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In this paper we study $g$-fractional diffusion on bounded domains in $\mathbb{R}^d$ with absorbing boundary conditions. We show the explicit representation of the solution and then we study the first passage time distribution, showing the dependence on the particular choice of the function $g$. Then, we specialize the analysis to the interesting case of a rectangular domain. Finally we briefly discuss the connection of this general theory with the physical application to the so-called fractional Dodson diffusion model recently discussed in the literature.

In the recent literature, the g-subdiffusion equation involving Caputo fractional derivatives with respect to another function has been studied in relation to anomalous diffusions with a continuous transition between different subdiffusive regimes. In this paper we study the problem of g-fractional diffusion in a bounded domain with absorbing boundaries. We find the explicit solution for the initial-boundary value problem and we study the first passage time distribution and the mean first-passage time (MFPT). An interestin outcome is the proof that with a particular choice of the function $g$ it is possible to obtain a finite MFPT, differently from the anomalous diffusion described by a fractional heat equation involving the classical Caputo derivative., Comment: Accepted by Phys. Rev. E

Besides the dynamical slowing down signaled by an enormous increase of the viscosity approaching the glass transition, structural glasses show interesting anomalous thermodynamic features at low temperatures that hint at peculiar deviations from Debye's law at low enough frequencies. Theory, numerical simulations, and experiments suggest that deviation from Debye's law is due to soft-localized glassy modes that populate the low-frequency spectrum. We study the localization properties of the low-frequency modes in a three-dimensional supercooled liquid model. The density of states $D(\omega)$ is computed considering the inherent structures of configurations well thermalized at parental temperatures close to the dynamical transition $T_\text d$. We observe a crossover in the probability distribution of the inverse of the participation ratio that happens approaching $T_\text d$ from high temperatures. We show that a similar crossover is observed at high parental temperature when the translational invariance of the system is explicitly broken by a random pinning field., Comment: 10 pages, 7 figures

We solve the problem of first-passage time for run-and-tumble particles in one dimension. Exact expression is derived for the mean first-passage time in the general case, considering external force-fields and chemotactic-fields, giving rise to space dependent swim-speed and tumble rate. Agreement between theoretical formulae and numerical simulations is obtained in the analyzed case studies -- constant and sinusoidal force fields, constant gradient chemotactic field. Reported findings can be useful to get insights into very different phenomena involving active particles, such as bacterial motion in external fields, intracellular transport, cell migration, animal foraging.

We numerically study the dynamics of run-and-tumble particles confined in two chambers connected by thin channels. Two dominant dynamical behaviors emerge: (i) an oscillatory pumping state, in which particles periodically fill the two vessels and (ii) a circulating flow state, dynamically maintaining a near constant population level in the containers when connected by two channels. We demonstrate that the oscillatory behaviour arises from the combination of a narrow channel, preventing bacteria reorientation, and a density dependent motility inside the chambers.

The random energy landscapes developed by speckle fields can be used to confine and manipulate a large number of micro-particles with a single laser beam. By means of molecular dynamics simulations, we investigate the static and dynamic properties of an active suspension of swimming bacteria embedded into speckle patterns. Looking at the correlation of the density fluctuations and the equilibrium density profiles, we observe a crossover phenomenon when the forces exerted by the speckles are equal to the bacteria's propulsion.

{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles or equivalently of very low concentrations. However, in situations of practical interest, the concentration of bacteria is always large enough to make interactions an important factor. Using molecular dynamics simulations, we study the dynamic structure factor of a model bacterial bath for increasing values of densities. We show that it is possible to reproduce the dynamics of density fluctuations in the system using a free run-and-tumble model with effective fitting parameters. We discuss the dependence of these parameters, e.g., the tumbling rate, tumbling time and self-propulsion velocity, on the density of the bath.

Self-propelling bacteria are a dream of nano-technology. These unicellular organisms are not just capable of living and reproducing, but they can swim very efficiently, sense the environment and look for food, all packaged in a body measuring a few microns. Before such perfect machines could be artificially assembled, researchers are beginning to explore new ways to harness bacteria as propelling units for micro-devices. Proposed strategies require the careful task of aligning and binding bacterial cells on synthetic surfaces in order to have them work cooperatively. Here we show that asymmetric micro-gears can spontaneously rotate when immersed in an active bacterial bath. The propulsion mechanism is provided by the self assembly of motile Escherichia coli cells along the saw-toothed boundaries of a nano-fabricated rotor. Our results highlight the technological implications of active matter's ability to overcome the restrictions imposed by the second law of thermodynamics on equilibrium passive fluids., Comment: 4 pages, 3 figures

