Numerical analysis of a mechanotransduction dynamical model reveals homoclinic bifurcations of extracellular matrix mediated oscillations of the mesenchymal stem cell fate

We perform one and two-parameter numerical bifurcation analysis of a mechanotransduction model approximating the dynamics of mesenchymal stem cell differentiation into neurons, adipocytes, myocytes and osteoblasts. For our analysis, we use as bifurcation parameters the stiffness of the extracellular matrix and parameters linked with the positive feedback mechanisms that up-regulate the production of the YAP/TAZ transcriptional regulators (TRs) and the cell adhesion area. Our analysis reveals a rich nonlinear behaviour of the cell differentiation including regimes of hysteresis and multistability, stable oscillations of the effective adhesion area, the YAP/TAZ TRs and the PPAR$\gamma$ receptors associated with the adipogenic fate, as well as homoclinic bifurcations that interrupt relatively high-amplitude oscillations abruptly. The two-parameter bifurcation analysis of the Andronov-Hopf points that give birth to the oscillating patterns predicts their existence for soft extracellular substrates ($<1kPa$), a regime that favours the neurogenic and the adipogenic cell fate. Furthermore, in these regimes, the analysis reveals the presence of homoclinic bifurcations that result in the sudden loss of the stable oscillations of the cell-substrate adhesion towards weaker adhesion and high expression levels of the gene encoding Tubulin beta-3 chain, thus favouring the phase transition from the adipogenic to the neurogenic fate

Construction of embedded fMRI resting state functional connectivity networks using manifold learning

We construct embedded functional connectivity networks (FCN) from benchmark resting-state functional magnetic resonance imaging (rsfMRI) data acquired from patients with schizophrenia and healthy controls based on linear and nonlinear manifold learning algorithms, namely, Multidimensional Scaling (MDS), Isometric Feature Mapping (ISOMAP) and Diffusion Maps. Furthermore, based on key global graph-theoretical properties of the embedded FCN, we compare their classification potential using machine learning techniques. We also assess the performance of two metrics that are widely used for the construction of FCN from fMRI, namely the Euclidean distance and the lagged cross-correlation metric. We show that the FCN constructed with Diffusion Maps and the lagged cross-correlation metric outperform the other combinations

Tuning the average path length of complex networks and its influence to the emergent dynamics of the majority-rule model

We show how appropriate rewiring with the aid of Metropolis Monte Carlo computational experiments can be exploited to create network topologies possessing prescribed values of the average path length (APL) while keeping the same connectivity degree and clustering coefficient distributions. Using the proposed rewiring rules we illustrate how the emergent dynamics of the celebrated majority-rule model are shaped by the distinct impact of the APL attesting the need for developing efficient algorithms for tuning such network characteristics.Comment: 10 figure

Focusing Revisited: an MN-dynamics Approach

The nonlinear Schr{\"o}dinger (NLS) equation is a ubiquitous example of an envelope wave equation for conservative, dispersive systems. We revisit here the problem of self-similar focusing of waves in the case of the focusing NLS equation through the prism of a dynamic renormalization technique (MN dynamics) that factors out self-similarity and yields a bifurcation view of the onset of focusing. As a result, identifying the focusing self-similar solution becomes a steady state problem. The discretized steady states are subsequently obtained and their linear stability is numerically examined. The calculations are performed in the setting of variable index of refraction, in which the onset of focusing appears as a supercritical bifurcation of a novel type of mixed Hamiltonian-dissipative dynamical system (reminiscent, to some extent, of a pitchfork bifurcation).Comment: 6 pages, 2 figure

Microscopic/stochastic timesteppers and coarse control: a kinetic Monte Carlo example

Coarse timesteppers provide a bridge between microscopic / stochastic system descriptions and macroscopic tasks such as coarse stability/bifurcation computations. Exploiting this computational enabling technology, we present a framework for designing observers and controllers based on microscopic simulations, that can be used for their coarse control. The proposed methodology provides a bridge between traditional numerical analysis and control theory on the one hand and microscopic simulation on the other

Reducing wildland fire hazard exploiting complex network theory. A case study analysis

We discuss a new systematic methodology to mitigate wildland fire hazard by appropriately distributing fuel breaks in space. In particular, motivated by the concept of information flow in complex networks we create a hierarchical allocation of the landscape patches that facilitate the fire propagation based on the Bonacich centrality. Reducing the fuel load in these critical patches results to lower levels of fire hazard. For illustration purposes we apply the proposed strategy to a real case of wildland fire. In particular we focus on the wildland fire that occurred in Spetses Island, Greece in 1990 and burned the one third of the forest. The efficiency of the proposed strategy is compared against the benchmark of random distribution of fuel breaks for a wide range of fuel breaks densities

Coarse-graining the dynamics of network evolution: the rise and fall of a networked society

We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be developed. We illustrate our approach through a particular social network model: the "rise and fall" of a networked society [1]: we implement our low-dimensional description computationally using the equation-free approach and show how it can be used to (a) accelerate simulations and (b) extract system-level stability/bifurcation information from the detailed dynamic model. We discuss other system-level tasks that can be enabled through such a computer-assisted coarse graining approach.Comment: 18 pages, 11 figure

Coarse Brownian Dynamics for Nematic Liquid Crystals: Bifurcation Diagrams via Stochastic Simulation

We demonstrate how time-integration of stochastic differential equations (i.e. Brownian dynamics simulations) can be combined with continuum numerical bifurcation analysis techniques to analyze the dynamics of liquid crystalline polymers (LCPs). Sidestepping the necessity of obtaining explicit closures, the approach analyzes the (unavailable in closed form) coarse macroscopic equations, estimating the necessary quantities through appropriately initialized, short bursts of Brownian dynamics simulation. Through this approach, both stable and unstable branches of the equilibrium bifurcation diagram are obtained for the Doi model of LCPs and their coarse stability is estimated. Additional macroscopic computational tasks enabled through this approach, such as coarse projective integration and coarse stabilizing controller design, are also demonstrated

Can social microblogging be used to forecast intraday exchange rates?

The Efficient Market Hypothesis (EMH) is widely accepted to hold true under certain assumptions. One of its implications is that the prediction of stock prices at least in the short run cannot outperform the random walk model. Yet, recently many studies stressing the psychological and social dimension of financial behavior have challenged the validity of the EMH. Towards this aim, over the last few years, internet-based communication platforms and search engines have been used to extract early indicators of social and economic trends. Here, we used Twitter's social networking platform to model and forecast the EUR/USD exchange rate in a high-frequency intradaily trading scale. Using time series and trading simulations analysis, we provide some evidence that the information provided in social microblogging platforms such as Twitter can in certain cases enhance the forecasting efficiency regarding the very short (intradaily) forex.Comment: This is a prior version of the paper published at NETNOMICS. The final publication is available at http://www.springer.com/economics/economic+theory/journal/1106