Transition from stochastic to deterministic behavior in calcium oscillations

Simulation and modeling is becoming more and more important when studying complex biochemical systems. Most often, ordinary differential equations are employed for this purpose. However, these are only applicable when the numbers of participating molecules in the biochemical systems are large enough to be treated as concentrations. For smaller systems, stochastic simulations on discrete particle basis are more accurate. Unfortunately, there are no general rules for determining which method should be employed for exactly which problem to get the most realistic result. Therefore, we study the transition from stochastic to deterministic behavior in a widely studied system, namely the signal transduction via calcium, especially calcium oscillations. We observe that the transition occurs within a range of particle numbers, which roughly corresponds to the number of receptors and channels in the cell, and depends heavily on the attractive properties of the phase space of the respective systems dynamics. We conclude that the attractive properties of a system, expressed, e.g., by the divergence of the system, are a good measure for determining which simulation algorithm is appropriate in terms of speed and realism

PLoS One

Quantitative analysis of the vascular network anatomy is critical for the understanding of the vasculature structure and function. In this study, we have combined microcomputed tomography (microCT) and computational analysis to provide quantitative three-dimensional geometrical and topological characterization of the normal kidney vasculature, and to investigate how 2 core genes of the Wnt/planar cell polarity, Frizzled4 and Frizzled6, affect vascular network morphogenesis. Experiments were performed on frizzled4 (Fzd4-/-) and frizzled6 (Fzd6-/-) deleted mice and littermate controls (WT) perfused with a contrast medium after euthanasia and exsanguination. The kidneys were scanned with a high-resolution (16 μm) microCT imaging system, followed by 3D reconstruction of the arterial vasculature. Computational treatment includes decomposition of 3D networks based on Diameter-Defined Strahler Order (DDSO). We have calculated quantitative (i) Global scale parameters, such as the volume of the vasculature and its fractal dimension (ii) Structural parameters depending on the DDSO hierarchical levels such as hierarchical ordering, diameter, length and branching angles of the vessel segments, and (iii) Functional parameters such as estimated resistance to blood flow alongside the vascular tree and average density of terminal arterioles. In normal kidneys, fractal dimension was 2.07±0.11 (n = 7), and was significantly lower in Fzd4-/- (1.71±0.04; n = 4), and Fzd6-/- (1.54±0.09; n = 3) kidneys. The DDSO number was 5 in WT and Fzd4-/-, and only 4 in Fzd6-/-. Scaling characteristics such as diameter and length of vessel segments were altered in mutants, whereas bifurcation angles were not different from WT. Fzd4 and Fzd6 deletion increased vessel resistance, calculated using the Hagen-Poiseuille equation, for each DDSO, and decreased the density and the homogeneity of the distal vessel segments. Our results show that our methodology is suitable for 3D quantitative characterization of vascular networks, and that Fzd4 and Fzd6 genes have a deep patterning effect on arterial vessel morphogenesis that may determine its functional efficiency

Dolocitev velikosti in globine kraterjev na Luni

Experimental work in the research of astronomical phenomena is often difficult or even impossible because of long-lasting processes or too distant objects and correspondingly too expensive equipment. In this paper, we present an example of observation of the Moon, which is our nearest astronomic object and therefore does not require professional astronomic equipment for observation. We focus on the observation of craters on the Moon, determining their lateral size and depth on the basis of photographs and simple calculations. The fieldwork with students of junior grade school education was performed within the framework of the optional subject Astronomy. An analysis of the results of the students’ experimental work, as well as of curricula on various levels of education, led us to conclusion that this kind of experimental work is suitable for incorporation in secondary school physics education. With some mathematical simplifications, however, the treatment of the topic can also be appropriate in primary school. Such experimental work enables students to gain specific natural science and mathematical competences that are also required for the study of other natural phenomena. (DIPF/Orig.

Topologically determined optimal stochastic resonance responses of spatially embedded networks

We have analyzed the stochastic resonance phenomenon on spatial networks of bistable and excitable oscillators, which are connected according to their location and the amplitude of external forcing. By smoothly altering the network topology from a scale-free (SF) network with dominating long-range connections to a network where principally only adjacent oscillators are connected, we reveal that besides an optimal noise intensity, there is also a most favorable interaction topology at which the best correlation between the response of the network and the imposed weak external forcing is achieved. For various distributions of the amplitudes of external forcing, the optimal topology is always found in the intermediate regime between the highly heterogeneous SF network and the strong geometric regime. Our findings thus indicate that a suitable number of hubs and with that an optimal ratio between short- and long-range connections is necessary in order to obtain the best global response of a spatial network. Furthermore, we link the existence of the optimal interaction topology to a critical point indicating the transition from a long-range interactions-dominated network to a more lattice-like network structure

Evolutionary and dynamical coherence resonances in the pair approximated prisoner\u27s dilemma game

Stochasticity has recently emerged as being a potent promoter of cooperative behaviour in systems developed under the framework of evolutionary game theory. In the spatial prisoner\u27s dilemma game, the fitness of players adopting the cooperative strategy was found to be resonantly dependent on the intensity of payoff fluctuations. Evidently, the phenomenon resembles classical coherence resonance, whereby the noise-induced order, or coherence, of the dynamics is substituted with the noise-induced prevalence of the \u27good\u27 strategy, thus marking a constructive effect of noise on the system. The connection between the former \u27dynamical\u27 coherence resonance and the latter so-called \u27evolutionary\u27 coherence resonance, however, has not yet been established. The two different definitions of coherence resonance appear to provoke some discomfort. The goal of the present paper is therefore, on one hand, to draw a clear line between the two different perceptions of coherence resonance, and on the other, to show that the two apparently disjoint phenomena, that are currently related only by name, can in fact be observed simultaneously, sharing an identical mechanism of emergence

How optimal synchronization of oscillators depends on the network structure and the individual dynamical properties of the oscillators

The problem of making a network of dynamical systems synchronize onto a common evolution is the subject of much ongoing research in several scientific disciplines. It is nowadays a well-known fact that the synchronization processes are gradually in influenced by the interaction topology between the dynamically interacting units. A complex coupling configuration can significantly affect the synchronization abilities of a networked system. However, the question arises what is the optimal network topology that provides enhancement of the synchronization features under given circumstances. In order to address this issue we make use of a network model in which we can smoothly tune the topology from a highly heterogeneous and efficient scale-free network to a homogeneous and less efficient network. The network is then populated with Poincaré oscillators, a paradigmatic model for limit-cycle oscillations. This oscillator model exhibits a parameter that enables changes of the limit cycle attraction and is thus immediately related to flexibility/rigidity properties of the oscillator. Our results reveal that for weak attractions of the limit cycle, intermediate homogeneous topology ensures maximal synchronization, whereas highly heterogeneous scale-free topology ensures maximal synchronization for strong attractions of the limit cycle. We argue that the flexibility/rigidity of individual nodes of the networks defines the topology, where maximal global coherence is achieved