Glass models on Bethe lattices

We consider ``lattice glass models'' in which each site can be occupied by at most one particle, and any particle may have at most l occupied nearest neighbors. Using the cavity method for locally tree-like lattices, we derive the phase diagram, with a particular focus on the vitreous phase and the highest packing limit. We also study the energy landscape via the configurational entropy, and discuss different equilibrium glassy phases. Finally, we show that a kinetic freezing, depending on the particular dynamical rules chosen for the model, can prevent the equilibrium glass transitions.Comment: 24 pages, 11 figures; minor corrections + enlarged introduction and conclusio

Edge usage, motifs and regulatory logic for cell cycling genetic networks

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression patterns? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeast, fission yeast and mammals. First, we show that the networks in each of the ensembles use just a few interactions that are repeatedly reused as building blocks. Second, we find an enrichment in network motifs that is similar in the two yeast cell cycle systems investigated. These motifs do not have autonomous functions, but nevertheless they reveal a regulatory logic for cell cycling based on a feed-forward cascade of activating interactions.Comment: 9 pages, 9 figures, to be published in Phys. Rev.

Symmetry-protected Topological Phases at Finite Temperature

We have applied the recently developed theory of topological Uhlmann numbers to a representative model of a topological insulator in two dimensions, the Qi-Wu-Zhang model. We have found a stable symmetry-protected topological (SPT) phase under external thermal fluctuations in two-dimensions. A complete phase diagram for this model is computed as a function of temperature and coupling constants in the original Hamiltonian. It shows the appearance of large stable phases of matter with topological properties compatible with thermal fluctuations or external noise and the existence of critical lines separating abruptly trivial phases from topological phases. These novel critical temperatures represent thermal topological phase transitions. The initial part of the paper comprises a self-contained explanation of the Uhlmann geometric phase needed to understand the topological properties that it may acquire when applied to topological insulators and superconductors.Comment: Contribution to the focus issue on "Artificial Graphene". Edited by Maciej Lewenstein, Vittorio Pellegrini, Marco Polini and Mordechai (Moti) Sege