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At least 1,657 records · Page 92Linked to original sources
PubMed2002

Growing scale-free networks with small-world behavior.

In the context of growing networks, we introduce a simple dynamical model that unifies the generic features of real networks: scale-free distribution of degree and the small-world effect. While the average shortest path length increases logarithmically as in random networks, the clustering coefficient assumes a large value independent of system size. We derive analytical expressions for the clustering coefficient in two limiting cases: random [C approximately (ln N)(2)/N] and highly clustered (C=5/6) scale-free networks.

Journal Article↗
PubMed2004

Hierarchy measures in complex networks.

Using each node's degree as a proxy for its importance, the topological hierarchy of a complex network is introduced and quantified. We propose a simple dynamical process used to construct networks which are either maximally or minimally hierarchical. Comparison with these extremal cases as well as with random scale-free networks allows us to better understand hierarchical versus modular features in several real-life complex networks. For random scale-free topologies the extent of topological hierarchy is shown to smoothly decline with gamma, the exponent of a degree distribution, reaching its highest possible value for gamma</=2 and quickly approaching zero for gamma>3.

Journal Article↗
PubMed2000

The dynamics of a neuronal culture of dissociated cortical neurons of neonatal rats.

Neuronal networks of dissociated cortical neurons from neonatal rats were cultured over a multielectrode dish with 64 active sites, which were used both for recording the electrical activity and for stimulation. After about 4 weeks of culture, a dense network of neurons had developed and their electrical activity was studied. When a brief voltage pulse was applied to one extracellular electrode, a clear electrical response was evoked over almost the entire network. When a strong voltage pulse was used, the response was composed of an early phase, terminating within 25 ms, and a late phase which could last several hundreds of milliseconds. Action potentials evoked during the early phase occurred with a precise timing with a small jitter and the electrical activity initiated by a localized stimulation diffused significantly over the network. In contrast, the late phase was characterized by the occurrence of clusters of electrical activity with significant spatio-temporal fluctuations. The late phase was suppressed by adding small amounts of D(-)-2-amino-5-phosphonovaleric acid to the extracellular medium, or by increasing the amount of extracellular Mg2+. The electrical activity of the network was substantially increased by the addition of bicuculline to the extracellular medium. The results presented here show that the neuronal network may exist in two different dynamical states: one state in which the neuronal network behaves as a non-chaotic deterministic system and another state where the system exhibits large spatio-temporal fluctuations, characteristic of stochastic or chaotic systems.

Action Potentials↗
PubMed2006

Self-associating block copolymer networks for microchip electrophoresis provide enhanced DNA separation via "inchworm" chain dynamics.

We describe a novel class of DNA separation media for microchip electrophoresis, "physically cross-linked" block copolymer networks, which provide rapid (<4.5 min) and remarkably enhanced resolution of DNA in a size range critical for genotyping. Linear poly(acrylamide-co-dihexylacrylamide) (LPA-co-DHA) comprising as little as 0.13 mol % dihexylacrylamide yields substantially improved electrophoretic DNA separations compared to matched molar mass linear polyacrylamide. Single-molecule videomicroscopic images of DNA electrophoresis reveal novel chain dynamics in LPA-co-DHA matrixes, resembling inchworm movement, to which we attribute the increased DNA resolution. Substantial improvements in DNA peak separation are obtained, in particular, in LPA-co-DHA solutions at polymer/copolymer concentrations near the interchain entanglement threshold. Higher polymer concentrations yield enhanced separations only for small DNA molecules (<120 base pairs). Hydrophobically cross-linked networks offer advantages over conventional linear polymers based on enhanced separation performance (or speed) and over chemically cross-linked gels because hydrophobic cross-links can be reversibly broken, allowing facile microchannel loading.

DNA↗
PubMed1999

Dynamic updating in DIAS-NIDDM and DIAS causal probabilistic networks.

Diabetes advisory system (DIAS) is a decision support system, which has been developed to provide advice on the amount of insulin injected by subjects with insulin-dependent diabetes mellitus (IDDM). DIAS employs a temporal causal probabilistic network (CPN) to implement a stochastic model of carbohydrate metabolism. The CPN network has recently been extended to provide also advice to subjects with noninsulin-dependent diabetes mellitus (NIDDM). However, due to increased complexity and size of the extended CPN the calculations became unfeasible. The CPN network was, therefore, simplified and a novel approach employed to generate conditional probability tables. The principles of dynamic CPN's were adopted and, in combination with the method of conditioning, learning, and forecasting, were implemented in a time- and memory-efficient way. An evaluation using experimental data was carried out to compare the original and revised DIAS implementations employing data collected by patients with IDDM, and to assess the a posteriori identifiability of model parameters in patients with NIDDM.

