Transport and nonequilibrium phase transitions in polygonal urn models.

We study the deterministic dynamics of N point particles moving at a constant speed in a 2D table made of two polygonal urns connected by an active rectangular channel, which applies a feedback control on the particles, inverting the horizontal component of their velocities when their number in the channel exceeds a fixed threshold. Such a bounce-back mechanism is non-dissipative: it preserves volumes in phase space. An additional passive channel closes the billiard table forming a circuit in which a stationary current may flow. Under specific constraints on the geometry and on the initial conditions, the large N limit allows nonequilibrium phase transitions between homogeneous and inhomogeneous phases. The role of ergodicity in making a probabilistic theory applicable is discussed for both rational and irrational urns. The theoretical predictions are compared with the numerical simulation results. Connections with the dynamics of feedback-controlled biological systems are highlighted.

Learning models for classifying Raman spectra of genomic DNA from tumor subtypes.

An early and accurate detection of different subtypes of tumors is crucial for an effective guidance to personalized therapy and in predicting the ability of tumor to metastasize. Here we exploit the Surface Enhanced Raman Scattering (SERS) platform, based on disordered silver coated silicon nanowires (Ag/SiNWs), to efficiently discriminate genomic DNA of different subtypes of melanoma and colon tumors. The diagnostic information is obtained by performing label free Raman maps of the dried drops of DNA solutions onto the Ag/NWs mat and leveraging the classification ability of learning models to reveal the specific and distinct physico-chemical interaction of tumor DNA molecules with the Ag/NW, here supposed to be partly caused by a different DNA methylation degree.

Quantitative analysis of phase formation and growth in ternary mixtures upon evaporation of one component.

We perform a quantitative analysis of Monte Carlo simulation results of phase separation in ternary blends upon evaporation of one component. Specifically, we calculate the average domain size and plot it as a function of simulation time to compute the exponent of the obtained power law. We compare and discuss results obtained by two different methods, for three different models: two-dimensional (2D) binary-state model (Ising model), 2D ternary-state model with and without evaporation. For the ternary-state models, we study additionally the dependence of the domain growth on concentration, temperature and initial composition. We reproduce the expected 1/3 exponent for the Ising model, while for the ternary-state model without evaporation and for the one with evaporation we obtain lower values of the exponent. It turns out that phase separation patterns that can form in this type of systems are complex. The obtained quantitative results give valuable insights towards devising computable theoretical estimations of size effects on morphologies as they occur in the context of organic solar cells.

Statistical Classification for Raman Spectra of Tumoral Genomic DNA.

We exploit Surface-Enhanced Raman Scattering (SERS) to investigate aqueous droplets of genomic DNA deposited onto silver-coated silicon nanowires, and we show that it is possible to efficiently discriminate between spectra of tumoral and healthy cells. To assess the robustness of the proposed technique, we develop two different statistical approaches, one based on the Principal Components Analysis of spectral data and one based on the computation of the ℓ2 distance between spectra. Both methods prove to be highly efficient, and we test their accuracy via the Cohen's κ statistics. We show that the synergistic combination of the SERS spectroscopy and the statistical analysis methods leads to efficient and fast cancer diagnostic applications allowing rapid and unexpansive discrimination between healthy and tumoral genomic DNA alternative to the more complex and expensive DNA sequencing.

Deterministic model of battery, uphill currents, and nonequilibrium phase transitions.

We consider point particles in a table made of two circular cavities connected by two rectangular channels, forming a closed loop under periodic boundary conditions. In the first channel, a bounce-back mechanism acts when the number of particles flowing in one direction exceeds a given threshold T. In that case, the particles invert their horizontal velocity, as if colliding with vertical walls. The second channel is divided in two halves parallel to the first but located in the opposite sides of the cavities. In the second channel, motion is free. We show that, suitably tuning the sizes of cavities of the channels and of T, nonequilibrium phase transitions take place in the N→∞ limit. This induces a stationary current in the circuit, thus modeling a kind of battery, although our model is deterministic, conservative, and time reversal invariant.

A lattice model for active-passive pedestrian dynamics: a quest for drafting effects.

We study the pedestrian escape from an obscure room using a lattice gas model with two species of particles. One species, called passive, performs a symmetric random walk on the lattice, whereas the second species, called active, is subject to a drift guiding the particles towards the exit. The drift mimics the awareness of some pedestrians of the geometry of the room and of the location of the exit. We provide numerical evidence that, in spite of the hard core interaction between particles-namely, there can be at most one particle of any species per site-adding a fraction of active particles in the system enhances the evacuation rate of all particles from the room. A similar effect is also observed when looking at the outgoing particle flux, when the system is in contact with an external particle reservoir that induces the onset of a steady state. We interpret this phenomenon as a discrete space counterpart of the drafting effect typically observed in a continuum set-up as the aerodynamic drag experienced by pelotons of competing cyclists.

