Publications

In critical systems, the effect of a localized perturbation affects points that are arbitrarily far from the perturbation location. In this paper, we study the effect of localized perturbations on the solution of the random dimer problem in two dimensions. By means of an accurate numerical analysis, we show that a local perturbation of the optimal covering induces an excitation whose size is extensive with finite probability. We compute the fractal dimension of the excitations and scaling exponents. In particular, excitations in random dimer problems on nonbipartite lattices have the same statistical properties of domain walls in spin glass. Excitations produced in bipartite lattices, instead, are compatible with a loop-erased self-avoiding random walk process. In both cases, we find evidence of conformal invariance of the excitations that is compatible with $SLE_{\kappa}$ with parameter $\kappa$ depending on the bipartiteness of the underlying lattice only.

We consider the problem of recovering an unknown $k$-factor, hidden in a weighted random graph. For $k=1$ this is the planted matching problem, while the $k=2$ case is closely related to the planted travelling salesman problem. The inference problem is solved by exploiting the information arising from the use of two different distributions for the weights on the edges inside and outside the planted sub-graph. We argue that, in the large size limit, a phase transition can appear between a full and a partial recovery phase as function of the signal-to-noise ratio. We give a criterion for the location of the transition.

We introduce a mean-field framework for the study of systems of interacting particles sharing a conserved quantity. The work generalises and unites the existing fields of asset-exchange models, often applied to socio-economic systems, and aggregation-fragmentation models, typically used in modelling the dynamics of clusters. An initial model includes only two-body collisions, which is then extended to include many-body collisions and spontaneous fragmentation. We derive self-consistency equations for the steady-state distribution, which can be solved using a population dynamics algorithm, as well as a full solution for the time evolution of the moments, corroborated with numerical simulations. The generality of the model makes it applicable to many problems and allows for the study of systems exhibiting more complex interactions that those typically considered. The work is relevant to the modelling of barchan dune fields in which interactions between the bedforms and spontaneous fragmentation due to changes in the wind are thought to lead to size-selection. Our work could also be applied in finding wealth distributions when agents can both combine assets as well as split into multiple subsidiaries.

Abstract: Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation, see e.g. Lodish et al. (Molecular cell biology, 8th edn, W.H. Freeman and Company, San Francisco, 2016). In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a totally asymmetric simple exclusion process coupled to a finite diffusive reservoir, which we call the ribosome transport model with diffusion. In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion is not a rate limiting factor in translation initiation because diffusion is fast enough in biological cells. Graphic abstract: [Figure not available: see fulltext.].

We explore glassy dynamics of dense assemblies of soft particles that are self-propelled by active forces. These forces have a fixed amplitude and a propulsion direction that varies on a timescale τp, the persistence timescale. Numerical simulations of such active glasses are computationally challenging when the dynamics is governed by large persistence times. We describe in detail a recently proposed scheme that allows one to study directly the dynamics in the large persistence time limit, on timescales around and well above the persistence time. We discuss the idea behind the proposed scheme, which we call “activity-driven dynamics”, as well as its numerical implementation. We establish that our prescription faithfully reproduces all dynamical quantities in the appropriate limit τp → ∞. We deploy the approach to explore in detail the statistics of Eshelby-like plastic events in the steady state dynamics of a dense and intermittent active glass.

During development, gene regulatory networks allocate cell fates by partitioning tissues into spatially organised domains of gene expression. How the sharp boundaries that delineate these gene expression patterns arise, despite the stochasticity associated with gene regulation, is poorly understood. We show, in the vertebrate neural tube, using perturbations of coding and regulatory regions, that the structure of the regulatory net- work contributes to boundary precision. This is achieved, not by reducing noise in individual genes, but by the configuration of the network modulating the ability of stochastic fluctuations to initiate gene expression changes. We use a computational screen to identify network properties that influence boundary precision, revealing two dynamical mechanisms by which small gene circuits attenuate the effect of noise in order to increase patterning precision. These results highlight design principles of gene regulatory networks that produce precise patterns of gene expression.

In this paper we study the out-of-equilibrium phase diagram of the quantum version of Derrida’s random energy model, which is the simplest model of mean-field spin glasses. We interpret its corresponding quantum dynamics in Fock space as a one-particle problem in very high dimension to which we apply different theoretical methods tailored for high-dimensional lattices: the forward-scattering approximation, a mapping to the Rosenzweig-Porter model, and the cavity method. Our results indicate the existence of two transition lines and three distinct dynamical phases: a completely many-body localized phase at low energy, a fully ergodic phase at high energy, and a multifractal "bad metal"phase at intermediate energy. In the latter, eigenfunctions occupy a diverging volume yet an exponentially vanishing fraction of the total Hilbert space. We discuss the limitations of our approximations and the relationship with previous studies.

In modern society people are being exposed to numerous information, with some of them being frequently repeated or more disruptive than others. In this paper we use a model of opinion dynamics to study how this news impact the society. In particular, our study aims to explain how the exposure of the society to certain events deeply change peopletextquoterights perception of the present and future. The evolution of opinions which we consider is influenced both by external information and the pressure of the society. The latter includes imitation, differentiation, homophily and its opposite, xenophobia. The combination of these ingredients gives rise to a collective memory effect, which is triggered by external information. In this paper we focus our attention on how this memory arises when the order of appearance of external news is random. We will show which characteristics a piece of news needs to have in order to be embedded in the societytextquoterights memory. We will also provide an analytical way to measure how many information a society can remember when an extensive number of news items is presented. Finally we will show that, when a certain piece of news is present in the societytextquoterights history, even a distorted version of it is sufficient to trigger the memory of the originally stored information.

Although the spectral properties of random graphs have been a long-standing focus of network theory, the properties of right eigenvectors of directed graphs have so far eluded an exact analytic treatment. We present a general theory for the statistics of the right eigenvector components in directed random graphs with a prescribed degree distribution and with randomly weighted links. We obtain exact analytic expressions for the inverse participation ratio and show that right eigenvectors of directed random graphs with a small average degree are localized. Remarkably, if the fourth moment of the degree distribution is finite, then the critical mean degree of the localization transition is independent of the degree fluctuations, which is different from localization in undirected graphs that is governed by degree fluctuations. We also show that in the high connectivity limit the distribution of the right eigenvector components is solely determined by the degree distribution. For delocalized eigenvectors, we recover in this limit the universal results from standard random matrix theory that are independent of the degree distribution, while for localized eigenvectors the eigenvector distribution depends on the degree distribution.

We focus on the energy landscape of a simple mean-field model of glasses and analyze activated barrier-crossing by combining the Kac-Rice method for high-dimensional Gaussian landscapes with dynamical field theory. In particular, we consider Langevin dynamics at low temperature in the energy landscape of the pure spherical p-spin model. We select as initial condition for the dynamics one of the many unstable index-1 saddles in the vicinity of a reference local minimum. We show that the associated dynamical mean-field equations admit two solutions: one corresponds to falling back to the original reference minimum, and the other to reaching a new minimum past the barrier. By varying the saddle we scan and characterize the properties of such minima reachable by activated barrier-crossing. Finally, using time-reversal transformations, we construct the two-point function dynamical instanton of the corresponding activated process.