We investigate mode-locking processes in lasers displaying a variable degree of structural randomness, from standard optical cavities to multiple-scattering media. By employing methods mutuated from spin-glass theory, we analyze the mean-field Hamiltonian and derive a phase-diagram in terms of the pumping rate and the degree of disorder. Three phases are found: i) paramagnetic, corresponding to a noisy continuous wave emission, ii) ferromagnetic, that describes the standard passive mode-locking, and iii) the spin-glass in which the phases of the electromagnetic field are frozen in a exponentially large number of configurations. The way the mode-locking threshold is affected by the amount of disorder is quantified. The results are also relevant for other physical systems displaying a random Hamiltonian, like Bose-Einstein condensates and nonlinear optical beams., Comment: 4 pages, 2 figures

The thermodynamics and topology of mean-field models with 2+k body interaction terms (generalizing XY model) are derived. Focusing on two particular cases (2+4 and 2+6 body interaction terms), a comparison between thermodynamic (phase transition energy, thermodynamically forbidden energy regions) and topological (singularity and curvature of saddle entropy) properties is performed. We find that i) a topological change is present at the phase transition energy; however, ii) only one topological change occurs, also for those models exhibiting two phase transitions; iii) the order of a phase transition is not completely signaled by the curvature of topological quantities., Comment: 7 pages, 9 figures

We report on a statistical approach to mode-locking transitions of nano-structured laser cavities characterized by an enhanced density of states. We show that the equations for the interacting modes can be mapped onto a statistical model exhibiting a first order thermodynamic transition, with the average mode-energy playing the role of inverse temperature. The transition corresponds to a phase-locking of modes. Extended modes lead to a mean-field like model, while in presence of localized modes, as due to a small disorder, the model has short range interactions. We show that simple scaling arguments lead to observable differences between transitions involving extended modes and those involving localized modes. We also show that the dynamics of the light modes can be exactly solved, predicting a jump in the relaxation time of the coherence functions at the transition. Finally, we link the thermodynamic transition to a topological singularity of the phase space, as previously reported for similar models., Comment: 10 pages, 5 figures

We study the nonlinear dynamics of a multi-mode random laser using the methods of statistical physics of disordered systems. A replica-symmetry breaking phase transition is predicted as a function of the pump intensity. We thus show that light propagating in a random non-linear medium displays glassy behavior, i.e. the photon gas has a multitude of metastable states and a non vanishing complexity, corresponding to mode-locking processes in random lasers. The present work reveals the existence of new physical phenomena, and demonstrates how nonlinear optics and random lasers can be a benchmark for the modern theory of complex systems and glasses., Comment: 5 pages, 1 figure

We numerically calculate the configurational entropy S_conf of a binary mixture of hard spheres, by using a perturbed Hamiltonian method trapping the system inside a given state, which requires less assumptions than the previous methods [R.J. Speedy, Mol. Phys. 95, 169 (1998)]. We find that S_conf is a decreasing function of packing fraction f and extrapolates to zero at the Kauzmann packing fraction f_K = 0.62, suggesting the possibility of an ideal glass-transition for hard spheres system. Finally, the Adam-Gibbs relation is found to hold., Comment: 10 pages, 6 figures

We address the question of the quantitative relationship between thermodynamic phase transitions and topological changes in the potential energy manifold analyzing two classes of one dimensional models, the Burkhardt solid-on-solid model and the Peyrard-Bishop model for DNA thermal denaturation, both in the confining and non-confining version. These models, apparently, do not fit [M.Kastner, Phys. Rev. Lett. 93, 150601 (2004)] in the general idea that the phase transition is signaled by a topological discontinuity. We show that in both models the phase transition energy v_c is actually non-coincident with, and always higher than, the energy v_theta at which a topological change appears. However, applying a procedure already successfully employed in other cases as the mean field phi^4 model, i.e. introducing a map M(v)=v_s from levels of the energy hypersurface V to the level of the stationary points "visited" at temperature T, we find that M(v_c)=v_theta. This result enhances the relevance of the underlying stationary points in determining the thermodynamics of a system, and extends the validity of the topological approach to the study of phase transition to the elusive one-dimensional systems considered here., Comment: 10 pages, 9 figures, to appear in PRE

We report a numerical study of saddles properties of the potential energy landscape for soft spheres with different softness, i.e. different power n of the interparticle repulsive potential. We find that saddle-based quantities rescale into master curves once energies and temperatures are scaled by mode-coupling temperature T_MCT, confirming and generalizing previous findings obtained for Lennard-Jones like models., Comment: 2 pages, 2 figures

