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PubMed1983

An interpretation of some whole plant water transport phenomena.

A treatment of water flow into and through plants to the evaporating surface of the leaves is presented. The model is driven by evaporation from the cell wall matrix of the leaves. The adsorptive and pressure components of the cell wall matric potential are analyzed and the continuity between the pressure component and the liquid tension in the xylem established. Continuity of these potential components allows linking of a root transport function, driven by the tension in the xylem, to the leaf water potential. The root component of the overall model allows for the solvent-solute interactions characteristic of a membrane-bound system and discussion of the interactions of environmental variables such as root temperature and soil water potentials. A partition function is developed from data in the literature which describes how water absorbed by the plant might be divided between transpiration and leaf growth over a range of leaf water potentials.Relationships between the overall system conductance and the conductance coefficients of the various plant parts (roots, xylem, leaf matrix) are established and the influence of each of these discussed.The whole plant flow model coupled to the partition function is used to simulate several possible relationships between leaf water potential and transpiration rate. The effects of changing some of the partition function coefficients, as well as the root medium water potential on these simulations is illustrated.In addition to the general usefulness of the model and its ability to describe a wide range of situations, we conclude that the relationships used, dealing with bulk fluid flow, diffusion, and solute transport, are adequate to describe the system and that analogically based theoretical systems, such as the Ohm's law analogy, probably ought to be abandoned for this purpose.

Journal Article↗

PubMed2000

Causes of climate change over the past 1000 years

Recent reconstructions of Northern Hemisphere temperatures and climate forcing over the past 1000 years allow the warming of the 20th century to be placed within a historical context and various mechanisms of climate change to be tested. Comparisons of observations with simulations from an energy balance climate model indicate that as much as 41 to 64% of preanthropogenic (pre-1850) decadal-scale temperature variations was due to changes in solar irradiance and volcanism. Removal of the forced response from reconstructed temperature time series yields residuals that show similar variability to those of control runs of coupled models, thereby lending support to the models' value as estimates of low-frequency variability in the climate system. Removal of all forcing except greenhouse gases from the approximately 1000-year time series results in a residual with a very large late-20th-century warming that closely agrees with the response predicted from greenhouse gas forcing. The combination of a unique level of temperature increase in the late 20th century and improved constraints on the role of natural variability provides further evidence that the greenhouse effect has already established itself above the level of natural variability in the climate system. A 21st-century global warming projection far exceeds the natural variability of the past 1000 years and is greater than the best estimate of global temperature change for the last interglacial.

Journal Article↗

PubMed2004

Vibrational dynamics of adsorbed molecules under conditions of photodesorption: pump-probe SFG spectra of CO/Pt(111).

Interaction of CO adsorbed on Pt(111) with electrons and phonons is studied experimentally by means of a pump-probe experiment where CO is probed by IR + visible sum frequency generation under a pump laser intensity that allows photodesorption. Vibrational spectra of CO internal stretch are obtained as a function of pump-probe delay. A two-temperature and anharmonic coupling model is used to extract from the spectra the real time variations of CO peak frequency and dephasing time. The main conclusions are the following: (i) The CO stretch is perturbed by two low-frequency modes, assigned to frustrated rotation and frustrated translation. (ii) The frustrated rotation is directly coupled to electrons photoexcited in Pt(111) by the pump laser. (iii) There is no evidence of Pt-CO stretch excitation in the spectra. The implications for the photodesorption dynamics are discussed.

Journal Article↗

PubMed2006

Heat transfer in Fitzhugh-Nagumo models.

An extended FitzHugh-Nagumo model coupled with dynamical heat transfer in tissue, as described by a bioheat equation, is derived and confronted with experiments. The main outcome of this analysis is that traveling pulses and spiral waves of electric activity produce temperature variations on the order of tens of mu degrees C. In particular, the model predicts that a spiral wave's tip, heating the surrounding medium as a consequence of the Joule effect, leads to characteristic hot spots. This process could possibly be used to have a direct visualization of the tip's position by using thermal detectors.

Action Potentials↗

PubMed2005

Attention-driven discrete sampling of motion perception.

In movies or on TV, a wheel can seem to rotate backwards, due to the temporal subsampling inherent in the recording process (the wagon wheel illusion). Surprisingly, this effect has also been reported under continuous light, suggesting that our visual system, too, might sample motion in discrete "snapshots." Recently, these results and their interpretation have been challenged. Here, we investigate the continuous wagon wheel illusion as a form of bistable percept. We observe a strong temporal frequency dependence: the illusion is maximal at alternation rates around 10 Hz but shows no spatial frequency dependence. We introduce an objective method, based on unbalanced counterphase gratings, for measuring this phenomenon and demonstrate that the effect critically depends on attention: the continuous wagon wheel illusion was almost abolished in the absence of focused attention. A motion-energy model, coupled with attention-dependent temporal subsampling of the perceptual stream at rates between 10 and 20 Hz, can quantitatively account for the observed data.

Attention↗

PubMed2005

[Estimation models for vegetation water content at both leaf and canopy levels].

Based on spectral indices method, this paper utilized the water content (Cw) and reflectance data of 67 fresh different type leaves from LOPEX' 93 database to establish the statistical model between leaf Cw and spectral indices at leaf level through 47 samples, and to test the model with the other 20 samples. The results suggested that fuel moisture content (FMC) and equivalent water thickness (EWT) as Cw demonstrators were different in reflectance spectral curves. The difference between FMC and EWT was large when they were utilized to retrieve the leaf Cw. The correlation coefficient between EWT and each spectral index was higher than FMC, but the forecast precision of FMC was better than that of EWT. The 7 spectral indices could all retrieve the leaf FMC accurately, but only the Ratio975, II and SR were suitable to estimate the leaf EWT. Spectral indices linear model on the strength of optimal subset regressions had the highest precision to retrieve the leaf Cw. Ratio975 might be the universal spectral index to estimate the leaf Cw. At canopy level, the simulated canopy spectra under different leaf area index (LAI) and Cw were derived from the PROSPECT and SAILH coupling models. In order to eliminate background influence and to precisely retrieve the Cw, soil-adjusted water index (SAWI) was proposed at the first time to indicate the information of near-infrared and short-wave infrared canopy reflectance. The ratio of SAWI and other spectral indices could dramatically eliminate the soil background, and effectively retrieve the vegetation Cw at canopy level. Spectral index (Ratio975 - 0.96)/(SAWI + 0.2) as improved Ratio975 could be used to compute the canopy Cw more precisely when LAI was ranging from 0.3 to 8.0 and Cw from 0.0001 to 0. 07cm.

Ecosystem↗

PubMed2005

Channel specific rate constants relevant to the thermal decomposition of disilane.

Rate constants for the thermal dissociation of Si2H6 are predicted with a novel transition state model. The saddle points for dissociation on the Si2H6 potential energy surface are lower in energy than the corresponding separated products, as confirmed by high level ab initio quantum mechanical calculations. Thus, the dissociations of Si2H6 to produce SiH2 + SiH4 (R1) and H3SiSiH + H2 (R2) both proceed through tight inner transition states followed by loose outer transition states. The present "dual" transition state model couples variational phase space theory treatments of the outer transition states with ab initio based fixed harmonic vibrator treatments of the inner transition states to obtain effective numbers of states for the two transition states acting in series. It is found that, at least near room temperature, such a dual transition state model is generally required for the proper description of each of the dissociations. Only at quite high temperatures, i.e., above 2000 K for (R1) and 600 K for (R2), does a single fixed inner transition state provide an adequate description. Similarly, only at quite low temperatures (below 100 and 10 K for (R1) and (R2), respectively) does a single outer transition state provide an adequate description. Pressure dependent rate constants are obtained from solutions to the multichannel master equation. These calculations confirm that dissociation channel (R2) is negligible under conditions relevant to the thermal chemical vapor deposition (CVD) processes. Rate constants for the chemical activation reactions, SiH2 + SiH4 --> Si2H6 (R-1) and SiH2 + SiH4 --> H3SiSiH + H2 (R3), are also evaluated within the dual transition state model. It is found that reaction R3 is the dominant channel for low pressures and high temperatures, i.e., below 100 Torr for temperatures above 1100 K.

Journal Article↗

PubMed2003

Turbulence detection in a stenosed artery bifurcation by numerical simulation of pulsatile blood flow using the low-Reynolds number turbulence model.

The pulsatile blood flow in a partially blocked artery is significantly altered as the flow regime changes through the cardiac cycle. This paper reports on the application of a low-Reynolds turbulence model for computation of physiological pulsatile flow in a healthy and stenosed carotid artery bifurcation. The human carotid artery was chosen since it has received much attention because atherosclerotic lesions are frequently observed. The Wilcox low-Re k-omega turbulence model was used for the simulation since it has proven to be more accurate in describing transition from laminar to turbulent flow. Using the FIDAP finite element code a validation showed very good agreement between experimental and numerical results for a steady laminar to turbulent flow transition as reported in a previous publication by the same authors. Since no experimental or numerical results were available in the literature for a pulsatile and turbulent flow regime, a comparison between laminar and low-Re turbulent calculations was made to further validate the turbulence model. The results of this study showed a very good agreement for velocity profiles and wall shear stress values for this imposed pulsatile laminar flow regime. To explore further the medical aspect, the calculations showed that even in a healthy or non-stenosed artery, small instabilities could be found at least for a portion of the pulse cycle and in different sections. The 40% and 55% diameter reduction stenoses did not significantly change the turbulence characteristics. Further results showed that the presence of 75% stenoses changed the flow properties from laminar to turbulent flow for a good portion of the cardiac pulse. A full 3D simulation with this low-Re-turbulence model, coupled with Doppler ultrasound, can play a significant role in assessing the degree of stenosis for cardiac patients with mild conditions.

Blood Flow Velocity↗

PubMedDate not supplied

Transport of three herbicides in ground water at Twin Lake test site, Chalk River, Ontario, Canada.

A field tracer test performed under natural flow conditions at the Twin Lake test site, Chalk River Laboratories of the Atomic Energy of Canada Ltd. in Chalk River, Ontario, Canada, using tritium and three herbicides (Chlortoluron, Terbuthylazine, and Pendimethalin) was interpreted using the dispersion equation with a combined reaction model. The reaction model couples an instantaneous equilibrium reaction governed by a linear adsorption isotherm with a reversible or irreversible kinetic reaction of the first order, and decay. An improved interpretation method consists of a simultaneous fitting of theoretical concentration and mass-recovery curves to the experimental data, which leads to a more reliable determining of reaction models and improves the accuracy of fitting. Tritium served as the reference tracer to determine the flow velocity, dispersivity, and the recovery of the herbicides. Chlortoluron was slightly delayed by equilibrium exchange with strongly reduced concentration due to an irreversible kinetic reaction and/or decay. Terbuthilazine was slightly delayed by equilibrium exchange, with strongly reduced concentration due to a reversible kinetic reaction with some influence of decay. A strong equilibrium reaction and a strong reversible kinetic reaction without degradation governed the transport of Pendimethalin, reducing considerably its concentration. The results obtained show that simulations based only on Kd and decay constant, especially if these parameters are found in the laboratory, may considerably differ from those performed with reaction parameters determined in properly performed field tests. The dominant reaction types, and the values of parameters found in the study, supply useful information on the transport of the investigated herbicides in sandy aquifers under natural flow conditions.

Aniline Compounds↗

PubMed2006

Prediction of signal peptides using bio-basis function neural networks and decision trees.

Signal peptide identification is of immense importance in drug design. Accurate identification of signal peptides is the first critical step to be able to change the direction of the targeting proteins and use the designed drug to target a specific organelle to correct a defect. Because experimental identification is the most accurate method, but is expensive and time-consuming, an efficient and affordable automated system is of great interest. In this article, we propose using an adapted neural network, called a bio-basis function neural network, and decision trees for predicting signal peptides. The bio-basis function neural network model and decision trees achieved 97.16% and 97.63% accuracy respectively, demonstrating that the methods work well for the prediction of signal peptides. Moreover, decision trees revealed that position P(1'), which is important in forming signal peptides, most commonly comprises either leucine or alanine. This concurs with the (P(3)-P(1)-P(1')) coupling model.

Algorithms↗

PubMed2004

Experimental validation of a tractable numerical model for focused ultrasound heating in flow-through tissue phantoms.

Heating from high intensity focused ultrasound (HIFU) can be used to control bleeding, both from individual blood vessels as well as from gross damage to the capillary bed. The presence of vascularity can limit one's ability to elevate the temperature owing to convective heat transport. In an effort to better understand the heating process in tissues with vascular structure we have developed a numerical simulation that couples models for ultrasound propagation, acoustic streaming, ultrasound heating and blood cooling in a Newtonian viscous medium. The 3-D simulation allows for the study of complicated biological structures and insonation geometries. We have also undertaken a series of in vitro experiments employing non-uniform flow-through tissue phantoms and designed to provide verification of the model predictions. We show that blood flow of 2 cm/s (6.4 ml/min through a 2.6 mm 'vessel') can reduce peak temperature in a vessel wall by 25%. We also show that HIFU intensities of 6.5 x 10(5) W/m2 can induce acoustic streaming with peak velocities up to 5 cm/s and this can reduce heating near a vessel wall by more than 10%. These results demonstrate that convective cooling is important in HIFU and can be accounted for within simulation models.

Algorithms↗

PubMed2005

The effect of residual Ca2+ on the stochastic gating of Ca2+-regulated Ca2+ channel models.

Single-channel models of intracellular Ca(2+) channels such as the inositol 1,4,5-trisphosphate receptor and ryanodine receptor often assume that Ca(2+)-dependent transitions are mediated by a constant background [Ca(2+)] as opposed to a dynamic [Ca(2+)] representing the formation and collapse of a localized Ca(2+) domain. This assumption neglects the fact that Ca(2+) released by open intracellular Ca(2+) channels may influence subsequent gating through the processes of Ca(2+)-activation or -inactivation. We study the effect of such "residual Ca(2+)" from previous channel opening on the stochastic gating of minimal and realistic single-channel models coupled to a restricted cytoplasmic compartment. Using Monte Carlo simulation as well as analytical and numerical solution of a system of advection-reaction equations for the probability density of the domain [Ca(2+)] conditioned on the state of the channel, we determine how the steady-state open probability (p(open)) of single-channel models of Ca(2+)-regulated Ca(2+) channels depends on the time constant for Ca(2+) domain formation and collapse. As expected, p(open) for a minimal model including Ca(2+) activation increases as the domain time constant becomes large compared to the open and closed dwell times of the channel, that is, on average the channel is activated by residual Ca(2+) from previous openings. Interestingly, p(open) for a channel model that is inactivated by Ca(2+) also increases as a function of the domain time constant when the maximum domain [Ca(2+)] is fixed, because slow formation of the Ca(2+) domain attenuates Ca(2+)-mediated inactivation. Conversely, when the source amplitude of the channel is fixed, increasing the domain time constant leads to elevated domain [Ca(2+)] and decreased open probability. Consistent with these observations, a realistic De Young-Keizer-like IP(3)R model responds to residual Ca(2+) with a steady-state open probability that is a monotonic function of the domain time constant, though minimal models that include both Ca(2+)-activation and -inactivation show more complex behavior. We show how the probability density approach described here can be generalized for arbitrarily complex channel models and for any value of the domain time constant. In addition, we present a comparatively simple numerical procedure for estimating p(open) for models of Ca(2+)-regulated Ca(2+) channels in the limit of a very fast or very slow Ca(2+) domain. When the ordinary differential equation for the [Ca(2+)] in a restricted cytoplasmic compartment is replaced by a partial differential equation for the buffered diffusion of intracellular Ca(2+) in a homogeneous isotropic cytosol, we find the dependence of p(open) on the buffer time constant is qualitatively similar to the above-mentioned results.

