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Results for “Coupled model”

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At least 163 records · Page 9Linked to original sources

PubMed1991

Reversible mechanosensitive ion pumping as a part of mechanoelectrical transduction.

To explain the ability of some mechanosensitive cells to reverse the process of mechanotransduction and to generate mechanical oscillations and emit sound, a piezo-conformational coupling model (PCC model) is proposed. The model includes a transport protein which changes either its volume (PV-coupling) or its area in the membrane (gamma A-coupling) when undergoing conformational transitions. Such a protein can interact with an oscillating pressure to pump ions and create a transmembrane gradient if the affinities of the protein for ions are different at the two sides of membrane. The frequency and concentration windows for mechanical energy transduction were determined. Under optimal conditions, the efficiency of energy transduction can approach the theoretical maximum of 100%. If the concentration gradient exceeds the static head value (quasi-equilibrium which can be built up and maintained by this transport system), the energy transduction reverses and the transporter becomes a generator of mechanical oscillations at the expense of a concentration gradient. Estimation of thermodynamic parameters of the pump shows that the PV-coupling model would require large pressure oscillations to work while the gamma A-coupling model could work in physiological conditions. The gamma A-coupling mechanism may be used by cells for two purposes. In the reverse mode, it can be a force generator for various applications. In the direct mode, it may serve bioenergetic purposes by harvesting the energy of mechanical oscillations and storing it in the form of a concentration gradient. This pump has an unusual thermodynamic feature: it can distinguish the two components of the electrochemical potential gradient,i.e., the concentration gradient and the electrical potential, the latter serving as a permissive switch to open, or close, the pump when the potential reaches the threshold value.Predictions of the PCC model and its probable involvement in biological mechanotransduction are dicussed.

Biological Transport, Active↗

PubMed2005

Frequency-selective response of periodically forced coupled FHN models via system size multi-resonance.

We consider system of globally coupled FitzHugh-Nagumo (FHN) models; each element is subjected to a subthreshold periodic signal and independent Gaussian white noise. With the variation of the system size, the spike train of the mean field of the system fires according to the period of the subthreshold external signal or to the interior time scale of the FHN model. The influence of the coupling strength is also investigated. It only influences the response of the mean field to external signal. If two external signals are injected to the system simultaneously, the least-common-multiple periods or other common multiples may be selected by different system sizes.

Computer Simulation↗

PubMedDate not supplied

Modeling flow and nitrate fate at catchment scale in Brittany (France).

In the intensive pig-farming (Sus scrofa) area of Brittany (western France), many surface and subsurface water resources are contaminated by nitrate (NO3) with concentrations that chronically exceed the European Community 50 mg L(-1) drinking standard. To ensure sustainable water supply, the fate of NO3 must be considered in both surface water and ground water. The fate of N was investigated in a Britain catchment, the Coët-Dan watershed, with an integrated management tool: the hydrological SWAT model coupled with the ground water model MODFLOW, and its companion contaminant and solute transport model MT3DMS. The model was validated with respect to water quantity during a 6-yr period and for the NO3 concentration during a 44-mo period, at two gauging stations in the catchment. The coupled models reproduced accurately the measurements. At the basin outlet, the Nash-Sutcliffe coefficients were 0.88 for monthly flow for the entire period and 0.87 for monthly N load. Alternative scenarios were simulated and showed potential benefits of decreasing manure application from 210 to 170 kg N ha(-1) as required by the European Commission Nitrates Directive.

Animals↗

PubMedDate not supplied

[Chronoinotropic reaction of the hypertrophied myocardium using an electromechanical coupling mathematical model].

Static and dynamic chrono-inotropic responses were recorded from both normal and hypertrophic rat auricular myocardium. The slope of the static force-frequency relation from hypertrophied heart was steeper than in the control hearts. The cellular mechanisms underlying changes in the force frequency response associated with hypertrophy of the heart were studied by means of a mathematical model of excitation-contraction coupling. The characteristic features of hypertrophied heart force-frequency relations are shown to be due to the enhanced volume of the intracellular Ca-stores in contrast to the total volume of the cardiomyocyte.

Animals↗

PubMed1999

Learning model for coupled neural oscillators.