Adult↗
PubMedDate not supplied

Declarative simulation of dynamicals systems: the 812 programming language and its application to the simulation of genetic networks.

A major part of biological processes can be modeled as dynamical systems (DS), that is, as a time-varying state. In this article, we advocate a declarative approach for prototyping the simulation of DS. We introduce the concepts of collection, stream and fabric. A fabric is a multi-dimensional object that represents the successive values of a structured set of variables. A declarative programming language, called 8 1/2 has been developed to support the concept of fabrics. Several examples of working 8 1/2 programs are given to illustrate the relevance of the fabric data structure for simulation applications and to show how recursive fabric definitions can be easily used to model various biological phenomena in a natural way (a resolution of PDE, a simulation in artificial life, the Turing diffusion-reaction process and various examples of genetic networks). In the conclusion, we recapitulate several lessons we have learned from the 8 1/2 project.

Programming Languages↗
PubMedDate not supplied

Dynamics of a hybrid system of a brain neural network and an artificial nonlinear oscillator.

In the brain, many functional modules interact with each other to execute complex information processing. Understanding the nature of these interactions is necessary for understanding how the brain functions. In this study, to mimic interacting modules in the brain, we constructed a hybrid system mutually coupling a hippocampal CA3 network as an actual brain module and a radial isochron clock (RIC) simulated by a personal computer as an artificial module. Return map analysis of the CA3-RIC system's dynamics showed the mutual entrainment and complex dynamics dependent on the coupling modes. The phase response curve of CA3 was modeled regarding the CA3 as a nonlinear oscillator. Using the phase response curves of CA3 and RIC, we reconstructed return maps of the hybrid system's dynamics. Although the reconstructed return maps almost agreed with the experimental data, there were deviations dependent on the coupling mode. In particular, we noted that the deviation was smaller under the bidirectional coupling conditions than during the one-way coupling from RIC to CA3. These results suggest that brain modules may flexibly change their dynamical properties through interaction with other modules.

Hippocampus↗
PubMed2004

Coherence in scale-free networks of chaotic maps.

We study fully synchronized states in scale-free networks of chaotic logistic maps as a function of both dynamical and topological parameters. Three different network topologies are considered: (i) a random scale-free topology, (ii) a deterministic pseudofractal scale-free network, and (iii) an Apollonian network. For the random scale-free topology we find a coupling strength threshold beyond which full synchronization is attained. This threshold scales as k(-mu) , where k is the outgoing connectivity and mu depends on the local nonlinearity. For deterministic scale-free networks coherence is observed only when the coupling strength is proportional to the neighbor connectivity. We show that the transition to coherence is of first order and study the role of the most connected nodes in the collective dynamics of oscillators in scale-free networks.

Journal Article↗
PubMedDate not supplied

In vitro angiogenesis is modulated by the mechanical properties of fibrin gels and is related to alpha(v)beta3 integrin localization.

This study deals with the role of the mechanical properties of matrices in in vitro angiogenesis. The ability of rigid fibrinogen matrices with fibrin gels to promote capillarylike structures was compared. The role of the mechanical properties of the fibrin gels was assessed by varying concentration of the fibrin gels. When the concentration of fibrin gels was decreased from 2 mg/ml to 0.5 mg/ml, the capillarylike network increased. On rigid fibrinogen matrices, capillarylike structures were not formed. The extent of the capillarylike network formed on fibrin gels having the lowest concentration depended on the number of cells seeded. The dynamic analysis of capillarylike network formation permitted a direct visualization of a progressive stretching of the 0.5 mg/ml fibrin gels. This stretching was not observed when fibrin concentration increases. This analysis shows that 10 h after seeding, a prearrangement of cells into ringlike structures was observed. These ringlike structures grew in size. Between 16 and 24 h after seeding, the capillarylike structures were formed at the junction of two ringlike structures. Analysis of the alpha(v)beta3 integrin localization demonstrates that cell adhesion to fibrinogen is mediated through the alpha(v)beta3 integrin localized into adhesion plaques. Conversely, cell adhesion to fibrin shows a diffuse and dot-contact distribution. We suggest that the balance of the stresses between the tractions exerted by the cells and the resistance of the fibrin gels triggers an angiogenic signal into the intracellular compartment. This signal could be associated with modification in the alpha(v)beta3 integrin distribution.

Biomechanical Phenomena↗
PubMed2001

Synchronization of Kauffman networks.

