SEARCH · PubMed Health

Results for “Coupled model”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources

PubMed1996

Motor protein mechanics: a stochastic model with minimal mechanochemical coupling.

A stochastic model for the action of motor proteins such as kinesin is presented. The mechanical components of the enzyme are 1) two identical head domains that bind to discrete sites on a microtubule and that are capable of undergoing a conformational change; and 2) an elastic element that connects each head to the rest of the molecule. We investigate the situation in which the strain dependence of the chemical reaction rates is minimal and the heads have independent biochemical cycles. The enzyme advances stochastically along a filament when one head detaches and diffuses to a new binding site, while the other head remains bound to the microtubule. We also investigate the case in which the chemical cycles of the heads are correlated so that the molecule shifts each head alternately. The predictions of the model are found to be in agreement with experimentally measured force-velocity relationships for kinesin-both when the force is applied externally and when the enzyme is loaded by a viscous drag. For reasonable values of the parameters, this agreement is quantitative. The molecular stepping characteristics observed in recent motility assays are also reproduced. A number of experiments are suggested that would provide a more stringent test of the model and help determine whether this simple picture is an appropriate description of motor proteins or whether models that include strain-dependent reaction rates or more complicated types of cooperation of the two heads need to be considered.

Animals↗

PubMed2005

A LabVIEW model incorporating an open-loop arterial impedance and a closed-loop circulatory system.

While numerous computer models exist for the circulatory system, many are limited in scope, contain unwanted features or incorporate complex components specific to unique experimental situations. Our purpose was to develop a basic, yet multifaceted, computer model of the left heart and systemic circulation in LabVIEW having universal appeal without sacrificing crucial physiologic features. The program we developed employs Windkessel-type impedance models in several open-loop configurations and a closed-loop model coupling a lumped impedance and ventricular pressure source. The open-loop impedance models demonstrate afterload effects on arbitrary aortic pressure/flow inputs. The closed-loop model catalogs the major circulatory waveforms with changes in afterload, preload, and left heart properties. Our model provides an avenue for expanding the use of the ventricular equations through closed-loop coupling that includes a basic coronary circuit. Tested values used for the afterload components and the effects of afterload parameter changes on various waveforms are consistent with published data. We conclude that this model offers the ability to alter several circulatory factors and digitally catalog the most salient features of the pressure/flow waveforms employing a user-friendly platform. These features make the model a useful instructional tool for students as well as a simple experimental tool for cardiovascular research.

Animals↗

PubMed2005

Parameterization of a dynamic specific activity model of 14C transfer from surface water-to-humans.

Carbon-14 is a particularly interesting radionuclide from the perspective of dose estimation because it mixes readily with stable CO2, and hence enters the food-chain as fundamental biomolecules. A model was developed for the situation of 14C releases to surface waters, where there are distinct changes in the water 14C activity concentrations throughout the year. The model computes the specific activity in water, phytoplankton, fish, crops, meat, milk and air, following a typical irrigation-based food-chain scenario. This paper describes the derivation of the required 14C-specific parameter values. Many of the key parameters are not commonly measured, at least not in the context of dose assessment. Thus, inference from other sources of data was required, and this is the scientific contribution described in this paper. The best estimates and appropriate measures of statistical dispersion are provided. This required consideration of both the temporal and spatial averaging domains to ensure they were correct for parameters as defined in the model. The model coupled with these parameter values represents several new developments for modelling 14C transfers.

Air Pollution, Radioactive↗

PubMed2006

The HC fragment of tetanus toxin forms stable, concentration-dependent dimers via an intermolecular disulphide bond.

Protein oligomerisation is a prerequisite for the toxicity of a number of bacterial toxins. Examples include the pore-forming cytotoxin streptolysin O, which oligomerises to form large pores in the membrane and the protective antigen of anthrax toxin, where a heptameric complex is essential for the delivery of lethal factor and edema factor to the cell cytosol. Binding of the clostridial neurotoxins to receptors on neuronal cells is well characterised, but little is known regarding the quaternary structure of these toxins and the role of oligomerisation in the intoxication process. We have investigated the oligomerisation of the receptor binding domain (H(C)) of tetanus toxin, which retains the binding and trafficking properties of the full-length toxin. Electrophoresis, size exclusion chromatography and mass spectrometry were used to demonstrate that H(C) undergoes concentration-dependent oligomerisation in solution. Reducing agents were found to affect H(C) oligomerisation and, using mutagenesis, Cys869 was shown to be essential for this process. Furthermore, the oligomeric state and quaternary structure of H(C) in solution was assessed using synchrotron small-angle X-ray scattering. Ab initio shape analysis and rigid body modelling coupled with mutagenesis data allowed the construction of an unequivocal model of dimeric H(C) in solution. We propose a possible mechanism for H(C) oligomerisation and discuss how this may relate to toxicity.

Binding Sites↗

PubMed2006

Simultaneous absorption of CO2 and H2S into aqueous blends of N-methyldiethanolamine and diethanolamine.

Removal of CO2 from gaseous streams by absorption with chemical reaction in the liquid phase is usually employed in industry as a method to retain atmospheric CO2 to combat the greenhouse effect. A broad spectrum of alkanolamines and, more recently, their mixtures are being employed for the removal of acid gases such as CO2, H2S, and COS from natural and industrial gas streams. In this research, simultaneous absorption of CO2 and H2S into aqueous blends of N-methyldiethanolamine and diethanolamine is studied theoretically and experimentally. The effect of contact time, temperature, and amine concentration on the rate of absorption and the selectivity were studied by absorption experiments in a wetted wall column at atmospheric pressure and constant feed gas ratio. The diffusion-reaction processes for CO2 and H2S mass transfer in blended amines are modeled according to Higbie's penetration theory with the assumption that all reactions are reversible. A rigorous parametric sensitivity test is done to quantify the effects of possible errors in the pertinent model parameters on the prediction accuracy of the absorption rates and enhancement factors. Model results based on the kinetics-equilibrium-mass transfer coupled model developed in this work are found to be in good agreement with the experimental results of rates of absorption of CO2 and H2S into (MDEA + DEA + H2O).

Air Pollutants↗

PubMed1989

Salmonella typhimurium virulence in a burned-mouse model.

Various features of salmonellosis were examined in a burned-mouse model. In this model, which uses an outbred mouse strain, a challenge dose of ca. 100 CFU with any of several strains of Salmonella typhimurium caused a fatal infection. A variety of mutated strains attenuated for virulence in Salmonella-susceptible parenterally infected mice were also attenuated in the burned-mouse model. When administered as live vaccines injected intraperitoneally the same attenuated strains provided between slight and complete protection against subsequent lethal challenge subcutaneously at the site of a burn. The correspondence of results obtained in the burned-mouse model with those seen in other mouse models coupled with the unique advantages of the burned-mouse model argue for the usefulness of the model in studies of salmonellosis and in testing of strains constructed for use as live vaccines.

Animals↗

PubMed2000

Left ventricular wall stress normalization in chronic pressure-overloaded heart: a mathematical model study.

It is generally accepted that the left ventricle (LV) hypertrophies (LVH) to normalize systolic wall stress (sigma(s)) in chronic pressure overload. However, LV filling pressure (P(v)) may be elevated as well, supporting the alternative hypothesis of end-diastolic wall stress (sigma(d)) normalization in LVH. We used an LV time-varying elastance model coupled to an arterial four-element lumped-parameter model to study ventricular-arterial interaction in hypertension-induced LVH. We assessed model parameters for normotensive controls and applied arterial changes as observed in hypertensive patients with LVH (resistance +40%, compliance -25%) and assumed 1) no cardiac adaptation, 2) normalization of sigma(s) by LVH, and 3) normalization of sigma(s) by LVH and increase in P(v), such that sigma(d) is normalized as well. In patients, systolic and diastolic blood pressures increase by approximately 40%, cardiac output (CO) is constant, and wall thickness increases by 30-55%. In scenarios 1 and 2, blood pressure increased by only 10% while CO dropped by 20%. In scenario 2, LV wall thickness increased by only 10%. The predictions of scenario 3 were in qualitative and quantitative agreement with in vivo human data. LVH thus contributes to the elevated blood pressure in hypertension, and cardiac adaptations include an increase in P(v), normalization of sigma(s), and preservation of CO in the presence of an impaired diastolic function.

Adaptation, Physiological↗

PubMed1996

Component stretching during oblique stimulation-evoked saccades: the role of the superior colliculus.

1. During oblique visually guided saccades, the peak velocity of each component is reduced from what it would be for a purely horizontal or vertical saccade of the same amplitude, and the durations of the components are prolonged. We tested predictions of two competing accounts of the neural basis of this "component stretching" phenomenon. Using a recent experimental approach, we electrically stimulated sites in the monkey superior colliculus (SC) immediately after either vertical or horizontal visually guided saccades. Under these conditions, the amplitude of one component (corresponding to the direction of the preceding movement, horizontal or vertical) of the stimulation-evoked saccade varies systematically, while the amplitude of the other component ("constant-amplitude component") remains essentially constant. These changes in saccade metrics occur even though both the locus and parameters of collicular stimulation are fixed. 2. As with visually guided saccades, the peak velocity of the constant-amplitude component in stimulation-evoked saccades decreased with increasing amplitude of the orthogonal component, while the duration of the constant-amplitude component increased with orthogonal amplitude. The component stretching effect in these stimulation-evoked saccades was qualitatively indistinguishable from component stretching in metrically matched, visually guided movements. Yet, unlike visually guided saccades, the locus of stimulation-induced activity was fixed from one stimulation-evoked saccade to the next. 3. Therefore component stretching in stimulation-evoked oblique saccades does not depend on the locus of activity in the collicular motor map. These results are inconsistent with the predictions of common source models of component stretching, but are consistent with cross-coupling models. We discuss the present results in the context of a new interpretation of collicular interaction with downstream saccadic controllers.

Animals↗

PubMed2006

Three-pulse photon echo of an excitonic dimer modeled via Redfield theory.

In this article the third-order response of an excitonically coupled dimer is studied. The three-pulse photon echo signals were calculated by extracting polarization components from the total polarization in the corresponding phase-matched directions. The total nonlinear response was obtained by numeric propagation of the density matrix, with the exciton-vibrational coupling modeled via Redfield relaxation theory. The full two-dimensional three-pulse photon echo signals and the peak shift were analyzed in terms of the density-matrix dynamics of coherence dephasing and population relaxation. The location of the two-exciton state was found to be essential for proper modeling of the three-pulse photon echo. In particular, an oscillation in the three-pulse photon echo peak shift is found if the two-exciton state is displaced. The oscillations can be related to the dynamics of the one-exciton coherences.

Journal Article↗

PubMed2006

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe-4S] cluster.

Desulfovibrio gigas ferredoxin II (DgFdII) is a small protein with a polypeptide chain composed of 58 amino acids, containing one Fe3S4 cluster per monomer. Upon studying the redox cycle of this protein, we detected a stable intermediate (FdIIint) with four 1H resonances at 24.1, 20.5, 20.8 and 13.7 ppm. The differences between FdIIox and FdIIint were attributed to conformational changes resulting from the breaking/formation of an internal disulfide bridge. The same 1H NMR methodology used to fully assign the three cysteinyl ligands of the [3Fe-4S] core in the oxidized state (DgFdIIox) was used here for the assignment of the same three ligands in the intermediate state (DgFdIIint). The spin-coupling model used for the oxidized form of DgFdII where magnetic exchange coupling constants of around 300 cm-1 and hyperfine coupling constants equal to 1 MHz for all the three iron centres were found, does not explain the isotropic shift temperature dependence for the three cysteinyl cluster ligands in DgFdIIint. This study, together with the spin delocalization mechanism proposed here for DgFdIIint, allows the detection of structural modifications at the [3Fe-4S] cluster in DgFdIIox and DgFdIIint.

Chromatography, High Pressure Liquid↗

PubMed1999

Vesicle deformation by an axial load: from elongated shapes to tethered vesicles.

A sufficiently large force acting on a single point of the fluid membrane of a flaccid phospholipid vesicle is known to cause the formation of a narrow bilayer tube (tether). We analyze this phenomenon by means of general mathematical methods allowing us to determine the shapes of strongly deformed vesicles including their stability. Starting from a free vesicle with an axisymmetric, prolate equilibrium shape, we consider an axial load that pulls (or pushes) the poles of the vesicle apart. Arranging the resulting shapes of strained vesicles in dependence of the axial deformation and of the area difference of monolayers, phase diagrams of stable shapes are presented comprising prolate shapes with or without equatorial mirror symmetry. For realistic values of membrane parameters, we study the force-extension relation of strained vesicles, and we demonstrate in detail how the initially elongated shape of an axially stretched vesicle transforms into a shape involving a membrane tether. This tethering transition may be continuous or discontinuous. If the free vesicle is mirror symmetric, the mirror symmetry is broken as the tether forms. The stability analysis of tethered shapes reveals that, for the considered vesicles, the stable shape is always asymmetric (polar), i.e., it involves only a single tether on one side of the main vesicle body. Although a bilayer tube formed from a closed vesicle is not an ideal cylinder, we show that, for most practical purposes, it is safe to assume a cylindrical geometry of tethers. This analysis is supplemented by the documentation of a prototype experiment supporting our theoretical predictions. It shows that the currently accepted model for the description of lipid-bilayer elasticity (generalized bilayer couple model) properly accounts for the tethering phenomenon.