Neurophysiological experiments have shown that many motor commands in living systems are generated by coupled neural oscillators. To coordinate the oscillators and achieve a desired phase relation with desired frequency, the intrinsic frequencies of component oscillators and coupling strengths between them must be chosen appropriately. In this paper we propose learning models for coupled neural oscillators to acquire the desired intrinsic frequencies and coupling weights based on the instruction of the desired phase pattern or an evaluation function. The abilities of the learning rules were examined by computer simulations including adaptive control of the hopping height of a hopping robot. The proposed learning rule takes a simple form like a Hebbian rule. Studies on such learning models for neural oscillators will aid in the understanding of the learning mechanism of motor commands in living bodies.

Action Potentials↗

PubMed2003

Synchronization of coupled rotators: Josephson junction ladders and the locally coupled Kuramoto model.

We show that the resistively shunted junction (RSJ) equations describing a ladder array of overdamped, critical-current disordered Josephson junctions that are current biased along the rungs of the ladder can be mapped onto a Kuramoto model with nearest neighbor, sinusoidal couplings. This result is obtained by an averaging method, in which the fast dynamics of the RSJ equations are integrated out, leaving the dynamics which describe the time scale over which neighboring junctions along the rungs of the ladder phase and frequency synchronize. We quantify the degree of frequency synchronization of the rung junctions by calculating the standard deviation of their time-averaged voltages, sigma(omega), and the phase synchronization is quantified by calculating the time average of the modulus of the Kuramoto order parameter, <|r|>. We test the results of our averaging process by comparing the values of sigma(omega) and <|r|> for the original RSJ equations and our averaged equations. We find excellent agreement for dc bias currents of I(B)/ greater, similar 3, where is the average critical current of the rung junctions, and critical current disorders of up to 10%. We also study the effects of thermal noise on the synchronization properties of the overdamped ladder. Finally, we find that including the effects of junction capacitance can lead to a discontinuous synchronization transition as the strength of the coupling between neighboring junctions is smoothly varied.

Journal Article↗

PubMedDate not supplied

A transport model with coupled ternary exchange and chemisorption retention for hydrazinium cations.

A numerical model was developed to describe the fate and transport of hydrazinium (N2H5+) and competing Ca2+ and H+ cations applied in acidic solutions to columns of Ca2+/H+-saturated sandy soil during steady saturated flow conditions. Instantaneous ternary H+-Ca2+-N2H5+ cation exchange using the Gaines-Thomas approach was combined with second-order, irreversible, kinetic chemisorption of exchange-phase N2H5+ ions as major retention mechanisms for N2H5+. Exchange-mediated chemisorption is assumed to occur as chemical binding of N2H5+ ions located on carboxyl-group exchange sites to nearby carbonyl groups, consequently decreasing the effective soil cation exchange capacity (CEC). Comparison of simulated and observed breakthrough curves (BTCs) for concentrations of N2H5+ and Ca2+ ions in column effluent was used in model evaluation. The cation transport model with cation exchange coupled with exchange-mediated chemisorption provided a valid first approximation for N2H5+ transport.

Absorption↗

PubMed2005

Analytic gradients for the spin-conserving and spin-flipping equation-of-motion coupled-cluster models with single and double substitutions.

Analytic gradient expressions for the spin-conserving and spin-flipping equation-of-motion coupled-cluster models with single and double substitutions are derived using a Lagrangian approach for the restricted and unrestricted Hartree-Fock references, both for the case of all orbitals being active in correlated calculations and for the frozen core and/or virtual orbitals. Details of the implementation within the Q-CHEM electronic structure package are discussed. The capabilities of the new code are demonstrated by application to cyclobutadiene.

Journal Article↗

PubMed2005

Store-operated Ca2+ entry: vesicle fusion or reversible trafficking and de novo conformational coupling?

Store-operated Ca2+ entry (SOCE), a mechanism regulated by the filling state of the intracellular Ca2+ stores, is a major pathway for Ca2+ influx. Hypotheses to explain the communication between the Ca2+ stores and plasma membrane (PM) have considered both the existence of small messenger molecules, such as a Ca2+-influx factor (CIF), and both stable and de novo conformational coupling between proteins in the Ca2+ store and PM. Alternatively, a secretion-like coupling model based on vesicle fusion and channel insertion in the PM has been proposed, which shares some properties with the de novo conformational coupling model, such as the role of the actin cytoskeleton and soluble N-ethylmaleimide (NEM)-sensitive-factor attachment proteins receptor (SNARE) proteins. Here we review recent progress made in the characterization of the de novo conformational coupling and the secretion-like coupling models for SOCE. We pay particular attention into the involvement of SNARE proteins and the actin cytoskeleton in both SOCE models. SNAREs are recognized as proteins involved in exocytosis, participating in vesicle transport, membrane docking, and fusion. As with secretion, a role for the cortical actin network in Ca2+ entry has been demonstrated in a number of cell types. In resting cells, the cytoskeleton may prevent the interaction between the Ca2+ stores and the PM, or preventing fusion of vesicles containing Ca2+ channels with the PM. These are processes in which SNARE proteins might play a crucial role upon cell activation by directing a precise interaction between the membrane of the transported organelle and the PM.