We analyze the synchronization transition for a pair of coupled identical Kauffman networks in the chaotic phase. The annealed model for Kauffman networks shows that synchronization appears through a transcritical bifurcation and provides an approximate description for the whole dynamics of the coupled networks. We show that these analytical predictions are in good agreement with numerical results for sufficiently large networks and study finite-size effects in detail. Preliminary analytical and numerical results for partially disordered networks are also presented.

Journal Article↗
PubMed2007

Exact subthreshold integration with continuous spike times in discrete-time neural network simulations.

Very large networks of spiking neurons can be simulated efficiently in parallel under the constraint that spike times are bound to an equidistant time grid. Within this scheme, the subthreshold dynamics of a wide class of integrate-and-fire-type neuron models can be integrated exactly from one grid point to the next. However, the loss in accuracy caused by restricting spike times to the grid can have undesirable consequences, which has led to interest in interpolating spike times between the grid points to retrieve an adequate representation of network dynamics. We demonstrate that the exact integration scheme can be combined naturally with off-grid spike events found by interpolation. We show that by exploiting the existence of a minimal synaptic propagation delay, the need for a central event queue is removed, so that the precision of event-driven simulation on the level of single neurons is combined with the efficiency of time-driven global scheduling. Further, for neuron models with linear subthreshold dynamics, even local event queuing can be avoided, resulting in much greater efficiency on the single-neuron level. These ideas are exemplified by two implementations of a widely used neuron model. We present a measure for the efficiency of network simulations in terms of their integration error and show that for a wide range of input spike rates, the novel techniques we present are both more accurate and faster than standard techniques.

Action Potentials↗
PubMed1993

Changes in mobility of chromaffin granules in actin network with its assembly and Ca(2+)-dependent disassembly by gelsolin.

As a final stage of cell signal transduction, secretory cells release hormones by exocytosis. Before secretory granules contact with the cell membrane for fusion, an actin-network barrier must dissociate as a prelude. To elucidate dynamical behaviors of secretory granules in actin networks, in vitro assembly and disassembly processes of actin networks were examined by means of dynamic light-scattering spectroscopy. We studied actin polymerization in the presence of chromaffin granules isolated from bovine adrenal medullas and found that the entanglement of actin filaments rapidly formed cages that confined granules in them. We also studied the effect of gelsolin, one of actin-severing proteins, on the network of actin filaments preformed in the presence of chromaffin granules. It turned out that the cages that confined granules rapidly disappeared when gelsolin was added in the presence of free Ca2+ ions. A semiquantitative analysis of dynamic light-scattering spectra permitted us to estimate the changes in the mobility (or the translational diffusion coefficient) of chromaffin granules in the actin network with its assembly and Ca(2+)-dependent disassembly by gelsolin. Based on the present results and some pieces of evidence in the literature, a model is proposed for biophysical situations before, during, and after an exocytotic event.

Actins↗
PubMed2002

Spatial and temporal dynamics of hedgerows in three agricultural landscapes of southern Quebec, Canada.

Noncrop areas such as hedgerows in agricultural landscapes can perform several ecological and agronomic functions (e.g., habitat, movement corridors, windbreak, etc.), but their dynamics and drivers of changes are often poorly known. We conducted a study in three agricultural landscapes of southern Quebec, Canada, to assess and compare the spatial and temporal (1958-1997) dynamics of three hedgerow networks in relation to geomorphic conditions (marine, glacial, and mixed deposit) and land-use changes. Hedgerow networks were mapped and described in terms of their structure (density, degree of connectivity, and presence of trees or shrubs) and their relationship to other components of the landscape (connection to woodland). Relationships were assessed in time and space using nonparametric correlation, Mantel test, and principal components analysis (PCA). Results show significant differences between hedgerow structure for the three landscapes and distinct temporal and spatial dynamics that can be related to changes in management practices and agricultural policies. On marine deposits, increases in hedgerow density did not always correspond to an increase in their degree of connectivity, suggesting a possible reduction in network quality. On glacial deposits, hedgerow density declined following abandonment of agricultural land, but rather than disappearing, these linear structures were integrated into adjacent brush or forested areas. Our analysis reveals the complex spatial and temporal dynamics of the hedgerow networks and highlights the need to take into account spatial attributes such as connectivity and connection to woodland to evaluate more accurately overall network quality.

Agriculture↗
PubMed1993

New physical concepts for cell amoeboid motion.

