Bayesian inference of epidemics on network

Jacopo Bindi

I study inference problems for irreversible stochastic epidemic models on network via Belief Propagation algorithm. Previous works derive equations which allow to compute posterior distributions of the time evolution of the state of each node given some observation. It has already been shown that this method outperforms previous ones in the particular case of finding "patient zero" of a SIR epidemic given an observation at a later unknown time. I study performances of this method on the inference of the time evolution of a SIR epidemic subsequent a given observation.

Experimental investigation of symmetry breaking in chemotactic directional sensing

Federica Chianale

Molecular probes for specific lipid species, present in the plasma membrane, allow the real time observation in living cells of the symmetry-breaking events occuring during cell migration. Indeed, the accumulation of PI(3,4,5)P3 at the leading edge is one of the earliest symmetry-breaking events and is functional for the stabilization of new cell protrusions. Based on experimental evidence, a positive feedback loop between actin polymerization and PI(3,4,5)P3 accumulation has been hypothesized in several cell models (Dictyostelium discoideum, neutrophils, fibroblasts); however, the molecular details underlying this positive feedback loop still remain to be identified. Taking advantage of a specific PI(3,4,5)P3 probe and of live TIRF microscopy, we are testing the hypothesis that a physical interaction between PI3K, the enzyme producing PI(3,4,5)P3, and WAVE proteins is responsible for the actin-PI(3,4,5)P3 positive feedback loop at the plasma membrane of extending lamellipodia.

Signal localization as a phase separation process

Andrea Gamba

It is well known that ultrasensitivity (Goldbeter & Koshland, 1981) is the core of many bistable switches in biological systems. It is not as well recognized that when ultrasensitive self-amplifying circuits are diffusively coupled in a spatially distributed system such as the cell plasmamembrane, they may induce its dynamic separation into distinct signaling phases. This basic mechanism lays behind the process of cell membrane polarization in many, diverse biological systems. Cell membrane polarization is implicated in basic biological phenomena such as differentiation, proliferation, migration and morphogenesis of unicellular and multicellular organisms. Physical models based on the coupling of membrane diffusion with bistable enzymatic dynamics can reproduce a broad range of symmetry-breaking events, such as those observed in eukaryotic directional sensing, the apico-basal polarization of epithelial cells, the polarization of budding and mating yeast.

Spatial disorder in the Voter Model

Claudio Borile

When we try to study the organization and the properties of ecological systems, non-equilibrium statistical physics is a natural candidate to develop a unified framework for understanding the emergent properties of these kind of systems. Simple interacting particle systems, such as the Voter Model (VM), have found a surprisingly good agreement with empirical data and proved to be a useful null-model that can be treated analytically. Despite the recent progress in this field, still a major issue in ecology and conservation ecology is to understand the effects of habitat fragmentation and heterogeneities on the biodiversity of an ecosystem. Motivated by this open problem, we study the effects of quenched spatial disorder on the long-time behavior of the VM and its nonlinear generalizations.

Topological transition in secondary structure of RNA-like polymer

Olga Valba, Moscow Institute of Physics and Technology (PhysTech)

In my report I will show that the secondary structures of random
heteropolymers undergo a topological transition. Namely, for c less than the critical value the fraction of "active'' nucleotides (which form the base pairs) tends to 1 as the length of the chain goes to infinity, signaling the formation of a virtually "perfect'' secondary structure without gaps. In turn,
for c > c_{cr} always a non-perfect structure with gaps is formed. It was proved mathematically that 2 < c_{cr} < 3; our current research deals with determination a value of transition point; it directly connects with developing new methods to generate random sequences with "effectively" non integer alphabet.
Our previous results have shown that transition point is very close to alphabet used by Nature in real RNAs. Such a critical behavior can point to some statistical exclusivity of natural alphabet.

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