Actins↗

PubMed2005

Transient high-frequency firing in a coupled-oscillator model of the mesencephalic dopaminergic neuron.

Dopaminergic neurons of the midbrain fire spontaneously at rates <10/s and ordinarily will not exceed this range even when driven with somatic current injection. When driven at higher rates, these cells undergo spike failure through depolarization block. During spontaneous bursting of dopaminergic neurons in vivo, bursts related to reward expectation in behaving animals, and bursts generated by dendritic application of N-methyl-d-aspartate (NMDA) agonists, transient firing attains rates well above this range. We suggest a way such high-frequency firing may occur in response to dendritic NMDA receptor activation. We have extended the coupled oscillator model of the dopaminergic neuron, which represents the soma and dendrites as electrically coupled compartments with different natural spiking frequencies, by addition of dendritic AMPA (voltage-independent) or NMDA (voltage-dependent) synaptic conductance. Both soma and dendrites contain a simplified version of the calcium-potassium mechanism known to be the mechanism for slow spontaneous oscillation and background firing in dopaminergic cells. The compartments differ only in diameter, and this difference is responsible for the difference in natural frequencies. We show that because of its voltage dependence, NMDA receptor activation acts to amplify the effect on the soma of the high-frequency oscillation of the dendrites, which is normally too weak to exert a large influence on the overall oscillation frequency of the neuron. During the high-frequency oscillations that result, sodium inactivation in the soma is removed rapidly after each action potential by the hyperpolarizing influence of the dendritic calcium-dependent potassium current, preventing depolarization block of the spike mechanism, and allowing high-frequency spiking.

Action Potentials↗

PubMed2000

Comparison of the effects of 5- and 6-HOAt on model peptide coupling reactions relative to the cases for the 4- and 7-Isomers.

Synthesis of 5- and 6-HOAt has completed the full set of the four HOAt isomers derived from HOBt by insertion of a single nitrogen atom in the benzenoid nucleus. Comparison of the reactivity of all four isomers in model peptide coupling reactions has confirmed the unique character of the 7-isomer in promoting selectivity and maintaining configuration at the reactive carboxylic acid residue.

Aniline Compounds↗

PubMed2000

Neoproterozoic 'snowball Earth' simulations with a coupled climate/ice-sheet model.

Ice sheets may have reached the Equator in the late Proterozoic era (600-800 Myr ago), according to geological and palaeomagnetic studies, possibly resulting in a 'snowball Earth'. But this period was a critical time in the evolution of multicellular animals, posing the question of how early life survived under such environmental stress. Here we present computer simulations of this unusual climate stage with a coupled climate/ice-sheet model. To simulate a snowball Earth, we use only a reduction in the solar constant compared to present-day conditions and we keep atmospheric CO2 concentrations near present levels. We find rapid transitions into and out of full glaciation that are consistent with the geological evidence. When we combine these results with a general circulation model, some of the simulations result in an equatorial belt of open water that may have provided a refugium for multicellular animals.

Animals↗

PubMed2001

Modeling dynamically heterogeneous coupled relaxations.

A model describing dynamically heterogeneous relaxation in complex coupled systems is presented. The model predicts the splitting of a high-temperature single Debye relaxation to a low-temperature bimodal relaxation. The bimodal process shows a crossover from a Debye-type relaxation to an approximately stretched-exponential relaxation. Some general features of relaxation in complex systems emerge from the predictions of the model, and a comparison of the model with experiments is reported.

Journal Article↗

PubMed2001

Phase diagram for the Winfree model of coupled nonlinear oscillators.

