and the associated supression of the critical temperature for Bose-Einstein condensation in the phase with a spontaneous periodic density modulation. Moreover, we determine the evolution of the polariton spectrum due to the coupling of the cavity photons and the atomic field near the self-organization transition, which is quite different above or below the Bose-Einstein condensation temperature. At low temperatures, the critical value of the Dicke-Hepp-Lieb transition decreases with temperature and thus thermal fluctuations can enhance the tendency to a periodic arrangement of the atoms.

cond-mat.quant-gas↗

arXiv2013

Critical velocity for a toroidal Bose-Einstein condensate flowing through a barrier

We consider the setup employed in a recent experiment (Ramanathan et al 2011 Phys. Rev. Lett. 106 130401) devoted to the study of the instability of the superfluid flow of a toroidal Bose-Einstein condensate in presence of a repulsive optical barrier. Using the Gross-Pitaevskii mean-field equation, we observe, consistently with what we found in Piazza et al (2009 Phys. Rev. A 80 021601), that the superflow with one unit of angular momentum becomes unstable at a critical strength of the barrier, and decays through the mechanism of phase slippage performed by pairs of vortex-antivortex lines annihilating. While this picture qualitatively agrees with the experimental findings, the measured critical barrier height is not very well reproduced by the Gross-Pitaevskii equation, indicating that thermal fluctuations can play an important role (Mathey et al 2012 arXiv:1207.0501). As an alternative explanation of the discrepancy, we consider the effect of the finite resolution of the imaging system. At the critical point, the superfluid velocity in the vicinity of the obstacle is always of the order of the sound speed in that region, $v_{\rm barr}=c_{\rm l}$. In particular, in the hydrodynamic regime (not reached in the above experiment), the critical point is determined by applying the Landau criterion inside the barrier region. On the other hand, the Feynman critical velocity $v_{\rm f}$ is much lower than the observed critical velocity. We argue that this is a general feature of the Gross-Pitaevskii equation, where we have $v_{\rm f}=ε c_{\rm l}$ with $ε$ being a small parameter of the model. Given these observations, the question still remains open about the nature of the superfluid instability.

cond-mat.quant-gas↗

arXiv2012

Sub shot-noise interferometry from measurements of the one-body density

We derive the asymptotic maximum-likelihood phase estimation uncertainty for any interferometric protocol where the positions of the probe particles are measured to infer the phase, but where correlations between the particles are not accessible. First, we apply our formula to the estimation of the phase acquired in the Mach-Zehnder interferometer and recover the well-know momentum formula for the phase sensitivity. Then, we apply our results to interferometers with two spatially separated modes, which could be implemented with a Bose-Einstein condensate trapped in a double-well potential. We show that in a simple protocol which estimates the phase from an interference pattern a sub shot-noise phase uncertainty of up to $Δθ\propto N^{-2/3}$ can be achieved. One important property of this estimation protocol is that its sensitivity does not depend on the value of the phase $θ$, contrary to the sensitivity given by the momentum formula for the Mach-Zehnder transformation. Finally, we study the experimental implementation of the above protocol in detail, by numerically simulating the full statistics as well as by considering the main sources of detection noise, and argue that the shot-noise limit could be surpassed with current technology.

quant-ph↗

arXiv2012

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into cumulus-type, i.e., those similar to puffy (white) clouds, and stratus-type, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an energy transfer mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by multi-trajectories; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach rarely visited but functionally-related states. We also show the role of disorder in spatial games of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks.

q-bio.MN↗

arXiv2010

Phase Estimation from Atom Position Measurements

We study the measurement of the position of atoms as a means to estimate the relative phase between two Bose-Einstein condensates. First, we consider $N$ atoms released from a double-well trap, forming an interference pattern, and show that a simple least-squares fit to the density gives a shot-noise limited sensitivity. The shot-noise limit can instead be overcome by using correlation functions of order $\sqrt{N}$ or larger. The measurement of the $N\mathrm{th}$-order correlation function allows to estimate the relative phase at the Heisenberg limit. Phase estimation through the measurement of the center-of-mass of the interference pattern can also provide sub-shot-noise sensitivity. Finally, we study the effect of the overlap between the two clouds on the phase estimation, when Mach-Zehnder interferometry is performed in a double-well.

