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Results for “Coupled model”

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PubMed2004

A unified biochemical and continuum mechanical red blood cell membrane bilayer--couple model.

We study the shapes and biochemical characteristics of human red blood cells using a unified biochemical and continuum mechanical model. In particular, we model the crenated, echinocytic shapes and show how they may shift due to changes in the pH and various amphipaths affecting the osmotic pressure by also utilizing pressure as an independent variable. In contrast to earlier works which advocate that biochemical factors may be attributable to mechanical control parameters, cytoskeletal elastic constants and effective relaxed bilayer area difference of outer plasma membrane and inner protein-based membrane skeleton, our unified model agrees well with Band 3 diffusion experimental root mean square distance data.

Anion Exchange Protein 1, Erythrocyte↗

PubMed1991

Mechanism of activation of A2 adenosine receptors. II. A restricted collision-coupling model of receptor-effector interaction.

Existing models describing the kinetics of receptor-effector interaction were found to be insufficient to account for the experimental findings on adenylate cyclase activation by A2 adenosine receptors described in the preceding manuscript [Mol. Pharmacol. 39: 517-523 (1991)]. We have, therefore, chosen another approach and have developed discrete computer simulations of receptor-effector interactions taking place on a spherical membrane. These simulations were based on the following principles: (a) receptors activate effectors in a catalytic manner, and (b) diffusion of receptors and effectors is slow, so that receptors will only activate effectors that are in their vicinity at the time of agonist occupation. Using several experimentally determined parameters, these simulations could reproduce the experimental findings on adenylate cyclase activation by A2 adenosine receptors described in the preceding manuscript. In addition, by appropriate choice of the simulation parameters, they are shown to accommodate the behavior of several other models of receptor-effector interactions.

Azides↗

PubMed2000

Status and improvements of coupled general circulation models

Coupled general circulation models (CGCMs) integrate our knowledge about atmospheric and oceanic circulation. Different versions of CGCMs are used to provide a better understanding of natural climate variability on interannual and decadal time scales, for extended weather forecasting, and for making seasonal climate scenario projections. They also help to reconstruct past climates, especially abrupt climate change processes. Model intercomparisons, new test data (mainly from satellites), more powerful computers, and parameterizations of atmospheric and oceanic processes have improved CGCM performance to such a degree that the model results are now used by many decision-makers, including governments. They are also fundamental for the detection and attribution of climate change.

Journal Article↗

PubMed2000

Duality relations for M coupled potts models

We establish explicit duality transformations for systems of M q-state Potts models coupled through their local energy density, generalizing known results for M=1,2,3. The M-dimensional space of coupling constants contains a self-dual submanifold of dimension D(M)=[M/2]. For the case M=4, the variation of the effective central charge along the self-dual surface is investigated by numerical transfer matrix techniques. Evidence is given for the existence of a family of critical points, corresponding to conformal field theories with an extended S(M) symmetry algebra.

Journal Article↗

PubMed1989

Extending relapse prevention models to couples.

A model is proposed which extends Marlatt's Relapse Prevention model to couples. The model includes macroscopic and microscopic levels of analysis. At the macroscopic level, it is proposed that the probability of client coping responses is affected by the quality of the client's social support network, the quality of primary intimate relationships, the density of reinforcement for abstinence, and the expectation of loss of reinforcement for drinking. At the microscopic level, it is proposed that spouses may engage in a variety of coping responses that may either facilitate client coping and help maintain changes in drinking, or which are nonfacilitative and increase the likelihood of relapse. Clinical implications of the model are discussed.

Alcoholism↗

PubMed2004

Measles metapopulation dynamics: a gravity model for epidemiological coupling and dynamics.

Infectious diseases provide a particularly clear illustration of the spatiotemporal underpinnings of consumer-resource dynamics. The paradigm is provided by extremely contagious, acute, immunizing childhood infections. Partially synchronized, unstable oscillations are punctuated by local extinctions. This, in turn, can result in spatial differentiation in the timing of epidemics and, depending on the nature of spatial contagion, may result in traveling waves. Measles epidemics are one of a few systems documented well enough to reveal all of these properties and how they are affected by spatiotemporal variations in population structure and demography. On the basis of a gravity coupling model and a time series susceptible-infected-recovered (TSIR) model for local dynamics, we propose a metapopulation model for regional measles dynamics. The model can capture all the major spatiotemporal properties in prevaccination epidemics of measles in England and Wales.

Demography↗

PubMed2005

Coupled design model of pre-denitrification systems.

A coupled model of biological and settling phases aimed at optimal design of pre-denitrification systems is presented. Each unknown is obtained in explicit form, and is expressed as a function of the system's required performance. A model taking into account both suspended and dissolved substrates is adopted for the biological phase, while the limiting solid flux theory is assumed for the design of the settling phase. Finally a relationship correlating the two phases is obtained expressing opportunely the sludge recycle flow and the sludge waste flow, without recourse to empirical parameters. The effect of different influent/effluent wastewater characteristics on the model's results is also analysed.

Models, Theoretical↗

PubMed2002

Modeling force development in the sarcomere in consideration of electromechanical coupling.

Models of the cellular force development simulate the contractive behavior of the sarcomere. In conjunction with electrophysiological models they can contribute to a better comprehension of physiology and pathologies. Aim of this study is to examine the coupling of cellular electrophysiological processes and force development. For that a graphical user interface was developed to simplify the parameterization and calculation of the models as well as to present the results graphically. A feedback mechanism is introduced to pay attention to close connections between force development and intracellular processes. On basis of various tests with different boundary conditions, new force models are developed, parameterized, validated and compared with models in literature. In future studies the results will be tested in multiple cell organization.

Actins↗

PubMed1997

Hodgkin-Huxley and partially coupled inactivation models yield different voltage dependence of block.

K+ channel blockers have been shown to exhibit complex time- and voltage-dependent effects on cardiac K+ currents. Whereas much attention has been focused on the state dependence of K+ channel block, how a particular channel model can alter the predicted time and voltage dependence of channel block remains unexplored. In this study, using two different model formalisms for the same cardiac transient outward current channel, we compare the effects of a theoretical open-state specific channel blocker on macroscopic currents. Model 1 is a Hodgkin-Huxley-like model, in which inactivation is an intrinsically voltage-dependent process and occurs independently of activation. Model 2 is a "partially coupled" model, in which inactivation is intrinsically voltage insensitive but requires channel activation before it can proceed. In the absence of drug (blocking agent), the two models reproduce the macroscopic current data. In the presence of blocking agent, the two models can differ substantially, with model 1 displaying much less block than model 2. We also examine simple mathematically convenient modifications to the Hodgkin-Huxley formalism, which reproduce some, but not all, of the use-dependent properties of block. Thus model formalism is important for analysis and simulation of state-specific drug-channel interactions.

Animals↗

PubMed1983

A continuum model for coupled cells.

A continuum model of diffusion-coupled cells that more accurately reflects the presence of low-permeability gap junctions between cells is analyzed. It is shown by a multi-scale analysis that to lowest order the slow evolution of the mean concentration is described by the usual ordinary differential equations for a discrete model. Furthermore, stable non-uniform steady solutions are shown to exist in the continuum model of a one component system, whereas this is impossible for the standard reaction-diffusion model of this system. It is also shown how to average the equations in this continuum model to obtain a system of reaction-diffusion equations with constant coefficients.

Animals↗

PubMed1995

Electroencephalogram and visual evoked potential generation in a mathematical model of coupled cortical columns.

This study deals with neurophysiologically based models simulating electrical brain activity (i.e., the electroencephalogram or EEG, and evoked potentials or EPs). A previously developed lumped-parameter model of a single cortical column was implemented using a more accurate computational procedure. Anatomically acceptable values for the various model parameters were determined, and a multi-dimensional exploration of the model parameter-space was conducted. It was found that the model could produce a large variety of EEG-like waveforms and rhythms. Coupling two models, with delays in the interconnections to simulate the synaptic connections within and between cortical areas, made it possible to replicate the spatial distribution of alpha and beta activity. EPs were simulated by presenting pulses to the input of the coupled models. In general, the responses were more realistic than those produced using a single model. Our simulations also suggest that the scalp-recorded EP is at least partially due to a phase reordering of the ongoing activity.

