Monte Carlo Algorithms for the Partition Function and Information Rates of Two-Dimensional Channels

The paper proposes Monte Carlo algorithms for the computation of the information rate of two-dimensional source/channel models. The focus of the paper is on binary-input channels with constraints on the allowed input configurations. The problem of numerically computing the information rate, and even the noiseless capacity, of such channels has so far remained largely unsolved. Both problems can be reduced to computing a Monte Carlo estimate of a partition function. The proposed algorithms use tree-based Gibbs sampling and multilayer (multitemperature) importance sampling. The viability of the proposed algorithms is demonstrated by simulation results

Generalized Belief Propagation for the Noiseless Capacity and Information Rates of Run-Length Limited Constraints

The performance of the generalized belief propagation algorithm for computing the noiseless capacity and mutual information rates of finite-size two-dimensional and three-dimensional run-length limited constraints is investigated. For each constraint, a method is proposed to choose the basic regions and to construct the region graph. Simulation results for the capacity of different constraints as a function of the size of the channel and mutual information rates of different constraints as a function of signal-to-noise ratio are reported. Convergence to the Shannon capacity is also discussed.Comment: 8 pages, 11 figure

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio