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Results for “coupled patch model”

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At least 19 recordsLinked to original sources

PubMed2000

Dispersal, Environmental Correlation, and Spatial Synchrony in Population Dynamics.

Many species exhibit widespread spatial synchrony in population fluctuations. This pattern is of great ecological interest and can be a source of concern when the species is rare or endangered. Both dispersal and spatial correlations in the environment have been implicated as possible causes of this pattern, but these two factors have rarely been studied in combination. We develop a spatially structured population model, simple enough to obtain analytic solutions for the population correlation, that incorporates both dispersal and environmental correlation. We ask whether these two synchronizing factors contribute additively to the total spatial population covariance. We find that there is always an interaction between these two factors and that this interaction is small only when one or both of the environmental correlation and the dispersal rate are small. The interaction is opposite in sign to the environmental correlation; so, in the normal case of positive environmental correlation across sites, the population synchrony will be lower than predicted by simply adding the effects of dispersal and environmental correlation. We also find that population synchrony declines as the strength of population regulation increases. These results indicate that dispersal and environmental correlation need to be considered in combination as explanations for observed patterns of population synchrony.

Moran effect↗

PubMed2005

Evaluating the accuracy and generality of a hybrid patch model.

Forest patch models have been used extensively to simulate vegetation development under current and changing environmental conditions. However, their physiological foundation is subject to criticism and recent validation experiments against long-term growth and yield data have shown major deficiencies in reproducing observed growth patterns of mixed-species forests. Here we describe the modified forest patch model PICUS Version 1.3, a model variant that couples the structurally detailed three-dimensional patch model PICUS Version 1.2 and the physiologically based stand-level production module of the 3-PG (Physiological Principles in Predicting Growth) model. The approach attempts to combine the ability of PICUS v1.2 to simulate forest dynamics on time scales relevant to forest succession with a simplified but successful production model based on the concept of radiation-use efficiency. We evaluated the hybrid model in a series of simulation experiments. Results indicated a realistic response to a climate sensitivity experiment: the response to environmental gradients was well captured both in terms of productivity on time scales of a rotation length and of forest succession over several hundreds of years. Testing against independent long- term growth and yield data revealed good correspondence between observed and predicted values of volume production and stand structure. Further model development should include a dynamic soil component to consider effects of nutrient cycling.

Climate↗

PubMed1996

Spatial heterogeneity in epidemic models.

Spatial heterogeneity is believed to play an important role in the persistence and dynamics of epidemics of childhood diseases because asynchrony between populations within different regions allows global persistence, even if the disease dies out locally. A simple multi-patch (metapopulation) model for spatial heterogeneity in epidemics is analysed and we examine conditions under which patches become synchronized. We show that the patches in non-seasonal deterministic models often oscillate in phase for all but the weakest between patch coupling. Synchronization is also seen for stochastic models, although slightly stronger coupling is needed to overcome the random effects. We demonstrate that the inclusion of seasonal forcing in deterministic models can lead to the maintenance of phase differences between patches. Complex dynamic behaviour is observed in the seasonally forced spatial model, along with the coexistence of many different behaviours. Compared to the non-spatial model, chaotic solutions are observed for weaker seasonal forcing; these solutions have a more realistic minimum number of infectives.

Child↗

PubMed2004

Plankton lattices and the role of chaos in plankton patchiness.

Spatiotemporal and interspecies irregularities in planktonic populations have been widely observed. Much research into the drivers of such plankton patches has been initiated over the past few decades but only recently have the dynamics of the interacting patches themselves been considered. We take a coupled lattice approach to model continuous-in-time plankton patch dynamics, as opposed to the more common continuum type reaction-diffusion-advection model, because it potentially offers a broader scope of application and numerical study with relative ease. We show that nonsynchronous plankton patch dynamics (the discrete analog of spatiotemporal irregularity) arise quite naturally for patches whose underlying dynamics are chaotic. However, we also observe that for parameters in a neighborhood of the chaotic regime, smooth generalized synchronization of nonidentical patches is more readily supported which reduces the incidence of distinct patchiness. We demonstrate that simply associating the coupling strength with measurements of (effective) turbulent diffusivity results in a realistic critical length of the order of 100 km, above which one would expect to observe unsynchronized behavior. It is likely that this estimate of critical length may be reduced by a more exact interpretation of coupling in turbulent flows.

Animals↗

PubMed1992

Analysis of electric field stimulation of single cardiac muscle cells.

Electrical stimulation of cardiac cells by imposed extracellular electric fields results in a transmembrane potential which is highly nonuniform, with one end of the cell depolarized and the other end hyperpolarized along the field direction. To date, the implications of the close proximity of oppositely polarized membranes on excitability have not been explored. In this work we compare the biophysical basis for field stimulation of cells at rest with that for intracellular current injection, using three Luo-Rudy type membrane patches coupled together as a lumped model to represent the cell membrane. Our model shows that cell excitation is a function of the temporal and spatial distribution of ionic currents and transmembrane potential. The extracellular and intracellular forms of stimulation were compared in greater detail for monophasic and symmetric biphasic rectangular pulses, with duration ranging from 0.5 to 10 ms. Strength-duration curves derived for field stimulation show that over a wide range of pulse durations, biphasic waveforms can recruit and activate membrane patches about as effectively as can monophasic waveforms having the same total pulse duration. We find that excitation with biphasic stimulation results from a synergistic, temporal summation of inward currents through the sodium channel in membrane patches at opposite ends of the cell. Furthermore, with both waveform types, a net inward current through the inwardly rectifying potassium channel contributes to initial membrane depolarization. In contrast, models of stimulation by intracellular current injection do not account for the nonuniformity of transmembrane potential and produce substantially different (even contradictory) results for the case of stimulation from rest.

Animals↗

PubMed1998

Pattern formation in a patch occupancy metapopulation model: a cellular automata approach.

The explicit consideration of space in ecological research is of paramount importance to understand the structure and functioning of ecological systems. In this paper we develop a simple spatially explicit metapopulation model in which colonization is constant and independent of the number of occupied patches (i.e. propagule-rain effect, Gotelli, 1991). Extinction, on the other hand, is modelled as a stochastic process whose intensity depends on the number of occupied patches in the neighborhood of each focal patch. Our model is the CA counterpart of two classical patch occupancy metapopulation models. We analytically prove this by showing that our CA converges to the differential equation in the mean-field approximation. The asymptotic behaviour of the system, expressed as the proportion of occupied patches, agrees with the equilibrium proportion of patches derived by using ODEs. In both models, the existence of a rescue-effect increases the range of extinction and colonization parameters over which the system attains complete occupancy of patches. However, in our model this result is strongly influenced by the degree of coupling among patches and is apparent only for local interactions. With local interactions and particular parameter values of colonization and extinction, self-organized spatio-temporal patterns emerge with a fractal-like clustering, even though the environment is spatially homogeneous. Our results point out that the importance of being spatial and discrete (Durrett & Levin, 1994a) in our model is a result of local interactions.

Ecology↗

PubMed2005

Inferences about information flow and dispersal for spatially extended population systems using time-series data.

This work explores an information-theoretic approach to drawing inferences about coupling of spatially extended ecological populations based solely on time-series of abundances. The efficacy of the approach, time-delayed mutual information, was explored using a spatially extended predator-prey model system in which populations at different patches were coupled via diffusive movement. The approach identified the relative magnitude and direction of information flow resulting from animal movement between populations, the change in information flow as a function of distance separating populations, and the diffusive nature of the information flow. In addition, when the diffusive movement was eliminated from the model, mutual information correctly provided no evidence of information flow, even when population synchrony was generated by a common environmental driving function. Thus, for this model system, time-delayed mutual information was useful in discriminating between the Moran effect and animal movement as causes of population synchrony, as well as in characterizing dispersal in terms of direction, relative speed and diffusive nature.

Computer Simulation↗

PubMed2001

Coupling particles and fields in a diffusive hybrid model.

A general scheme to patch together discrete and continuous descriptions of diffusion within the same physical space is studied. In the discrete description, diffusion is described by microscopic random walkers on a lattice; in the continuous description, diffusion is described through the macroscopic diffusion equation. The coupling scheme is based on the mutual exchange of mass flux across the discrete-continuous interface. Detailed tests of the scheme, coupling particle, and field descriptions are particularly illustrative for the diffusion problem. Both the nonequilibrium transport behavior and the equilibrium fluctuations of the combined discrete-continuous system are in agreement with theoretical predictions.

Journal Article↗

PubMed1995

Estimation of the junctional resistance between electrically coupled receptor cells in Necturus taste buds.