Animals↗

PubMed1997

Structure of a laccase-mediated product of coupling of 2,4-diamino-6-nitrotoluene to guaiacol, a model for coupling of 2,4,6-trinitrotoluene metabolites to a humic organic soil matrix.

This work presents laccase-mediated model reactions for coupling of reduced 2,4,6-trinitrotoluene (TNT) metabolites to an organic soil matrix. The structure of an isolated coupling product of 2,4-diamino-6-nitrotoluene (2,4-DANT) to guaiacol as humic constituent was determined. Among several structures, the compound was identified conclusively to be the trinuclear coupling product 5-(2-amino-3-methyl-4-nitroanilino)-3,3(prm1)-dimethoxy-4,4(prm1)-diphenoqu inone. The compound has a weight of 409 g mol(sup-1) and may serve as a model reaction for the biogenic formation of bound residues in soil from TNT by coupling aminotoluenes (reduced TNT metabolites) to humic constituents. A linear correlation of the substrate consumption to the enzyme activity was detected. Based on this observation, the described reaction of 2,4-DANT coupling to guaiacol may be used for determination of laccase activity since the reaction was not inhibited by other compounds of culture supernatants. We propose a two-step mechanism for the coupling reaction because 2,4-DANT was not transformed by laccases in the absence of guaiacol and guaiacol oxidation was independent of the presence of 2,4-DANT. The first reaction step is a laccase-mediated dimerization of two guaiacol monomers with subsequent oxidation to a diphenoquinone. The second step is the nucleophilic addition of 2,4-DANT to the ortho position of the carbonyl group of the diphenoquinone structure.

Journal Article↗

PubMed2003

Evaluation of the influence of anisotropic indirect nuclear spin-spin coupling tensors on effective residual dipolar couplings for model peptides.

Residual dipolar couplings (RDCs) observed between nuclear spins in molecules in partially oriented media have become a valuable source of information for NMR spectroscopists seeking to structurally characterize biological macromolecules. Examination of the form of the direct (D) and indirect (J) nuclear spin-spin coupling Hamiltonians indicates that all observed RDCs contain an unknown contribution from the anisotropic part of J (Delta J) in addition to the direct dipolar contribution, DPQ. Here, we evaluate the influence of DeltaJ on RDCs through a series of DFT calculations on model peptides. Very small corrections to one-bond RDCs measured between heavy atoms in peptides and proteins are recommended: +0.51% for N-C' spin pairs, and +0.45% for C alpha-C' spin pairs. The corrections to RDCs involving at least one proton are negligible. This latter point is likely to be equally applicable to nucleic acids and oligosaccharides in addition to peptides and proteins. Finally, the orientations of the J(N, C') and J(C alpha, C') tensors in the molecular framework are reported for glycylglycine.

Anisotropy↗

PubMed2003

The effects of changes of intermolecular coupling on glass transition dynamics in polymer thin films and glass-formers confined in nanometer pores.

Intermolecular coupling plays an important role in determining the dynamics and the mobility of polymeric and non-polymeric glass-formers. The breadth of the dispersion is an indicator of the intermolecular coupling strength. The coupling model relates intermolecular coupling through the breadth of the dispersion to the dynamics of bulk glass-formers. When a glass-former is confined in nanometer pores or in thin films and if there is absence of chemical and physical interactions with the wall, intermolecular coupling is reduced, resulting in an increase of mobility. The coupling model is used to account for such changes of relaxation time of 1) ortho-terphenyl and poly(dimethyl siloxane) confined in nanometer pores, 2) polymer thin film confined between two impenetrable walls from Monte Carlo simulation, and 3) polymer film confined by perfectly smooth and purely repulsive potential acting on the repeat units from molecular-dynamics simulation. The model continues to explain the opposite effects observed when there is an increase of intermolecular coupling due to the presence of chemical or physical interaction with the walls.

Journal Article↗

PubMed2005

Relation between the alpha-relaxation and Johari-Goldstein beta-relaxation of a component in binary miscible mixtures of glass-formers.

