Rescaling invariance and anomalous energy transport in a small vertical column of grains.

It is well known that energy dissipation and finite size can deeply affect the dynamics of granular matter, often making usual hydrodynamic approaches problematic. Here we report on the experimental investigation of a small model system, made of ten beads constrained into a 1D geometry by a narrow vertical pipe and shaken at the base by a piston excited by a periodic wave. Recording the beads motion with a high frame rate camera allows to investigate in detail the microscopic dynamics and test hydrodynamic and kinetic models. Varying the energy, we explore different regimes from fully fluidized to the edge of condensation, observing good hydrodynamic behavior down to the edge of fluidization, despite the small system size. Density and temperature fields for different system energies can be collapsed by suitable space and time rescaling, and the expected constitutive equation holds very well when the particle diameter is considered. At the same time, the balance between dissipated and fed energy is not well described by commonly adopted dependence due to the up-down symmetry breaking. Our observations, supported by the measured particle velocity distributions, show a different phenomenological temperature dependence, which yields equation solutions in agreement with experimental results.

Revealing the Nonequilibrium Nature of a Granular Intruder: The Crucial Role of Non-Gaussian Behavior.

The characterization of the distance from equilibrium is a debated problem in particular in the treatment of experimental signals. If the signal is a one-dimensional time series, such a goal becomes challenging. A paradigmatic example is the angular diffusion of a rotator immersed in a vibro-fluidized granular gas. Here, we experimentally observe that the rotator's angular velocity exhibits significant differences with respect to an equilibrium process. Exploiting the presence of two relevant timescales and non-Gaussian velocity increments, we quantify the breakdown of time-reversal asymmetry, which would vanish in the case of a 1D Gaussian process. We deduce a new model for the massive probe, with two linearly coupled variables, incorporating both Gaussian and Poissonian noise, the latter motivated by the rarefied collisions with the granular bath particles. Our model reproduces the experiment in a range of densities, from dilute to moderately dense, with a meaningful dependence of the parameters on the density. We believe the framework proposed here opens the way to a more consistent and meaningful treatment of out-of-equilibrium and dissipative systems.

Thermodynamic bounds for diffusion in nonequilibrium systems with multiple timescales.

We derive a thermodynamic uncertainty relation bounding the mean squared displacement of a Gaussian process with memory, driven out of equilibrium by unbalanced thermal baths and/or by external forces. Our bound is tighter with respect to previous results and also holds at finite time. We apply our findings to experimental and numerical data for a vibrofluidized granular medium, characterized by regimes of anomalous diffusion. In some cases our relation can distinguish between equilibrium and nonequilibrium behavior, a nontrivial inference task, particularly for Gaussian processes.

Collective Drifts in Vibrated Granular Packings: The Interplay of Friction and Structure.

We simulate vertically shaken dense granular packings with horizontal periodic boundary conditions. A coordinated translating motion of the whole medium emerges when the horizontal symmetry is broken by disorder or defects in the packing and the shaking is weak enough to conserve the structure. We argue that such a drift originates in the interplay between structural symmetry breaking and frictional forces transmitted by the vibrating plate. A nonlinear ratchet model with stick slips reproduces many faces of the phenomenon. The collective motion discussed here underlies phenomena observed recently with vibrofluidized granular materials, such as persistent rotations and anomalous diffusion.

Vicsek model by time-interlaced compression: A dynamical computable information density.

Collective behavior, both in real biological systems and in theoretical models, often displays a rich combination of different kinds of order. A clear-cut and unique definition of "phase" based on the standard concept of the order parameter may therefore be complicated, and made even trickier by the lack of thermodynamic equilibrium. Compression-based entropies have been proved useful in recent years in describing the different phases of out-of-equilibrium systems. Here, we investigate the performance of a compression-based entropy, namely, the computable information density, within the Vicsek model of collective motion. Our measure is defined through a coarse graining of the particle positions, in which the key role of velocities in the model only enters indirectly through the velocity-density coupling. We discover that such entropy is a valid tool in distinguishing the various noise regimes, including the crossover between an aligned and misaligned phase of the velocities, despite the fact that velocities are not explicitly used. Furthermore, we unveil the role of the time coordinate, through an encoding recipe, where space and time localities are both preserved on the same ground, and find that it enhances the signal, which may be particularly significant when working with partial and/or corrupted data, as is often the case in real biological experiments.

