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Results for “spatiotemporal coupling”

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At least 289 records · Page 16Linked to original sources

PubMed1999

Complex patterns predicted in an in vitro experimental model system for the evolution of molecular cooperation.

An isothermal biochemical in vitro amplification system with two trans-cooperatively coupled amplifying DNA molecules was investigated homogeneously using a hierarchy of kinetic models and as a simplified reaction-diffusion system. In our model of this recently developed experimental system, no reaction mechanism higher than second order occurs, yet numerical simulations show a variety of complex spatiotemporal patterns which arise in response to finite amplitude perturbations in a flow reactor. In a certain domain of the kinetic parameters the system shows self-replicating spots. These spots can stabilize the cooperative amplification in such evolving systems against emerging parasites. The results are of high relevance for experimental studies on these functional in vitro ecosystems in spatially resolved microstructured reactors.

Journal Article↗

PubMed1997

Sensing and refilling calcium stores in an excitable cell.

Inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ mobilization leads to depletion of the endoplasmic reticulum (ER) and an increase in Ca2+ entry. We show here for the gonadotroph, an excitable endocrine cell, that sensing of ER Ca2+ content can occur without the Ca2+ release-activated Ca2+ current (Icrac), but rather through the coupling of IP3-induced Ca2+ oscillations to plasma membrane voltage spikes that gate Ca2+ entry. Thus we demonstrate that capacitative Ca2+ entry is accomplished through Ca(2+)-controlled Ca2+ entry. We develop a comprehensive model, with parameter values constrained by available experimental data, to simulate the spatiotemporal behavior of agonist-induced Ca2+ signals in both the cytosol and ER lumen of gonadotrophs. The model combines two previously developed models, one for ER-mediated Ca2+ oscillations and another for plasma membrane potential-driven Ca2+ oscillations. Simulations show agreement with existing experimental records of store content, cytosolic Ca2+ concentration ([Ca2+]i), and electrical activity, and make a variety of new, experimentally testable predictions. In particular, computations with the model suggest that [Ca2+]i in the vicinity of the plasma membrane acts as a messenger for ER content via Ca(2+)-activated K+ channels and Ca2+ pumps in the plasma membrane. We conclude that, in excitable cells that do not express Icrac, [Ca2+]i profiles provide a sensitive mechanism for regulating net calcium flux through the plasma membrane during both store depletion and refilling.

Animals↗

PubMed2004

Coherent spin manipulation without magnetic fields in strained semiconductors.

A consequence of relativity is that in the presence of an electric field, the spin and momentum states of an electron can be coupled; this is known as spin-orbit coupling. Such an interaction opens a pathway to the manipulation of electron spins within non-magnetic semiconductors, in the absence of applied magnetic fields. This interaction has implications for spin-based quantum information processing and spintronics, forming the basis of various device proposals. For example, the concept of spin field-effect transistors is based on spin precession due to the spin-orbit coupling. Most studies, however, focus on non-spin-selective electrical measurements in quantum structures. Here we report the direct measurement of coherent electron spin precession in zero magnetic field as the electrons drift in response to an applied electric field. We use ultrafast optical techniques to spatiotemporally resolve spin dynamics in strained gallium arsenide and indium gallium arsenide epitaxial layers. Unexpectedly, we observe spin splitting in these simple structures arising from strain in the semiconductor films. The observed effect provides a flexible approach for enabling electrical control over electron spins using strain engineering. Moreover, we exploit this strain-induced field to electrically drive spin resonance with Rabi frequencies of up to approximately 30 MHz.

Journal Article↗

PubMed1999

Comparative analysis of three murine G-protein coupled receptors activated by sphingosine-1-phosphate.

The cloning and analysis of the first identified lysophosphatidic acid (LPA) receptor gene, lpA1 (also referred to as vzg-1 or edg-2), led us to identify homologous murine genes that might also encode receptors for related lysophospholipid ligands. Three murine genomic clones (designated lpB1, lpB2, and lpB3) were isolated, corresponding to human/rat Edg-1, rat H218/AGR16, and human edg-3, respectively. Based on the amino acid similarities of their predicted proteins (44-52% identical), the three lpB genes could be grouped into a separate G-protein coupled receptor subfamily, distinct from that containing the LPA receptor genes lpA1 and lpA2. Unlike lpA1 and lpA2, which contain multiple coding exons, all lpB members contained a single coding exon. Heterologous expression of individual lpB members in a hepatoma cell line (RH7777), followed by 35S-GTPgammaS incorporation assays demonstrated that each of the three LPB receptors conferred sphingosine-1-phosphate-dependent, but not lysophosphatidic acid-dependent, G-protein activation. Northern blot and in situ hybridization analyses revealed overlapping as well as distinct expression patterns in both embryonic and adult tissues. This comparative characterization of multiple sphingosine-1-phosphate receptor genes and their spatiotemporal expression patterns will aid in understanding the biological roles of this enlarging lysophospholipid receptor family.

Amino Acid Sequence↗

PubMed1992

Phenomenology of boiling: A coupled map lattice model.

A minimal model for boiling is proposed. With increasing temperature of a bottom plate, the model shows three successive phases; conduction, nucleate, and film boiling. In the nucleate regime the heat flux increases with the temperature of the bottom plate, while it decreases in the film boiling regime. In the boiling phase, the maximum Lyapunov exponent is positive, implying that the boiling phenomena are spatiotemporally chaotic.

Journal Article↗

PubMed2001

Breakdown of universality in transitions to spatiotemporal chaos.

We show that the transition from laminar to active behavior in extended chaotic systems can vary from a continuous transition in the universality class of directed percolation with infinitely many absorbing states to what appears as a first-order transition. The latter occurs when finite lifetime nonchaotic structures, called "solitons," dominate the dynamics. We illustrate this scenario in an extension of the deterministic Chaté-Manneville coupled map lattice model and in a soliton including variant of the stochastic Domany-Kinzel cellular automaton.

Journal Article↗

PubMed2002

Spatiotemporal consistency of human mandibular and head-neck movement trajectories during jaw opening-closing tasks.

Previous studies of spatial and temporal coordination between human mandibular and head-neck movements during single as well as rhythmic jaw opening-closing tasks suggest that these movements are regulated by central nervous commands common for jaw and neck muscles. The present study evaluated the spatiotemporal consistency of concomitant mandibular and head-neck movements during repeated single jaw opening-closing tasks, in short- as well as long-term perspectives and at different speeds. The subjects were seated in an upright position without head support. They were instructed to perform single maximal jaw opening-closing movements, repeated ten times for fast and slow speed, respectively. Recordings were made at two sessions. A wireless optoelectronic technique was used to record three-dimensional mandibular and head-neck movements. The spatiotemporal consistency of repeated movement trajectories of the mandible (both in relation to the head and in space) and of the head-neck was quantitatively assessed by a spatiotemporal index (STI). In addition, mean movement trajectory patterns were compared for speed and recording sessions (expressed as correlation coefficient, r). The results showed relatively small STI (high degree of spatiotemporal consistency) and high r (reproducible trajectory patterns) values, both in short- and long-term perspectives, for concomitant mandibular and head-neck movements. The data were not generally speed related. In conclusion, the present results suggest a high degree of spatiotemporal consistency of the kinematic patterns of mandibular and head-neck movements during jaw opening-closing, in short- as well as long-term perspectives. They also indicate that underlying neural processes are invariant in nature. The results give further support to the notion of a tight functional coupling between the human jaw and the neck motor systems during natural jaw function.

Adult↗

PubMed2006

A two-promoter system of gene expression in C. elegans.

The development of multicellular organisms requires precise spatiotemporal gene expression and the expression of cell/tissue specific isoforms of some genes. This task may require more efficient genome organization in Caenorhabditis elegans and other organisms with relatively small genome size. The SL1 leader sequence is trans-spliced to many mRNAs in C. elegans. We hypothesize that introns coupled to internal SL1 acceptors contain independent promoters. We identify 238 genes that have introns coupled to internal SL1 acceptors. We find that the mean length of the internal SL1-coupled introns is significantly longer than the genome mean. For twelve of the genes, evidence exists that the intronic promoter provides tissue specificity different from that of the primary promoter. We estimate that 2.7% of the genome is regulated through this two-promoter system. We propose that internal SL1-coupled introns function as independent promoters and that this two-promoter system represents a major mechanism in C. elegans, in addition to alternative splicing, that serves to promote tissue-specific expression of protein isoforms. Our finding of the frequent coupling between an internal SL1 and a large immediately upstream intron will make promoters and transcription start sites predictable.

Animals↗

PubMed2006

Modeling of pattern regulation in melanophores.

Melanosomes, pigment granules in melanophores, play a principal role in physiological color adaptation of fish and frog. Melanophores regulate melanosome trafficking on cytoskeletal filaments to generate a range of spatiotemporal patterns. Here, we present the first comprehensive model of spatiotemporal evolution of melanosome patterns. The model encompasses both physical and biochemical aspects of melanosome dynamics. It consists of (i) a kinetic description of biochemical reactions involved in intracellular signaling, (ii) a system of macroscopic reaction-diffusion-convection equations for melanosome concentration, and (iii) a set of constitutive relationships for coupling transport with the biochemical network. The model relates molecular-level regulatory actions to cell-level melanosome distribution, allowing unification of existing experimental observations and qualitative hypotheses into an integrated, consistent framework. The model reproduces salient features of melanosome patterns, both during transient and steady state. It gives useful insights into how cells coordinate motor-assisted transport to maintain and adapt spatial organization of intracellular organelles. In particular, we calculate the optimal transition paths from aggregation to dispersion in fish melanophores. The calculations suggest that fish melanophores optimally control intracellular signaling to maximize the efficiency of motor-assisted transport during dispersion.

Adaptation, Physiological↗

PubMed2002

Dynamical behavior of a complex fluid near an out-of-equilibrium transition: approaching simple rheological chaos.

We report here an extensive study of sustained oscillations of the viscosity of a complex fluid near an out-of-equilibrium transition. Using well defined protocols, we perform rheological measurements of the onion texture near a layering transition in a Couette flow. This complex fluid exhibits sustained oscillations of the viscosity, on a large time scale (500 s) at controlled stress. These oscillations are directly correlated to an oscillating microstructural change of the texture of the fluid. We observe a great diversity of dynamical behavior and show that there is a coupling with spatial effects in the inverted Delta v direction. This is in agreement with a careful analysis of the temporal series of the viscosity with the dynamical system theory. This analysis indicates that the observed dynamical responses do not strictly correspond to three-dimensional chaotic states, probably because some spatiotemporal effects are present and are likely to play an important role.

Journal Article↗

PubMed2003

Dissipating step bunches during crystallization under transport control.

In studies of crystal formation by the generation and spreading of layers, equidistant step trains are considered unstable-bunches and other spatiotemporal patterns of the growth steps are viewed as ubiquitous. We provide an example to the opposite. We monitor the spatiotemporal dynamics of steps and the resulting step patterns during crystallization of the proteins ferritin and apoferritin using the atomic force microscope. The variations in step velocity and density are not correlated, indicating the lack of a long-range attraction between the steps. We show that (i) because of its coupling to bulk transport, nucleation of new layers is chaotic and occurs at the facet edges, where the interfacial supersaturation is higher; (ii) step bunches self-organize via the competition for supply from the solution; and, (iii) bunches of weakly interacting steps decay as they move along the face. Tests by numerical modeling support the conclusions about the mechanisms underlying our observations. The results from these systems suggest that during crystallization controlled by transport, with weakly or noninteracting growth steps, the stable kinetic state of the surface is an equidistant step train, and step bunches only arise during nucleation of new layers. Since nucleation only occurs at a few sites on the surface, the surface morphology may be controllably patterned or smoothened by locally controlling nucleation.

Journal Article↗

PubMed2002

Nonlinear dynamics of direction-selective recurrent neural media.

The direction selectivity of cortical neurons can be accounted for by asymmetric lateral connections. Such lateral connectivity leads to a network dynamics with characteristic properties that can be exploited for distinguishing in neurophysiological experiments this mechanism for direction selectivity from other possible mechanisms. We present a mathematical analysis for a class of direction-selective neural models with asymmetric lateral connections. Contrasting with earlier theoretical studies that have analyzed approximations of the network dynamics by neglecting nonlinearities using methods from linear systems theory, we study the network dynamics with nonlinearity taken into consideration. We show that asymmetrically coupled networks can stabilize stimulus-locked traveling pulse solutions that are appropriate for the modeling of the responses of direction-selective neurons. In addition, our analysis shows that outside a certain regime of stimulus speeds the stability of these solutions breaks down, giving rise to lurching activity waves with specific spatiotemporal periodicity. These solutions, and the bifurcation by which they arise, cannot be easily accounted for by classical models for direction selectivity.

Animals↗

PubMed2003

Coupling fields and underlying space curvature: an augmented Lagrangian approach.

We demonstrate a systematic implementation of coupling between a scalar field and the geometry of the space which carries the field. This naturally gives rise to a feedback mechanism between the field and the geometry. We develop a systematic model for the feedback in a general form, inspired by a specific implementation in the context of molecular dynamics (the so-called Rahman-Parrinello molecular dynamics, or RP-MD). We use a generalized Lagrangian that allows for the coupling of the space's metric tensor to the scalar field, and add terms motivated by RP-MD. We present two implementations of the scheme: one in which the metric is only time-dependent (which gives rise to an ordinary differential equation for its temporal evolution), and the other with spatiotemporal dependence (wherein the metric's evolution is governed by a partial differential equation). Numerical results are reported for the (1+1)-dimensional model with a nonlinearity of the sine-Gordon type.

Journal Article↗

PubMed2006

Minimal model for chaotic shear banding in shear thickening fluids.

We present a minimal model for spatiotemporal oscillation and rheochaos in shear thickening complex fluids at zero Reynolds number. In the model, a tendency towards inhomogeneous flows in the form of shear bands combines with a slow structural dynamics, modeled by delayed stress relaxation. Using Fourier-space numerics, we study the nonequilibrium "phase diagram" of the fluid as a function of a steady mean (spatially averaged) stress, and of the relaxation time for structural relaxation. We find several distinct regions of periodic behavior (oscillating bands, traveling bands, and more complex oscillations) and also regions of spatiotemporal rheochaos. A low-dimensional truncation of the model retains the important physical features of the full model (including rheochaos) despite the suppression of sharply defined interfaces between shear bands. Our model maps onto the FitzHugh-Nagumo model for neural network dynamics, with an unusual form of long-range coupling.

Journal Article↗

PubMed2003

Transient activation in a network of coupled map neurons.

The focus of this Letter is on the activity of a network of neurons pairwise coupled by inhibitory connections. Each neuron is represented by a two-dimensional map capable, when isolated, of a rich variety of complex dynamical regimes. It is shown that the network exhibits a stimulus-dependent sequential activation and inactivation of subgroups of neurons. This complex behavior is rather similar to some spatiotemporal features observed in the first stages of the olfaction process in some insects and suggests the possibility of large scale simulation of these processes by using reasonable computational capabilities.

Action Potentials↗

PubMed2003

Local dimension and finite time prediction in spatiotemporal chaotic systems.

We show how a recently introduced statistic [Patil et al., Phys. Rev. Lett. 81, 5878 (2001)] provides a direct relationship between dimension and predictability in spatiotemporal chaotic systems. Regions of low dimension are identified as having high predictability and vice versa. This conclusion is reached by using methods from dynamical systems theory and Bayesian modeling. In this work we emphasize on the consequences for short time forecasting and examine the relevance for factor analysis. Although we concentrate on coupled map lattices and coupled nonlinear oscillators for convenience, any other spatially distributed system could be used instead, such as turbulent fluid flows.

Journal Article↗

PubMed2005

Neurovascular coupling investigated with two-dimensional optical imaging spectroscopy in rat whisker barrel cortex.

Optical imaging slit spectroscopy is a powerful method for estimating quantitative changes in cerebral haemodynamics, such as deoxyhaemoglobin, oxyhaemoglobin and blood volume (Hbr, HbO2 and Hbt, respectively). Its disadvantage is that there is a large loss of spatial data as one image dimension is used to encode spectral wavelength information. Single wavelength optical imaging, on the other hand, produces high-resolution spatiotemporal maps of brain activity, but yields only indirect measures of Hbr, HbO2 and Hbt. In this study we perform two-dimensional optical imaging spectroscopy (2D-OIS) in rat barrel cortex during contralateral whisker stimulation to obtain two-dimensional maps over time of Hbr, HbO2 and Hbt. The 2D-OIS was performed by illuminating the cortex with four wavelengths of light (575, 559, 495 and 587 nm), which were presented sequentially at a high frame rate (32 Hz). The contralateral whisker pad was stimulated using two different durations: 1 and 16 s (5 Hz, 1.2 mA). Control experiments used a hypercapnic (5% CO2) challenge to manipulate baseline blood flow and volume in the absence of corresponding neural activation. The 2D-OIS method allowed separation of artery, vein and parenchyma regions. The magnitude of the haemodynamic response elicited varied considerably between different vascular compartments; the largest responses in Hbt were in the arteries and the smallest in the veins. Phase lags in the HbO2 response between arteries and veins suggest that a process of upstream signalling maybe responsible for dilating the arteries. There was also a consistent increase in Hbr from arterial regions after whisker stimulation.

Algorithms↗

PubMed2002

Calcium secretion coupling at calyx of Held governed by nonuniform channel-vesicle topography.

Phasic transmitter release at synapses in the mammalian CNS is regulated by local [Ca2+] transients, which control the fusion of readily releasable vesicles docked at active zones (AZs) in the presynaptic membrane. The time course and amplitude of these [Ca2+] transients critically determine the time course and amplitude of the release and thus the frequency and amplitude tuning of the synaptic connection. As yet, the spatiotemporal nature of the [Ca2+] transients and the number and location of release-controlling Ca2+ channels relative to the vesicles, the "topography" of the release sites, have remained elusive. We used a time-dependent model to simulate Ca2+ influx, three-dimensional buffered Ca2+ diffusion, and the binding of Ca2+ to the release sensor. The parameters of the model were constrained by recent anatomical and biophysical data of the calyx of Held. Comparing the predictions of the model with previously measured release probabilities under a variety of experimental conditions, we inferred which release site topography is likely to operate at the calyx: At each AZ one or a few clusters of Ca2+ channels control the release of the vesicles. The distance of a vesicle to the cluster(s) varies across the multiple release sites of a single calyx (ranging from 30 to 300 nm; average approximately 100 nm). Assuming this topography, vesicles in different locations are exposed to different [Ca2+] transients, with peak amplitudes ranging from 0.5 to 40 microm (half-width approximately 400 microsec) during an action potential. Consequently the vesicles have different release probabilities ranging from <0.01 to 1. We demonstrate how this spatially heterogeneous release probability creates functional advantages for synaptic transmission.

Brain Stem↗