The coupling model was applied to describe the alpha-relaxation dynamics of each component in perfectly miscible mixtures A(1-x)B(x) of two different glass-formers A and B. An important element of the model is the change of the coupling parameter of each component with the composition, x, of the mixture. However, this change cannot be determined directly from the frequency dispersion of the alpha-relaxation of each component because of the broadening caused by concentration fluctuations in the mixture, except in the limits of low concentrations of either component, x --> 0 and x --> 1. Fortunately, the coupling model has another prediction. The coupling parameter of a component, say A, in the mixture determines tau(alpha)/tau(JG), the ratio of the alpha-relaxation time, tau(alpha), to the Johari-Goldstein (JG) secondary relaxation time, tau(JG), of the same component A. This prediction enables us to obtain the coupling parameter, n(A), of component A from the isothermal frequency spectrum of the mixture that shows both the alpha-relaxation and the JG beta-relaxation of component A. We put this extra prediction into practice by calculating n(A) of 2-picoline in binary mixtures with either tri-styrene or o-terphenyl from recently published broadband dielectric relaxation data of the alpha-relaxation and the JG beta-relaxation of 2-picoline. The results of n(A) obtained from the experimental data show its change with composition, x, follows the same pattern as assumed in previous works that address only the alpha-relaxation dynamics of a component in binary mixtures based on the coupling model. There is an alternative view of the thrust of the present work. If the change of n(A) with composition, x, in considering the alpha-relaxation of component A is justified by other means, the theoretical part of the present work gives a prediction of how the ratio tau(alpha)/tau(JG) of component A changes with composition, x. The data of tau(alpha) and tau(JG) of 2-picoline mixed with tri-styrene or o-terphenyl provide experimental support for the prediction.

Journal Article↗

PubMed1997

Stability and Intermittency in Large-Scale Coupled Oscillator Models for Perceptual Segmentation

The coupled map lattice, a system of locally coupled nonlinear maps, is proposed as a model for perceptual segmentation. Patterns of synchronized activity are obtained in the model from high-dimensional, deterministic chaos. These patterns correspond to segmented topographical mappings of the visual field. The chaotic dynamic has a dual role of contributing to pattern creation in unsynchronized states and of noise revolting against stabilization in synchronized states. The dynamic allows rapid transitions between unsynchronized and synchronized states. Their stability characteristics are explored using analytical tools and numerical simulations. Stability or instability are shown to be determined by network coupling strength, in proportion to the rate of chaotic divergence. The introduction of adaptive connections, in combination with stimulus-controlled oscillation, enables stable or meta-stable patterns of synchronized activity to occur, depending on the perceptual structure in the visual field. For a perceptually ambiguous pattern, the system switches between alternative meta-stable segmentations. The switching-time distribution obtained from the model was found in agreement with those observed in the experimental literature. Copyright 1997 Academic Press. Copyright 1997 Academic Press

Journal Article↗

PubMed2001

Weak and strong dynamic scaling in a one-dimensional driven coupled-field model: effects of kinematic waves.

We study the coupled dynamics of the displacement fields in a one-dimensional coupled-field model for drifting crystals, first proposed by Lahiri and Ramaswamy [Phys. Rev. Lett. 79, 1150 (1997)]. We present some exact results for the steady state and the current in the lattice version of the model for a special subspace in the parameter space, within the region where the model displays kinematic waves. We use these results to construct the effective continuum equations corresponding to the lattice model. These equations decouple at the linear level in terms of the eigenmodes. We examine the long-time, large-distance properties of the correlation functions of the eigenmodes by using symmetry arguments, Monte Carlo simulations, and self-consistent mode-coupling methods. For most parameter values, the scaling exponents of the Kardar-Parisi-Zhang equation are obtained. However, for certain symmetry-determined values of the coupling constants the two eigenmodes, although nonlinearly coupled, are characterized by two distinct dynamic exponents. We discuss the possible application of the dynamic renormalization group in this context.

Journal Article↗

PubMed2005

Modelling biological complexity: a physical scientist's perspective.

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter. The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.

Animals↗