Biophysical Phenomena↗

PubMed2000

The actin cytoskeleton in store-mediated calcium entry.

Store-mediated Ca2+ entry is the main pathway for Ca2+ influx in platelets and many other cells. Several hypotheses have considered both direct and indirect coupling mechanisms between the endoplasmic reticulum and the plasma membrane. Here we pay particular attention to new insights into the regulation of store-mediated Ca2+ entry: the role of the cytoskeleton in a secretion-like coupling model. In this model, Ca2+ entry may be mediated by a reversible trafficking and coupling of the endoplasmic reticulum with the plasma membrane, that shows close parallels to the events mediating secretion. As with secretion, the actin cytoskeleton plays an inhibitory role in the activation of Ca2+ entry by preventing the approach and coupling of the endoplasmic reticulum with the plasma membrane, making cytoskeletal remodelling a key event in the activation of Ca2+ entry. We also review recent advances investigating the regulation of store-mediated Ca2+ entry by small GTPases and phosphoinositides, which might be involved in the store-mediated Ca2+ entry pathway through roles in the remodelling of the cytoskeleton.

Actins↗

PubMed2000

[Evaluation of commercial UHT milk and optimization of industrial process].

From the nutrition al point of view milk is one of the most complete food in the diet of mammals. It contains nearly all the nutrients necessary to sustain life, but milk can deteriorate very easily, either by microbiological contamination or by biochemical reactions during processing and/or storage. The objective of this research study was to design a modified UHT treatment to achieve commercial sterilization and maximize the stabilization of the heat-treated product during storage. To search for a modified UHT process, a mathematical model coupled with an optimization routine (complex method) was developed. The mathematical model considers Kinetics for the inactivation of Bacillus stearothermophilus and several quality factors. To attain the objective function, several commercial UHT milk were analyzed and for the computer search the minimization of hydroxy methyl furfural (HMF) formation was considered and also including constraints for protease and lipase inactivation. The complex optimization procedure was implemented to search for the optimum modified UHT treatment.. One of the optimum modified UHT treatments was the combination of two pre-treatment (3.16 minutes at 62.30 degrees C and 6 minutes at 75 degrees C) in addition with a UHT treatment (0.75 s at 148.8 degrees C). This treatment attains the maximum product stability with a negligible effect on composition and color formation in the treated milk (HMF formation less than 3 mg/mL).

Animals↗

PubMed2005

Solvent effects on the vibronic one-photon absorption profiles of dioxaborine heterocycles.

The vibronic profiles of one-photon absorption spectra of dioxaborine heterocycles in gas phase and solution have been calculated at the Hartree-Fock and density-functional-theory levels. The polarizable continuum model has been applied to simulate the solvent effect, while the linear coupling model is used to compute the Franck-Condon and Herzberg-Teller contributions. It is found that a good agreement between theory and experiment can be achieved when the solvent effect and electron correlation are taken into account simultaneously. For the first excited charge-transfer state, the maximum of its Herzberg-Teller profile is blueshifted from that of the Franck-Condon profile. The shifted energy is found to be around 0.2 eV, which agrees well with the measured energy difference between two- and one-photon absorptions of the first excited state.

Journal Article↗

PubMed2002

A Levy flight-random walk model for bioturbation.