We study the thermodynamics and the properties of the stationary points (saddles and minima) of the potential energy for a phi^4 mean field model. We compare the critical energy Vc (i.e. the potential energy V(T) evaluated at the phase transition temperature Tc) with the energy V{theta} at which the saddle energy distribution show a discontinuity in its derivative. We find that, in this model, Vc >> V{theta}, at variance to what has been found in the literature for different mean field and short ranged systems. By direct calculation of the energy Vs(T) of the ``inherent saddles'', i.e. the saddles visited by the equilibrated system at temperature T, we find that Vs(Tc) ~ V{theta}. Thus, we argue that the thermodynamic phase transition is related to a change in the properties of the inherent saddles rather then to a change of the topology of the potential energy surface at T=Tc. Finally, we discuss the approximation involved in our analysis and the generality of our method., Comment: 14 pages, 9 figures

By numerical simulation of a Lennard-Jones like liquid driven by a velocity gradient \gamma we test the fluctuation relation (FR) below the (numerical) glass transition temperature T_g. We show that, in this region, the FR deserves to be generalized introducing a numerical factor X(T,\gamma)<1 that defines an ``effective temperature'' T_{FR}=T/X. On the same system we also measure the effective temperature T_{eff}, as defined from the generalized fluctuation-dissipation relation, and find a qualitative agreement between the two different nonequilibrium temperatures., Comment: Version accepted for publication on Phys.Rev.E; major changes, 1 figure added

We discuss the microscopic definition of entropy production rate in a model of a dissipative system: a sheared fluid in which the kinetic energy is kept constant via a Gaussian thermostat. The total phase space contraction rate is the sum of two statistically independent contributions: the first one is due to the work of the conservative forces, is independent of the driving force and does not vanish at zero drive, making the system non-conservative also in equilibrium. The second is due to the work of the dissipative forces, and is responsible for the average entropy production; the distribution of its fluctuations is found to verify the Fluctuation Relation of Gallavotti and Cohen. The distribution of the fluctuations of the total phase space contraction rate also verify the Fluctuation Relation. It is compared with the same quantity calculated in the isoenergetic ensemble: we find that the two ensembles are equivalent, as conjectured by Gallavotti. Finally, we discuss the implication of our results for experiments trying to verify the validity of the FR., Comment: 8 pages, 4 figures

Lennard-Jones glasses (made on a computer by quenching from liquid state coordinates) are studied in harmonic approximation. Vibrational eigenfrequencies and eigenvectors are found by exact diagonalization for models with periodic boundaries and N=(500, 2048, and 6980) atoms. We analyze the density of states, mobility edge, and bond-stretching character of the normal modes. In agreement with older work of Grest, Nagel, and Rahman, the upper 7% of modes are localized, and the rest, delocalized. We find that modes can not be differentiated by any property or quantum number except their eigenfrequency. More specifically, in a given narrow frequency interval, all modes are globally identical. Transverse or longitudinal character, for example, disappears., Comment: 4 pages, 4 embedded figures

The study of the effects of the density variations on the vibrational dynamics in vitreous silica is presented. A detailed analysis of the dynamical structure factor, as well as of the current spectra, allows the identification of a flattened transverse branch which is highly sensitive to the density variations. The experimental variations on the intensity and position of the Boson Peak (BP) in v-SiO2 as a function of density are reproduced and interpreted as being due to the shift and disappearance of the latter band. The BP itself is found to correspond to the lower energy tail of the excess states due to the piling up of vibrational modes at energies corresponding to the flattening of the transverse branch., Comment: 6 pages, 5 figures

Features of the energy landscape sampled by supercooled liquids are numerically analyzed for several Lennard-Jones like model systems. The properties of quasisaddles (minima of the square gradient of potential energy W=|grad V|^2), are shown to have a direct relationship with the dynamical behavior, confirming that the quasisaddle order extrapolates to zero at the mode-coupling temperature T_MCT. The same result is obtained either analyzing all the minima of W or the saddles (absolute minima of W), supporting the conjectured similarity between quasisaddles and saddles, as far as the temperature dependence of the properties influencing the slow dynamics is concerned. We find evidence of universality in the shape of the landscape: plots for different systems superimpose into master curves, once energies and temperatures are scaled by T_MCT. This allows to establish a quantitative relationship between T_MCT and potential energy barriers for LJ-like systems, and suggests a possible generalization to different model liquids., Comment: 8 pages, 5 figures