Engineered swift equilibration of a Brownian gyrator.

In the context of stochastic thermodynamics, a minimal model for nonequilibrium steady states has been recently proposed: the Brownian gyrator (BG). It describes the stochastic overdamped motion of a particle in a two-dimensional harmonic potential, as in the classic Ornstein-Uhlenbeck process, but considering the simultaneous presence of two independent thermal baths. When the two baths have different temperatures, the steady BG exhibits a rotating current, a clear signature of nonequilibrium dynamics. Here, we consider a time-dependent potential, and we apply a reverse-engineering approach to derive exactly the required protocol to switch from an initial steady state to a final steady state in a finite time τ. The protocol can be built by first choosing an arbitrary quasistatic counterpart, with few constraints, and then adding a finite-time contribution which only depends upon the chosen quasistatic form and which is of order 1/τ. We also get a condition for transformations which, in finite time, conserve internal energy, useful for applications such as the design of microscopic thermal engines. Our study extends finite-time stochastic thermodynamics to transformations connecting nonequilibrium steady states.

Intra-operative enteroscopy for the identification of obscure bleeding source caused by gastrointestinal angiodysplasias: through a balloon-tip trocar is better.

AIM: Intra-operative enteroscopy (IE) is a valid diagnostic tool which can be adopted in order to identify the precise location of bleeding gastrointestinal angiodysplasias (GIADs) of the small bowel. We describe a novel IE technique that may increase the diagnostic yield by maintaining a steady distension of the bowel and that prevents microtrauma to the intestinal mucosa and spillage of enteric content into the operative field. METHODS: After laparotomy, a centimetric transverse enterotomy is performed approximately at the middle of the small bowel. A 12-mm trocar with balloon is then introduced and insufflated. The small bowel is gently distended by carbon dioxide insufflation. Through the trocar, a paediatric colonscope is then inserted and the enteroscopy is performed either retrogradely to the duodenum or anterogradely to the caecum. Once located, surgery is tailored to the precise site of bleeding, with a consequent sparing of intestinal resection. RESULTS: IE with 12-mm trocar with balloon was adopted in four elderly patients undergoing surgery for bleeding GIADs. The length of small bowel resection ranged from 10 to 200 cm, depending on the number of GIADs. Operating time ranged from 210 to 275 min. Intra-operative blood loss was nil. No patient developed organ-space or wound infections. There was no recurrence of bleeding from the midgut. CONCLUSION: Performing IE through a balloon trocar may increase the diagnostic accuracy of the procedure with the benefit of reducing the risk of traumatic injury to the bowel and the risk of surgical site infection.

Spontaneous Velocity Alignment in Motility-Induced Phase Separation.

We study a system of purely repulsive spherical self-propelled particles in the minimal setup inducing motility-induced phase separation (MIPS). We show that, even if explicit alignment interactions are absent, a growing order in the velocities of the clustered particles accompanies MIPS. Particles arrange into aligned or vortexlike domains whose size increases as the persistence of the self-propulsion grows, an effect that is quantified studying the spatial correlation function of the velocities. We explain the velocity alignment by unveiling a hidden alignment interaction of the Vicsek-like form, induced by the interplay between steric interactions and self-propulsion.

Dynamical Collective Memory in Fluidized Granular Materials.

Recent experiments with rotational diffusion of a probe in a vibrated granular media revealed a rich scenario, ranging from a dilute gas to a dense liquid with cage effects and an unexpected superdiffusive behavior at large times. Here we set up a simulation that reproduces quantitatively the experimental observations and allows us to investigate the properties of the host granular medium, a task not feasible in the experiment. We discover a persistent collective rotational mode which emerges at a high density and a low granular temperature: a macroscopic fraction of the medium slowly rotates, randomly switching direction after very long times. Such a rotational mode of the host medium is the origin of the probe's superdiffusion. Collective motion is accompanied by a kind of dynamical heterogeneity at intermediate times (in the cage stage) followed by a strong reduction of fluctuations at late times, when superdiffusion sets in.

Anomalous mobility of a driven active particle in a steady laminar flow.