Junctional resistance between coupled receptor cells in Necturus taste buds was estimated by modeling the results from single patch pipette voltage clamp studies on lingual slices. The membrane capacitance and input resistance of coupled taste receptor cells were measured to monitor electrical coupling and the results compared with those calculated by a simple model of electrically coupled taste cells. Coupled receptor cells were modeled by two identical receptor cells connected via a junctional resistance. On average, the junctional resistance was approximately 200-300 M omega. This was consistent with the electrophysiological recordings. A junctional resistance of 200-300 M omega is close to the threshold for Lucifer yellow dye-coupling detection (approximately 500 M omega). Therefore, the true extent of coupling in taste buds might be somewhat greater than that predicted from Lucifer yellow dye coupling. Due to the high input resistance of single taste receptor cells (> 1 G omega), a junctional resistance of 200-300 M omega assures a substantial electrical communication between coupled taste cells, suggesting that the electrical activity of coupled cells might be synchronized.

Animals↗

PubMed1998

Spatial structure, environmental heterogeneity, and population dynamics: analysis of the coupled logistic map.

Spatial extent can have two important consequences for population dynamics: It can generate spatial structure, in which individuals interact more intensely with neighbors than with more distant conspecifics, and it allows for environmental heterogeneity, in which habitat quality varies spatially. Studies of these features are difficult to interpret because the models are complex and sometimes idiosyncratic. Here we analyze one of the simplest possible spatial population models, to understand the mathematical basis for the observed patterns: two patches coupled by dispersal, with dynamics in each patch governed by the logistic map. With suitable choices of parameters, this model can represent spatial structure, environmental heterogeneity, or both in combination. We synthesize previous work and new analyses on this model, with two goals: to provide a comprehensive baseline to aid our understanding of more complex spatial models, and to generate predictions about the effects of spatial structure and environmental heterogeneity on population dynamics. Spatial structure alone can generate positive, negative, or zero spatial correlations between patches when dispersal rates are high, medium, or low relative to the complexity of the local dynamics. It can also lead to quasiperiodicity and hyperchaos, which are not present in the nonspatial model. With density-independent dispersal, spatial structure cannot destabilize equilibria or periodic orbits that would be stable in the absence of space. When densities in the two patches are uncorrelated, the probability that the population in a patch reaches extreme low densities is reduced relative to the same patch in isolation; this "rescue effect" would reduce the probability of metapopulation extinction beyond the simple effect of spreading of risk. Pure environmental heterogeneity always produces positive spatial correlations. The dynamics of the entire population is approximated by a nonspatial model with mean patch characteristics. This approximation worsens as the difference between the patches increases and the dispersal rate decreases: Under extreme conditions, destabilization of equilibria and periodic orbits occurs at mean parameter values lower than those predicted by the mean parameters. Apparent within-patch dynamics are distorted: The local population appears to have the wrong growth parameter and a constant number of immigrants (or emigrants) per generation. Adding environmental heterogeneity to spatial structure increases the occurrence of spatially correlated population dynamics, but the resulting temporal dynamics are more complex than would be predicted by the mean parameter values. The three classes of spatial pattern (positive, negative, and zero correlation), while still mathematically distinct, become increasingly similar phenomenologically.

Animals↗

PubMed1993

Passive current flow and morphology in the terminal arborizations of the posterior pituitary.

1. Patch-clamp techniques were used to study the morphology and electrotonic properties of the terminal arborizations of the posterior pituitary. 2. Neurobiotin-labeling experiments revealed axons and swellings connected to the structure that was patch clamped. The large swellings were en passant and situated along axons in a topological arrangement identical to that of the small varicosities. Axons had many varicosities and few branches, reflecting a predominant architectural motif of beads on a string rather than berries on a bush. 3. Cable theory was used to analyze passive current transients produced by voltage steps under whole-cell clamp. Most charging transients were not consistent with an equivalent cylinder representation as posited by the Rall model for a motoneuron. A few charging transients were consistent with the Rall model and provided estimates for basic membrane and cable properties. 4. Some of the charging transients that violated predictions of the Rall model were consistent with an alternative model, in which the patch-clamped swelling was assumed to be coupled to another swelling by a segment of axon. This model was called the Dumbbell model, and it, together with the neurobiotin-labeling experiments, indicated that a significant number of large swellings were less than one length constant away from another large swelling. 5. Large swellings can have diameters approximately 30 times larger than the diameters of the connecting axons. These swellings lie along the axon such that action potentials must propagate through them to spread excitation through the entire terminal arborization. These large swellings could be sites where action-potential propagation is more likely to fail. 6. The information presented here about neurohypophysial nerve terminals should be useful in further investigations of how terminal arborization geometry and membrane properties influence neurosecretion and synaptic transmission.

Animals↗

PubMed2006

The role of habitat disturbance and recovery in metapopulation persistence.

Classical metapopulation theory assumes a static landscape. However, empirical evidence indicates many metapopulations are driven by habitat succession and disturbance. We develop a stochastic metapopulation model, incorporating habitat disturbance and recovery, coupled with patch colonization and extinction, to investigate the effect of habitat dynamics on persistence. We discover that habitat dynamics play a fundamental role in metapopulation dynamics. The mean number of suitable habitat patches is not adequate for characterizing the dynamics of the metapopulation. For a fixed mean number of suitable patches, we discover that the details of how disturbance affects patches and how patches recover influences metapopulation dynamics in a fundamental way. Moreover, metapopulation persistence is dependent not only on the average lifetime of a patch, but also on the variance in patch lifetime and the synchrony in patch dynamics that results from disturbance. Finally, there is an interaction between the habitat and metapopulation dynamics, for instance declining metapopulations react differently to habitat dynamics than expanding metapopulations. We close, emphasizing the importance of using performance measures appropriate to stochastic systems when evaluating their behavior, such as the probability distribution of the state of the metapopulation, conditional on it being extant (i.e., the quasistationary distribution).

Environment↗

PubMed2006

Assessment of QT liabilities in drug development.

Since the publication, in 1997, of the CPMP (Committee for Proprietary Medicinal Products) Points to Consider document on "The assessment of potential for QT prolongation by non-cardiovascular medicinal products," both regulatory bodies and the pharmaceutical industry have paid increasing attention to the conduct of careful preclinical studies on the subject. Regulatory attention has focused on the drafting of Safety Pharmacology guidelines through the ICH (International Conference on Harmonization) process, which resulted in approval by the ICH and acceptance by the three main regions (USA, Europe, and Japan) of the ICH S7A guideline. The guideline does not deal only with cardiovascular studies and does not provide guidance on QT investigations. This part has been deferred to a second guideline (ICH S7B). Nevertheless, pharmaceutical companies have implemented screening strategies aimed at selecting compounds that do not present QT liabilities. These strategies can differ according to the pharmaceutical class, while experimental models differ according to the stage of development of the compound. Several in vitro models are employed in discovery (radioligand binding, high-throughput patch clamp, efflux, and fluorescence assays). These models, coupled with in silico methods, allow companies to screen a high number of compounds. Other in vitro models, applied later in the R&D process (action potential duration, APD, in Purkinje fibers or papillary muscle and the isolated heart) are useful in better describing the activity of compounds on cardiac ion channels. The most robust and accepted in vivo test is represented by telemetry studies in conscious non-rodents.

Animals↗

PubMed2007

Theoretical model of human apolipoprotein B100 tertiary structure.

Low density lipoprotein (LDL) particles are the main cholesterol carriers in human plasma. The organization of the particle, composed of apolar lipids and phospholipid monolayer stabilized by apolipoprotein B100 (apoB), is highly complex and still unknown. ApoB is an extremely large protein (4563 amino acids) and very little is known about its structure. A 3D model of the N-terminal region has been recently proposed and has provided interesting insights about the physico-chemical properties of the protein and putative interaction zones with lipids. In the present article, we propose the first tentative 3D modelling for most remaining residues. All predicted features emerging from the models are confronted with agreement to experimental data available. Using different up-to-date prediction methods, we decomposed the protein into eight domains and predicted 3D structure for each of them. The analysis of hydrophobic patches, polar regions, coupled with functional predictions based on the 3D models, gives new clues to understanding of the functional role of apoB. We suggest precise regions putatively involved in the lipid interactions, and discuss the position of apoB on the LDL particle. Finally, we propose relative organization of the domains, providing a shape quite compatible with the low resolution electron microscopy map.

Amino Acid Sequence↗

PubMed2006

Clustering and coupled gating modulate the activity in KcsA, a potassium channel model.