cond-mat.quant-gas↗

arXiv2010

A simple Monte Carlo model for crowd dynamics

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 (ii) a rearrangement of the rest of the group through a Monte Carlo dynamics. The rules for the combined steps are determined by the specific setting of the granular flow, so that our scheme should be easily adapted to describe crowd dynamics issues of many sorts, from stampedes in panic scenarios to organized flow around obstacles or through bottlenecks. We validate our scheme by computing the serving times statistics of a group of agents crowding to be served around a desk. In the case of a size homogeneous crowd, we recover intuitive results prompted by physical sense. However, as a further illustration of our theoretical framework, we show that heterogeneous systems display a less obvious behavior, as smaller agents feature shorter serving times. Finally, we analyze our results in the light of known properties of non-equilibrium hard-disk fluids and discuss general implications of our model.

physics.soc-ph↗

arXiv2010

Phase Estimation With Interfering Bose-Condensed Atomic Clouds

We investigate how to estimate from atom-position measurements the relative phase of two Bose-Einstein condensates released from a double-well potential. We demonstrate that the phase estimation sensitivity via the fit of the average density to the interference pattern is fundamentally bounded by shot noise. This bound can be overcome by estimating the phase from the measurement of $\sqrt N$ (or higher) correlation function. The optimal estimation strategy requires the measurement of the $N$-th order correlation function. We also demonstrate that a second estimation method -- based on the detection of the center of mass of the interference pattern -- provides sub shot-noise sensitivity. Yet, the implementation of both protocols might be experimentally challenging.

cond-mat.quant-gas↗

arXiv2009

Rabi Interferometry and Sensitive Measurement of the Casimir-Polder Force with Ultra-Cold Gases

We show that Rabi oscillations of a degenerate fermionic or bosonic gas trapped in a double-well potential can be exploited for the interferometric measurement of external forces at micrometer length scales. The Rabi interferometer is less sensitive, but easier to implement, than the Mach-Zehnder since it does not require dynamical beam-splitting/recombination processes. As an application we propose a measurement of the Casimir-Polder force acting between the atoms and a dielectric surface. We find that even if the interferometer is fed with a coherent state of relatively small number of atoms, and in the presence of realistic experimental noise, the force can be measured with a sensitivity sufficient to discriminate between thermal and zero-temperature regimes of the Casimir-Polder potential. Higher sensitivities can be reached with spin squeezed states.

quant-ph↗

arXiv2009

Long-range energy transfer in proteins

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, like in the case of the visual pigment rhodopsin, or through the breaking of a chemical bond, as in the presence of adenosine triphosphate (ATP). Such energy, in turn, has to be transmitted to specific locations, often several tens of Angstroms away from where it is initially released. Here we show, within the framework of a coarse-grained nonlinear network model, that energy in a protein can jump from site to site with high yields, covering in many instances remarkably large distances. Following single-site excitations, few specific sites are targeted, systematically within the stiffest regions. Such energy transfers mark the spontaneous formation of a localized mode of nonlinear origin at the destination site, which acts as an efficient energy-accumulating centre. Interestingly, yields are found to be optimum for excitation energies in the range of biologically relevant ones.

q-bio.BM↗

arXiv2009

Energy transfer in nonlinear network models of proteins

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 sites, while depressing transfer to generic locations. Remarkably, transfer can be mediated by the self-localization of discrete breathers at distant locations from the kick, acting as efficient energy-accumulating centers.

cond-mat.soft↗

arXiv2009

Vibrational entropy and the structural organization of proteins

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 the Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force constants displayed by protein arrangements and also incorporates side-chain degrees of freedom. Our analysis shows that vibrational entropy per unit residue correlates with the content of secondary structure. Furthermore, we assess the individual contribution to vibrational entropy of the novel features of our scheme as compared with the predictions of state-of-the-art network models. This analysis highlights the importance of properly accounting for the intrinsic hierarchy in force strengths typical of the different atomic bonds that build up and stabilize protein scaffolds. Finally, we discuss possible implications of our findings in the context of protein aggregation phenomena.

q-bio.BM↗