In 1967 Winfree proposed a mean-field model for the spontaneous synchronization of chorusing crickets, flashing fireflies, circadian pacemaker cells, or other large populations of biological oscillators. Here we give the first bifurcation analysis of the model, for a tractable special case. The system displays rich collective dynamics as a function of the coupling strength and the spread of natural frequencies. Besides incoherence, frequency locking, and oscillator death, there exist hybrid solutions that combine two or more of these states. We present the phase diagram and derive several of the stability boundaries analytically.

Journal Article↗

PubMed2005

Monte Carlo simulation of a strongly coupled XY model in three dimensions.

Many experimental studies, over the past two decades, have constantly reported a critical behavior for the transition from the smectic- A phase of liquid crystals to the hexatic- B phase with non- XY critical exponents. However, according to symmetry arguments this transition must belong to the XY universality class. Using an optimized Monte Carlo simulation technique based on the multihistogram method, we have investigated the phase diagram of a coupled XY model, proposed by Bruinsma and Aeppli [Phys. Rev. Lett. 48, 1625 (1982)], in three dimensions. The simulation results demonstrate the existence of a tricritical point for this model, in which two different orderings are established simultaneously. This result verifies the accepted idea that the large specific heat anomaly exponent observed for the SmA-HexB transition could be due to the occurrence of this transition in the vicinity of a tricritical point.

Journal Article↗

PubMed2003

Is the somitogenesis clock really cell-autonomous? A coupled-oscillator model of segmentation.

A striking pattern of oscillatory gene expression, related to the segmentation process (somitogenesis), has been identified in chick, mouse, and zebrafish embryos. Somitogenesis displays great autonomy, and it is generally assumed in the literature that somitogenesis-related oscillations are cell-autonomous in chick and mouse. We point out in this article that there would be many biological reasons to expect some mechanism of coupling between cellular oscillators, and we present a model with such coupling, but which also has autonomous properties. Previous experiments can be re-interpreted in light of this model, showing that it is possible to reconcile both autonomous and non-autonomous aspects. We also show that experimental data, previously interpreted as supporting a purely negative-feedback model for the mechanism of the oscillations, is in fact more compatible with this new model, which relies essentially on positive feedback.

Animals↗

PubMed1997

How does the crayfish swimmeret system work? Insights from nearest-neighbor coupled oscillator models.

Rhythmic movements of crayfish swimmerets are coordinated by a neural circuit that links their four abdominal ganglia. Each swimmeret is driven by its own small local circuit, or pattern-generating module. We modeled this network as a chain of four oscillators, bidirectionally coupled to their nearest neighbors, and tested the model's ability to reproduce experimentally observed changes in intersegmental phases and in period caused by differential excitation of selected abdominal ganglia. The choices needed to match the experimental data lead to the following predictions: coupling between ganglia is asymmetric; the ascending and descending coupling have approximately equal strengths; intersegmental coupling does not significantly affect the frequency of the system; and excitation affects the intrinsic frequencies of the oscillators and might also change properties of intersegmental coupling.

Animals↗

PubMedDate not supplied

Coupling basin- and site-scale inverse models of the Española aquifer.

Large-scale models are frequently used to estimate fluxes to small-scale models. The uncertainty associated with these flux estimates, however, is rarely addressed. We present a case study from the Española Basin, northern New Mexico, where we use a basin-scale model coupled with a high-resolution, nested site-scale model. Both models are three-dimensional and are analyzed by codes FEHM and PEST. Using constrained nonlinear optimization, we examine the effect of parameter uncertainty in the basin-scale model on the nonlinear confidence limits of predicted fluxes to the site-scale model. We find that some of the fluxes are very well constrained, while for others there is fairly large uncertainty. Site-scale transport simulation results, however, are relatively insensitive to the estimated uncertainty in the fluxes. We also compare parameter estimates obtained by the basin- and site-scale inverse models. Differences in the model grid resolution (scale of parameter estimation) result in differing delineation of hydrostratigraphic units, so the two models produce different estimates for some units. The effect is similar to the observed scale effect in medium properties owing to differences in tested volume. More important, estimation uncertainty of model parameters is quite different at the two scales. Overall, the basin inverse model resulted in significantly lower estimates of uncertainty, because of the larger calibration dataset available. This suggests that the basin-scale model contributes not only important boundary condition information but also improved parameter identification for some units. Our results demonstrate that caution is warranted when applying parameter estimates inferred from a large-scale model to small-scale simulations, and vice versa.

Calibration↗