Investigation about the mechanisms involved in the onset of type 2 diabetes in absence of familiarity is the focus of a research project which has led to the development of a computational model that recapitulates the aetiology of the disease.

We consider the Erdös-Rényi random graph G(n,p) and we analyze the simple irreversible epidemic process on the graph, known in the literature as bootstrap percolation. We give a quantitative version of some results by Janson et al. (2012), providing a fine asymptotic analysis of the final size A_n of active nodes, under a suitable super-critical regime. More specifically, we establish large deviation principles for the sequence of random variables n-A_n/f (n) with explicit rate functions and allowing the scaling function f to vary in the widest possible range.

Single-cell RNA-seq (scRNAseq) is a powerful tool to study heterogeneity of cells. Recently, several clustering based methods have been proposed to identify distinct cell populations. These methods are based on different statistical models and usually require to perform several additional steps, such as preprocessing or dimension reduction, before applying the clustering algorithm. Individual steps are often controlled by method-specific parameters, permitting the method to be used in different modes on the same datasets, depending on the user choices.

Molecular dynamics (MD) has become one of the most powerful tools of investigation in soft matter. Despite such success, simulations of large molecular environments are mostly run using the approximation of closed systems without the possibility of exchange of matter. Due to the molecular complexity of soft matter systems, an optimal simulation strategy would require the application of concurrent multiscale resolution approaches such that each part of a large system can be considered as an open subsystem at a high resolution embedded in a large coarser reservoir of energy and particles.

Competition between biological species in marine environments is affected by the motion of the surrounding fluid. An effective 2D compressibility can arise, for example, from the convergence and divergence of water masses at the depth at which passively traveling photosynthetic organisms are restricted to live. In this report, we seek to quantitatively study genetics under flow. To this end, we couple an off-lattice agent-based simulation of two populations in 1D to a weakly compressible velocity field--first a sine wave and then a shell model of turbulence.

In Rayleigh-Bénard convection (RBC) for fluids with Prandtl number Pr1, rotation beyond a critical (small) rotation rate is known to cause a sudden enhancement of heat transfer, which can be explained by a change in the character of the boundary layer (BL) dynamics near the top and bottom plates of the convection cell. Namely, with increasing rotation rate, the BL signature suddenly changes from Prandtl-Blasius type to Ekman type.

Marine species reproduce and compete while being advected by turbulent flows. It is largely unknown, both theoretically and experimentally, how population dynamics and genetics are changed by the presence of fluid flows. Discrete agent-based simulations in continuous space allow for accurate treatment of advection and number fluctuations, but can be computationally expensive for even modest organism densities. In this report, we propose an algorithm to overcome some of these challenges. We first provide a thorough validation of the algorithm in one and two dimensions without flow.

Recent numerical analyses to optimize the design of microfluidic devices for more effective entrapment or segregation of surrogate circulating tumor cells (CTCs) from healthy cells have been reported in the literature without concurrently accommodating the non-Newtonian nature of the body fluid and the non-uniform geometric shapes of the CTCs.