Competitive nucleation in reversible probabilistic cellular automata.

The problem of competitive nucleation in the framework of probabilistic cellular automata is studied from the dynamical point of view. The dependence of the metastability scenario on the self-interaction is discussed. An intermediate metastable phase, made of two flip-flopping chessboard configurations, shows up depending on the ratio between the magnetic field and the self-interaction. A behavior similar to the one of the stochastic Blume-Capel model with Glauber dynamics is found.

Residence time of symmetric random walkers in a strip with large reflective obstacles.

We study the effect of a large obstacle on the so-called residence time, i.e., the time that a particle performing a symmetric random walk in a rectangular (two-dimensional, 2D) domain needs to cross the strip. We observe complex behavior: We find out that the residence time does not depend monotonically on the geometric properties of the obstacle, such as its width, length, and position. In some cases, due to the presence of the obstacle, the mean residence time is shorter with respect to the one measured for the obstacle-free strip. We explain the residence time behavior by developing a one-dimensional (1D) analog of the 2D model where the role of the obstacle is played by two defect sites having smaller probability to be crossed with respect to all the other regular sites. The 1D and 2D models behave similarly, but in the 1D case we are able to compute exactly the residence time, finding a perfect match with the Monte Carlo simulations.

Stationary uphill currents in locally perturbed zero-range processes.

Uphill currents are observed when mass diffuses in the direction of the density gradient. We study this phenomenon in stationary conditions in the framework of locally perturbed one-dimensional zero range processes (ZRPs). We show that the onset of currents flowing from the reservoir with smaller density to the one with larger density can be caused by a local asymmetry in the hopping rates on a single site at the center of the lattice. For fixed injection rates at the boundaries, we prove that a suitable tuning of the asymmetry in the bulk may induce uphill diffusion at arbitrarily large, finite volumes. We also deduce heuristically the hydrodynamic behavior of the model and connect the local asymmetry characterizing the ZRP dynamics to a matching condition relevant for the macroscopic problem.

Blockage-induced condensation controlled by a local reaction.

We consider the setup of stationary zero range models and discuss the onset of condensation induced by a local blockage on the lattice. We show that the introduction of a local feedback on the hopping rates allows us to control the particle fraction in the condensed phase. This phenomenon results in a current versus blockage parameter curve characterized by two nonanalyticity points.

Lattice model of reduced jamming by a barrier.

We study an asymmetric simple exclusion process in a strip in the presence of a solid impenetrable barrier. We focus on the effect of the barrier on the residence time of the particles, namely, the typical time needed by the particles to cross the whole strip. We explore the conditions for reduced jamming when varying the environment (different drifts, reservoir densities, horizontal diffusion walks, etc.). In particular, we discover an interesting nonmonotonic behavior of the residence time as a function of the barrier length. Besides recovering by means of both the lattice dynamics and the mean-field model well-known aspects like the faster-is-slower effect and the intermittence of the flow, we propose also a birth-and-death process and a reduced one-dimensional (1D) model with variable barrier permeability to capture the behavior of the residence time with respect to the parameters.

Kink localization under asymmetric double-well potentials.

We study diffuse phase interfaces under asymmetric double-well potential energies with degenerate minima and demonstrate that the limiting sharp profile, for small interface energy cost, on a finite space interval is in general not symmetric and its position depends exclusively on the second derivatives of the potential energy at the two minima (phases). We discuss an application of the general result to porous media in the regime of solid-fluid segregation under an applied pressure and describe the interface between a fluid-rich and a fluid-poor phase.

Monte Carlo study of gating and selection in potassium channels.

The study of selection and gating in potassium channels is a very important issue in modern biology. Indeed, such structures are known in essentially all types of cells in all organisms where they play many important functional roles. The mechanism of gating and selection of ionic species is not clearly understood. In this paper we study a model in which gating is obtained via an affinity-switching selectivity filter. We discuss the dependence of selectivity and efficiency on the cytosolic ionic concentration and on the typical pore open state duration. We demonstrate that a simple modification in the way in which the selectivity filter is modeled yields larger channel efficiency.

Phase coexistence in consolidating porous media.

The appearance of the fluid-rich phase in saturated porous media under the effect of an external pressure is investigated. For this purpose we introduce a two field second gradient model allowing the complete description of the phenomenon. We study the coexistence profile between poor and rich fluid phases and we show that for a suitable choice of the parameters nonmonotonic interfaces show up at coexistence.