We study, via extensive numerical simulations, the force-velocity curve of an active particle advected by a steady laminar flow, in the nonlinear response regime. Our model for an active particle relies on a colored noise term that mimics its persistent motion over a time scale [Formula: see text]. We find that the active particle dynamics shows non-trivial effects, such as negative differential and absolute mobility (NDM and ANM, respectively). We explore the space of the model parameters and compare the observed behaviors with those obtained for a passive particle ([Formula: see text]) advected by the same laminar flow. Our results show that the phenomena of NDM and ANM are quite robust with respect to the details of the considered noise: in particular for finite [Formula: see text] a more complex force-velocity relation can be observed.

Controlled Viscosity in Dense Granular Materials.

We experimentally investigate the fluidization of a granular material subject to mechanical vibrations by monitoring the angular velocity of a vane suspended in the medium and driven by an external motor. On increasing the frequency, we observe a reentrant transition, as a jammed system first enters a fluidized state, where the vane rotates with high constant velocity, and then returns to a frictional state, where the vane velocity is much lower. While the fluidization frequency is material independent, the viscosity recovery frequency shows a clear dependence on the material that we rationalize by relating this frequency to the balance between dissipative and inertial forces in the system. Molecular dynamics simulations well reproduce the experimental data, confirming the suggested theoretical picture.

Lattice Model to Derive the Fluctuating Hydrodynamics of Active Particles with Inertia.

We derive the hydrodynamic equations with fluctuating currents for the density, momentum, and energy fields for an active system in the dilute limit. In our model, nonoverdamped self-propelled particles (such as grains or birds) move on a lattice, interacting by means of aligning dissipative forces and excluded volume repulsion. Our macroscopic equations, in a specific case, reproduce a transition line from a disordered phase to a swarming phase and a linear dispersion law accounting for underdamped wave propagation. Numerical simulations up to a packing fraction ∼10% are in fair agreement with the theory, including the macroscopic noise amplitudes. At a higher packing fraction, a dense-diluted coexistence emerges. We underline the analogies with the granular kinetic theories, elucidating the relation between the active swarming phase and granular shear instability.

Anomalous force-velocity relation of driven inertial tracers in steady laminar flows.

We study the nonlinear response to an external force of an inertial tracer advected by a two-dimensional incompressible laminar flow and subject to thermal noise. In addition to the driving external field F, the main parameters in the system are the noise amplitude [Formula: see text] and the characteristic Stokes time [Formula: see text] of the tracer. The relation velocity vs. force shows interesting effects, such as negative differential mobility (NDM), namely a non-monotonic behavior of the tracer velocity as a function of the applied force, and absolute negative mobility (ANM), i.e. a net motion against the bias. By extensive numerical simulations, we investigate the phase chart in the parameter space of the model, [Formula: see text], identifying the regions where NDM, ANM and more common monotonic behaviors of the force-velocity curve are observed.

Self-propulsion against a moving membrane: Enhanced accumulation and drag force.

Self-propulsion (SP) is a main feature of active particles (AP), such as bacteria or biological micromotors, distinguishing them from passive colloids. A renowned consequence of SP is accumulation at static interfaces, even in the absence of hydrodynamic interactions. Here we address the role of SP in the interaction between AP and a moving semipermeable membrane. In particular, we implement a model of noninteracting AP in a channel crossed by a partially penetrable wall, moving at a constant velocity c. With respect to both the cases of passive colloids with c>0 and AP with c=0, the AP with finite c show enhancement of accumulation in front of the obstacle and experience a largely increased drag force. This effect is understood in terms of an effective potential localised at the interface between particles and membrane, of height proportional to cτ/ξ, where τ is the AP's reorientation time and ξ the width characterizing the surface's smoothness (ξ→0 for hard core obstacles). An approximate analytical scheme is able to reproduce the observed density profiles and the measured drag force, in very good agreement with numerical simulations. The effects discussed here can be exploited for automatic selection and filtering of AP with desired parameters.

Nonlinear Response of Inertial Tracers in Steady Laminar Flows: Differential and Absolute Negative Mobility.