Amoeboid motion of cells is an essential mechanism in the function of many biological organisms (e.g., the regiment of scavenger cells in the immune defense system of animals). This process involves rapid chemical polymerization (with numerous protein constituents) to create a musclelike contractile network that advances the cell over the surface. Significant progress has been made in the biology and biochemistry of motile cells, but the physical dynamics of cell spreading and contraction are not well understood. The reason is that general approaches are formulated from complex mass, momentum, and chemical reaction equations for multiphase-multicomponent flow with the nontrivial difficulty of moving boundaries. However, there are strong clues to the dynamics that allow bold steps to be taken in simplifying the physics of motion. First, amoeboid cells often exhibit exceptional kinematics, i.e., steady advance and retraction of local fixed-shape patterns. Second, recent evidence has shown that cell projections "grow" by polymerization along the advancing boundary of the cell. Together, these characteristics represent a local growth process pinned to the interfacial contour of a contractile network. As such, the moving boundary becomes tractable, but subtle features of the motion lead to specific requirements for the chemical nature of the boundary polymerization process. To demonstrate these features, simple examples for limiting conditions of substrate interaction (i.e., "strong" and "weak" adhesion) are compared with data from experimental studies of yeast particle engulfment by blood granulocytes and actin network dynamics in fishscale keratocytes.

Animals↗
PubMed2001

In vivo detection of cytokeratin filament network breakdown in cells treated with the phosphatase inhibitor okadaic acid.

We have previously described vulva carcinoma-derived A-431 subclone AK13-1, which stably expresses fluorescently labeled cytokeratin filaments (CKFs). Time-lapse fluorescence microscopy of these cells permits the continuous monitoring of the dynamics of the CKF cytoskeleton in vivo. To study mechanisms and principles of CKF disassembly as it occurs, e.g., during mitosis and liver disease, we have treated cells with the phosphatase inhibitor okadaic acid (OA), which induces complete CKF network breakdown within 3-5 h without significantly affecting the organization of the actin- and tubulin-based cytofilaments. In time-lapse movies, we find that the network breakdown starts at the cell periphery and proceeds toward the cell center, where residual filaments become compacted into a prominent perinuclear ring. The progressing disassembly is paralleled by an increase of diffuse fluorescence throughout the cytoplasm and the appearance of non-filamentous spheroidal aggregates. They are formed in the filament-free cell periphery from non-filamentous precursors and can sometimes be detected in the proximity of desmosomes. Other aggregates are either found in close apposition to CKFs or are generated directly from the compacted perinuclear material. Primary granules later fuse, thereby producing structures of considerable size. We show that CKF network breakdown and granule formation rely on metabolic energy and that the continued presence of OA is needed for its completion. We conclude that phosphorylation/dephosphorylation is an important mechanism regulating CKF network dynamics in vivo with far-reaching implications for the understanding of epithelial plasticity and pathology.

Adenosine Triphosphate↗
PubMed2004

Liquid-crystal microlens arrays using patterned polymer networks.

A real-time dynamically tunable-focus microlens array made from a polymer-liquid-crystal (LC) composite is demonstrated. The polymer was first patterned in microlens array cavities by lamination, and the LC-monomer mixture was then injected to the molded polymer cavities and finally stabilized by UV light-induced networks. Using this new fabrication method, we demonstrated a lens with a spherical shape and a glazed surface. This LC-based microlens can reach approximately 100% light efficiency for linearly polarized light. The saturation voltage of the lens is approximately 60 Vrms, and the response time is approximately 30 ms.

Journal Article↗
PubMed2006

Evolutionary changes of metabolic networks and their biosynthetic capacities.

The metabolic networks of different species show a large variety in their structural design. In this work, the evolution of functional properties of metabolism in relation with metabolic network structure is investigated. The metabolism of ancestral species is inferred from the metabolism of contemporary species using a Bayesian network model for metabolism evolution. Subsequently, these networks are analysed with the recently developed method of network expansion. This method allows for a structural analysis of metabolic networks as well as a quantification of network functions in terms of their synthesising capacities when they are provided with certain external resources. The evolutionary dynamics of one particular network function: the metabolic expansion of glucose is investigated.

Adaptation, Physiological↗
PubMed2004

Network-induced oscillatory behavior in material flow networks and irregular business cycles.

Network theory is rapidly changing our understanding of complex systems, but the relevance of topological features for the dynamic behavior of metabolic networks, food webs, production systems, information networks, or cascade failures of power grids remains to be explored. Based on a simple model of supply networks, we offer an interpretation of instabilities and oscillations observed in biological, ecological, economic, and engineering systems. We find that most supply networks display damped oscillations, even when their units--and linear chains of these units--behave in a nonoscillatory way. Moreover, networks of damped oscillators tend to produce growing oscillations. This surprising behavior offers, for example, a different interpretation of business cycles and of oscillating or pulsating processes. The network structure of material flows itself turns out to be a source of instability, and cyclical variations are an inherent feature of decentralized adjustments.

Journal Article↗