Different patterns of channel activity have been detected by patch clamping excised membrane patches from reconstituted giant liposomes containing purified KcsA, a potassium channel from prokaryotes. The more frequent pattern has a characteristic low channel opening probability and exhibits many other features reported for KcsA reconstituted into planar lipid bilayers, including a moderate voltage dependence, blockade by Na(+), and a strict dependence on acidic pH for channel opening. The predominant gating event in this low channel opening probability pattern corresponds to the positive coupling of two KcsA channels. However, other activity patterns have been detected as well, which are characterized by a high channel opening probability (HOP patterns), positive coupling of mostly five concerted channels, and profound changes in other KcsA features, including a different voltage dependence, channel opening at neutral pH, and lack of Na(+) blockade. The above functional diversity occurs correlatively to the heterogeneous supramolecular assembly of KcsA into clusters. Clustering of KcsA depends on protein concentration and occurs both in detergent solution and more markedly in reconstituted membranes, including giant liposomes, where some of the clusters are large enough (up to micrometer size) to be observed by confocal microscopy. As in the allosteric conformational spread responses observed in receptor clustering (Bray, D. and Duke, T. (2004) Annu. Rev. Biophys. Biomol. Struct. 33, 53-73) our tenet is that physical clustering of KcsA channels is behind the observed multiple coupled gating and diverse functional responses.

Bacterial Proteins↗

PubMed2005

The effect of migration on metapopulation stability is qualitatively unaffected by demographic and spatial heterogeneity.

Coupled map lattices (CMLs), using two coupled logistic equations, have been extensively used to model the dynamics of two-patch ecological systems. Such studies have revealed that migration rate plays an important role in determining the dynamics of the system, particularly when the two maps differ in their intrinsic growth rate parameter, r. However, under more realistic assumptions, a metapopulation can be expected to consist of more than two subpopulations, each with its own demographic parameters, which will in part be a function of the environment of that patch. The role of the spatial arrangement of heterogeneous (i.e. with different r values) subpopulations in shaping the dynamics of such a metapopulation has rarely been investigated. Here, we study the effect of demographic and spatial heterogeneity on the stability of one- and two-dimensional systems of 64 coupled Ricker maps with different r values, under periodic and absorbing boundary conditions. We show that the effects of migration rate on metapopulation stability do not depend upon either the precise spatial arrangement of the subpopulations in the lattice, or on the presence of a moderate proportion of vacant (uninhabitable) patches in the lattice. The results, thus, suggest that metapopulation models are robust to variation in spatial arrangement of patch quality and, hence, of demographic parameters. We also show that for any given arrangement of the patches, maximum stability of the metapopulation occurs when the migration levels are intermediate, a result that agrees well with previous studies on two-map CML systems.

Animals↗

PubMed1994

Effects of simulated potassium blockade on the dynamics of triggered cardiac activity.

Under certain conditions, drugs that partially block transmembrane potassium currents in ventricular myocytes predispose patients to ventricular tachyarrhythmias. Although the precise mechanisms by which potassium blockade initiates tachyarrhythmias are unknown, it is believed that early afterdepolarizations (EADs) may play a role. Using the Luo-Rudy kinetic model of the ventricular action potential, we examine the effect of potassium blockade on the likelihood of observing triggered cardiac activity in a system of two coupled kinetic patches. We found that (i) phase 2 EADs are capable of triggering full action potentials in neighboring tissue if the patches are separated by a relatively large resistive barrier, and (ii) partial potassium blockade can either increase or decrease triggering probabilities depending on coupling resistivity. To understand the dynamic contribution of potassium blockade to triggered activity, the two-patch model is decomposed into two single patches. In one of the patches we compute the stability properties of simulated EADs (arising from phase 2 of the ventricular action potential) as a function of potassium blockade. The EAD stability properties are then related to the frequency-amplitude response of the neighboring patch. From the analysis of the decomposed system we found (iii) that increases in triggering probabilities brought about by potassium blockade may result from frequency and amplitude shifts of stable EAD oscillations. The first finding suggests a mechanism by which potassium blockade could induce EAD-triggered arrhythmias within the setting of chronic myocardial infarction. The second and third findings may partially explain why potassium blockade is antiarrhythmic in some patients, and proarrhythmic in others.

Action Potentials↗

PubMed2006

Analysing radio-frequency coil arrays in high-field magnetic resonance imaging by the combined field integral equation method.

We present the combined field integral equation (CFIE) method for analysing radio-frequency coil arrays in high-field magnetic resonance imaging (MRI). Three-dimensional models of coils and the human body were used to take into account the electromagnetic coupling. In the method of moments formulation, we applied triangular patches and the Rao-Wilton-Glisson basis functions to model arbitrarily shaped geometries. We first examined a rectangular loop coil to verify the CFIE method and also demonstrate its efficiency and accuracy. We then studied several eight-channel receive-only head coil arrays for 7.0 T SENSE functional MRI. Numerical results show that the signal dropout and the average SNR are two major concerns in SENSE coil array design. A good design should be a balance of these two factors.

Algorithms↗