Levy flights are employed in a lattice model of contaminant migration by bioturbation, the reworking of sediment by benthic organisms. The model couples burrowing, foraging, and conveyor-belt feeding with molecular diffusion. The model correctly predicts a square-root dependence on bioturbation rates over a wide range of biomass densities. The model is used to predict the effect of bioturbation on the redistribution of contaminants in laboratory microcosms containing pyrene-inoculated sediments and the tubificid oligochaete Limnodrilus hoffmeisteri. The model predicts the dynamic flux from the sediment and in-bed concentration profiles that are consistent with observations. The sensitivity of flux and concentration profiles to the specific mechanisms of bioturbation are explored with the model. The flux of pyrene to the overlying water was largely controlled by the simulated foraging activities.

Animals↗

PubMed2002

Lattice-spin mechanism in colossal magnetoresistive manganites.

We present a single-orbital double-exchange model, coupled with cooperative phonons (the so called breathing modes of the oxygen octahedra in manganites). The model is studied with Monte Carlo simulations. For a finite range of doping and coupling constants, a first-order metal-insulator phase transition is found, which coincides with the paramagnetic-ferromagnetic phase transition. The insulating state is due to the self-trapping of every carrier within an oxygen octahedron distortion.

Journal Article↗

PubMed2004

DFT-based pseudo-Jahn-Teller coupling studies on the steric and energetic lone pair effect of four- and five-coordinate halide molecules and complexes with central ions from the fifth, sixth, and seventh main groups.

The energetical and stereochemical effect of the s(2) lone pair in the title molecules and complexes is investigated using a pseudo-Jahn-Teller coupling model with parameters adjusted to energies and wave functions from DFT calculations. Vibronic coupling parameters were calculated and compared with those of the coordination number (CN) 3. Inspecting the correlation between the chemical hardness and the vibronic coupling energy (hardness rule), it is found that the tendency to distort decreases with increasing CN. While all considered molecules AX(3) (A(III) = P to Bi; X(-) = F to I) undergo lone pair deformations (D(3h)---> C(3v)), only part of the AX(4)(-) and BX(4) species (B(IV) = S to Po) do so (T(d)---> C(2v)-and even less the ones with CN = 5 (D(3h)---> C(2v) (congruent with C(4v)), AX(5)(2-), BX(5)(-), and CF(5) (C(V); Cl to I). The distorted polyhedra of minimum energy possess usually the butterfly C(2v) shape (CN = 4, tau(2)(zeta) displacement path) and a C(2v) = C(4v)geometry (CN = 5, epsilon' (epsilon) distortion path). A further symmetry lowering to C(s) occurs, if the central ion becomes too small with respect to the ligands (ionic size influence, PCl(Br)(4)(-), PCl(5)(2-)), with the tendency to reduce the CN toward 3 + 1 and 4 + 1, respectively. For CN = 4 the various stationary points of, for example, compressed and elongated C(3v), C(4v), etc. in the multidimensional ground-state potential surface have been characterized. Though of higher energy than the absolute C(2v) minimum, they are shown to govern the dynamics and reactivity of the CN = 4 species to a large extent. To simulate the chemical environment (positively charged counterions, polar solvents), the DFT calculations were performed using the polarizable continuum model COSMO (conductor-like screening model). Though the electronic energy gain upon distortion is not significantly affected by the solvent, the total stabilization energy is distinctly enhanced, frequently leading to lone pair deformations of otherwise electronically stable species. All results obtained by the combined vibronic/DFT approach are well in accord with available experimental data.

Journal Article↗

PubMed2005

Prospective validation of two models predicting pregnancy leading to live birth among untreated subfertile couples.

BACKGROUND: Models predicting clinical outcome need external validation before they can be applied safely in daily practice. This study aimed to validate two models for the prediction of the chance of treatment-independent pregnancy leading to live birth among subfertile couples. METHODS: The first model uses the woman's age, duration and type of subfertility, percentage of progressive sperm motility and referral status. The second model in addition uses the result of the post-coital test (PCT). For validation, these characteristics were collected prospectively in two University hospitals for 302 couples consulting for subfertility. The models' ability to distinguish between women who became pregnant and women who did not (discrimination) and the agreement between predicted and observed probabilities of treatment-independent pregnancy (calibration) were assessed. RESULTS: The discrimination of both models was slightly lower in the validation sample than in the original sample which provided the model. Calibration was good: the observed and predicted probabilities of treatment-independent pregnancy leading to live birth did not differ for both models. CONCLUSIONS: The chance of pregnancy leading to live birth was reliably estimated in the validation sample by both models. The use of PCT improved the discrimination of the models. These models can be useful in counselling subfertile couples.

Birth Rate↗