We analyze the dynamics and the geometric properties of the Potential Energy Surfaces (PES) of the k-Trigonometric Model (kTM), defined by a fully-connected k-body interaction. This model has no thermodynamic transition for k=1, a second order one for k=2, and a first order one for k>2. In this paper we i) show that the single particle dynamics can be traced back to an effective dynamical system (with only one degree of freedom); ii) compute the diffusion constant analytically; iii) determine analytically several properties of the self correlation functions apart from the relaxation times which we calculate numerically; iv) relate the collective correlation functions to the ones of the effective degree of freedom using an exact Dyson-like equation; v) using two analytical methods, calculate the saddles of the PES that are visited by the system evolving at fixed temperature. On the one hand we minimize |grad V|^2, as usually done in the numerical study of supercooled liquids and, on the other hand, we compute the saddles with minimum distance (in configuration space) from initial equilibrium configurations. We find the same result from the two calculations and we speculate that the coincidence might go beyond the specific model investigated here., Comment: 36 pages, 13 figures

The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from liquid down to the supercooled regime, from T =2 down to T =0.46. One thousand of independent configurations along the time evolution have been examined at each investigated temperature. From the starting configuration we searched the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of saddle, other quantities show some signature of the approaching of the dynamical arrest temperature., Comment: 15 pages, 8 figures, to be published on Journal of Physics: Cond. Matt

We use the saddle-approach, recently introduced in the numerical investigation of simple model liquids, in the analysis of a mean-field solvable system. The investigated system is the k-trigonometric model, a k-body interaction mean field system, that generalizes the trigonometric model introduced by Madan and Keyes [J. Chem. Phys. 98, 3342 (1993)] and that has been recently introduced to investigate the relationship between thermodynamics and topology of the configuration space. We find a close relationship between the properties of saddles (stationary points of the potential energy surface) visited by the system and the dynamics. In particular the temperature dependence of saddle order follows that of the diffusivity, both having an Arrhenius behavior at low temperature and a similar shape in the whole temperature range. Our results confirm the general usefulness of the saddle-approach in the interpretation of dynamical processes taking place in interacting systems., Comment: 7 pages, 8 figures

We present a numerical simulation study of the density-dependence (rho = 2.2 - 4.0 g/cm^3) of the high-energy collective dynamics in vitreous silica at mesoscopic wavevectors (Q = 1 - 18 nm^-1). The density-dependence of the longitudinal and transverse current spectra provides evidence that the excess modes observed in the density of states of this and many other glasses, i.e. the Boson Peak, arises from the high-Q limit of the quasi-transverse acoustic branch. This conclusion emerges from the comparison of the numerical results with the experimentally observed energy-shift and intensity variation of the Boson Peak with increasing density., Comment: 8 pages, 4 figures

We show that the presence and the location of first order phase transitions in a thermodynamic system can be deduced by the study of the topology of the potential energy function, V(q), without introducing any thermodynamic measure. In particular, we present the thermodynamics of an analytically solvable mean-field model with a k-body interaction which -depending on the value of k- displays no transition (k=1), second order (k=2) or first order (k>2) phase transition. This rich behavior is quantitatively retrieved by the investigation of a topological invariant, the Euler characteristic, of some submanifolds of the configuration space. Finally, we conjecture a direct link between the Euler characteristic and the thermodynamic entropy., Comment: 6 pages, 2 figures

We present a numerical simulation study of a simple monatomic Lennard-Jones liquid under shear flow, as a function of both temperature and shear rate. By investigating different observables we find that i) It exists a line in the (temperature-shear) plane that sharply marks the boarder between an ``equilibrium'' and a ``shear-controlled'' region for both the dynamic and the thermodynamic quantities; and ii) Along this line the structural relaxation time, is proportional to the inverse shear rate, i.e. to the typical time-scale introduced by the shear flow. Above the line the liquid dynamics is unaffected by the shear flow, while below it both temperature and shear rate control the particle motion., Comment: 14 pages, 5 figures

The supercooled dynamics of a Lennard-Jones model liquid is numerically investigated studying relevant points of the potential energy surface, i.e. the minima of the square gradient of total potential energy $V$. The main findings are: ({\it i}) the number of negative curvatures $n$ of these sampled points appears to extrapolate to zero at the mode coupling critical temperature $T_c$; ({\it ii}) the temperature behavior of $n(T)$ has a close relationship with the temperature behavior of the diffusivity; ({\it iii}) the potential energy landscape shows an high regularity in the distances among the relevant points and in their energy location. Finally we discuss a model of the landscape, previously introduced by Madan and Keyes [J. Chem. Phys. {\bf 98}, 3342 (1993)], able to reproduce the previous findings., Comment: To be published in J. Chem. Phys