We study the mobility and the diffusion coefficient of an inertial tracer advected by a two-dimensional incompressible laminar flow, in the presence of thermal noise and under the action of an external force. We show, with extensive numerical simulations, that the force-velocity relation for the tracer, in the nonlinear regime, displays complex and rich behaviors, including negative differential and absolute mobility. These effects rely upon a subtle coupling between inertia and applied force that induces the tracer to persist in particular regions of phase space with a velocity opposite to the force. The relevance of this coupling is revisited in the framework of nonequilibrium response theory, applying a generalized Einstein relation to our system. The possibility of experimental observation of these results is also discussed.

The biomolecular corona of nanoparticles in circulating biological media.

When nanoparticles come into contact with biological media, they are covered by a biomolecular 'corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (≈40 cm s(-1)). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.

Ratchet effect driven by Coulomb friction: the asymmetric Rayleigh piston.

The effect of Coulomb friction is studied in the framework of collisional ratchets. It turns out that the average drift of these devices can be expressed as the combination of a term related to the lack of equipartition between the probe and the surrounding bath, and a term featuring the average frictional force. We illustrate this general result in the asymmetric Rayleigh piston, showing how Coulomb friction can induce a ratchet effect in a Brownian particle in contact with an equilibrium bath. An explicit analytical expression for the average velocity of the piston is obtained in the rare collision limit. Numerical simulations support the analytical findings.

Nonequilibrium and information: the role of cross correlations.

We discuss the relevance of information contained in cross correlations among different degrees of freedom, which is crucial in nonequilibrium systems. In particular we consider a stochastic system where two degrees of freedom X{1} and X{2}-in contact with two different thermostats-are coupled together. The production of entropy and the violation of equilibrium fluctuation-dissipation theorem (FDT) are both related to the cross correlation between X{1} and X{2}. Information about such cross correlation may be lost when single-variable reduced models for X_{1} are considered. Two different procedures are typically applied: (a) one totally ignores the coupling with X{2}; and (b) one models the effect of X{2} as an average memory effect, obtaining a generalized Langevin equation. In case (a) discrepancies between the system and the model appear both in entropy production and linear response; the latter can be exploited to define effective temperatures, but those are meaningful only when time scales are well separated. In case (b) linear response of the model well reproduces that of the system; however the loss of information is reflected in a loss of entropy production. When only linear forces are present, such a reduction is dramatic and makes the average entropy production vanish, posing problems in interpreting FDT violations.

Pebbles and PebbleJuggler: software for accurate, unbiased, and fast measurement and analysis of nanoparticle morphology from transmission electron microscopy (TEM) micrographs.

Pebbles is a user-friendly software program which implements an accurate, unbiased, and fast method to measure the morphology of a population of nanoparticles (NPs) from TEM micrographs. The morphological parameters of the projected NP shape are obtained by fitting intensity models to the TEM micrograph. Pebbles can be used either in automatic mode, where both fitting and validation are reliably carried out with minimal human intervention, and in manual mode, where the user has full control on the fitting and validation steps. Accuracy in diameter measurement has been shown to be ≲1%. When operated in automatic mode, Pebbles can be very fast. The effective speed of 1 NP s⁻¹ has been achieved in favorable cases (packed monolayer of NPs). Since Pebbles is based on a local modeling procedure, it successfully treats cases such as low contrast NPs, NPs with significant diffraction scattering, and inhomogeneous background which often make conventional thresholding procedures fail. Pebbles is accompanied by PebbleJuggler, a software program for the statistical analysis of the sets of best-fit NP models created by Pebbles. Effort has been devoted to make Pebbles and PebbleJuggler the most user-friendly and the least user-tedious we could. Pebbles and PebbleJuggler are available at http://pebbles.istm.cnr.it.

Nonequilibrium fluctuations in a driven stochastic Lorentz gas.

We study the stationary state of a one-dimensional kinetic model where a probe particle is driven by an external field E and collides, elastically or inelastically, with a bath of particles at temperature T. We focus on the stationary distribution of the velocity of the particle, and of two estimates of the total entropy production Δs(tot). One is the entropy production of the medium Δs(m), which is equal to the energy exchanged with the scatterers, divided by a parameter θ, coinciding with the particle temperature at E=0. The other is the work W done by the external field, again rescaled by θ. At small E, a good collapse of the two distributions is found: in this case, the two quantities also verify the fluctuation relation (FR), indicating that both are good approximations of Δs(tot). Differently, for large values of E, the fluctuations of W violate the FR, while Δs(m) still verifies it.