Numerical simulation is employed to study dynamical heterogeneities in model harmonic glasses whose atoms interact via three variants of the Lennard-Jones potential (monoatomic full Lennard-Jones, soft spheres, binary mixture). Heterogeneities are observed to exist in all three kinds of glasses, and in some cases they are observed to depend on temperature. The dimension of the heterogeneities is studied for the full Lennard-Jones case., Comment: 3 pages, 5 PS figures; submitted to Phys. Rev. Lett

The aging dynamics of a simple model glass is numerically investigated observing how it takes place in the potential energy landscape $V$. Partitioning the landscape in basins of minima of $|\nabla V|^2$, we are able to elucidate some interesting topological properties of the aging process. The main result is the characterization of the long time behavior as a jump dynamics between basins of attraction of minima. Moreover we extract some information about the landscape itself, determining quantitatively few parameters describing it, such as the mean energy barrier value and the mean square distance between adjacent minima., Comment: 8th International Workshop on Disordered Systems, Andalo (Trento), Italy, March 2001

We numerically investigate the aging dynamics of a monatomic Lennard-Jones glass, focusing on the topology of the potential energy landscape which, to this aim, has been partitioned in basins of attraction of stationary points (saddles and minima). The analysis of the stationary points visited during the aging dynamics shows the existence of two distinct regimes: i) at short times, tt_c, the system mainly lies in basins pertaining to minima of slowly decreasing energy. The dynamics for t>t_c can be represented by a simple random walk on a network of minima with a jump probability proportional to the inverse of the waiting time., Comment: 4 pages, 5 postscript figures

We numerically investigate the supercooled dynamics of two simple model liquids exploiting the partition of the multi-dimension configuration space in basins of attraction of the stationary points (inherent saddles) of the potential energy surface. We find that the inherent saddles order and potential energy are well defined functions of the temperature T. Moreover, decreasing T, the saddle order vanishes at the same temperature (T_MCT) where the inverse diffusivity appears to diverge as a power law. This allows a topological interpretation of T_MCT: it marks the transition from a dynamics between basins of saddles (T>T_MCT) to a dynamics between basins of minima (T

Three classes of harmonic disorder systems (Lennard-Jones like glasses, percolators above threshold, and spring disordered lattices) have been numerically investigated in order to clarify the effect of different types of disorder on the mechanism of high frequency sound attenuation. We introduce the concept of frustration in structural glasses as a measure of the internal stress, and find a strong correlation between the degree of frustration and the exponent alpha that characterizes the momentum dependence of the sound attenuation $Gamma(Q)$$\simeq$$Q^\alpha$. In particular, alpha decreases from about d+1 in low-frustration systems (where d is the spectral dimension), to about 2 for high frustration systems like the realistic glasses examined., Comment: Revtex, 4 pages including 4 figures

The off-equilibrium dynamics of a monatomic Lennard-Jones glass is investigated after sudden isothermal density jumps (crunch) from well equilibrated liquid configurations towards the glassy state. The generalized fluctuation-dissipation relation has been studied and the temperature dependence of the violation factor m is found in agreement with the one step replica symmetry breaking scenario, i.e. at low temperature m(T) is found proportional to T up to an off-equilibrium effective temperature T_eff, where m(T_eff)=1. We report T_eff as a function of the density and compare it with the glass transition temperatures T_g as determined by equilibrium calculations., Comment: 4 pages,4 figures

We analyze the properties of a Lennard-Jones system at the level of the potential energy landscape. After an exhaustive investigation of the topological features of the landscape of the systems, obtained studying small size sample, we describe the dynamics of the systems in the multi-dimensional configurational space by a simple model. This consider the configurational space as a connected network of minima where the dynamics proceeds by jumps described by an appropriate master equation. Using this model we are able to reproduce the long time dynamics and the low temperature regime. We investigate both the equilibrium regime and the off-equilibrium one, finding those typical glassy behavior usually observed in the experiments such as: {\it i)} stretched exponential relaxation, {\it ii)} temperature-dependent stretching parameter, {\it iii)} breakdown of the Stokes-Einstein relation, and {\it iv)} appearance of a critical temperature below which one observes deviation from the fluctuation-dissipation relation as consequence of the lack of equilibrium in the system., Comment: 11 pages (Latex), 9 ps figures