Animals↗

PubMed2004

Frame transformation relations for fluxional symmetric rotor dimers.

The theory of frame transformation relation connecting body oriented angular momentum states and lab weakly coupled momentum states have been extended from rotor-electron to rotor-dimer systems. Coupling schemes are analyzed for weak and strong cases of correlation between lab and two different rotor body frames. It is shown that the frame transformation relation is a purely quantum effect at low angular momentum but an approach to a classical limit for high J. Symmetry analysis of frame transformation is compared to eigensolutions of model coupling Hamiltonian.

Journal Article↗

PubMed1997

1H and (13)C NMR Studies of an Oxidized HiPIP.

1H-(13)C HETCOR NMR spectra have been recorded for the oxidized HiPIP I from Ectothiorhodospira halophila for which an extended (1)H assignment was available. The hyperfine shifts of the alpha and beta carbons of the coordinated cysteines, as well as those of their attached protons, have been discussed in terms of the current magnetic coupling models and of the mechanisms of spin density delocalization. Through HSQC spectra preceded by a proton 180 degrees pulse, the nonselective T(1) values of the protons have been accurately obtained. It is shown how the nuclear T(1) values can be used as constraints, together with NOEs, for solution structure determination even when the present magnetic coupling scheme occurs. The oxidized cluster is shown to have an effective relaxation time much shorter than that in the reduced state.

Journal Article↗

PubMed1998

Isothermal and non-isothermal polymerization of a new bone cement.

A new bone cement based on poly(ethylmethacrylate) (PEMA), hydroxyapatite powder (HA) and n-butylmethacrylate monomer (n-BMA) has been studied using isothermal and non-isothermal polymerization. Methacrylate monomers are highly reactive and release a considerable amount of heat during polymerization. A quantitative understanding of the methacrylate polymerization is necessary because the thermal history of the polymerization has considerable influence on the final properties of a bone cement. In the first part, polymerization kinetics are analysed by means of differential scanning calorimetry (DSC). DSC data are used to evaluate a phenomenological model describing the cure kinetics of this new bone cement. In the second part, a kinetic model coupled with the energy balance is used to obtain temperature and degree of conversion profiles in the bone-cement-prosthesis system, under non-isothermal conditions, as function of initial temperature and thickness of the cement. Material properties, boundary and initial conditions and the kinetic behaviour are the input data for the numerically solved heat-transfer model. The temperature at the bone/cement interface, can be considered as a weak point, often responsible for total joint replacement failure. For this particular bone cement exhibiting a low exotherm and low glass transition temperature, the interfacial temperature is lower than the threshold level for thermal tissue damage (50 degrees C). The conversion occurs almost completely, avoiding problems with unreacted monomers that can be released by the cement, giving rise to tissue damage.

Journal Article↗

PubMed1994

Managing change in an interdisciplinary inpatient unit: an action research approach.

This case study describes the application of the action research model to managing change in an interdisciplinary inpatient unit. Special attention is given to potential resistances to the process and methods for addressing these. A needs assessment instrument assessing 40 program domains produced the initial data from which direction for change was derived. Active participation by all members in each phase of the process was found to contribute positively to the development and implementation of change efforts. Results indicate that the use of the model coupled with participation by the client group promoted positive staff morale, open communication, lower staff turnover, team problem solving, and improved goal attainment.

Data Collection↗

PubMed2005

Use of stochastic models to assess the effect of environmental factors on microbial growth.

We present a novel application of a stochastic ecological model to the study and analysis of microbial growth dynamics as influenced by environmental conditions in an extensive experimental data set. The model proved to be useful in bridging the gap between theoretical ideas in ecology and an applied problem in microbiology. The data consisted of recorded growth curves of Escherichia coli grown in triplicate in a base medium with all 32 possible combinations of five supplements: glucose, NH(4)Cl, HCl, EDTA, and NaCl. The potential complexity of 2(5) experimental treatments and their effects was reduced to 2(2) as just the metal chelator EDTA, the presumed osmotic pressure imposed by NaCl, and the interaction between these two factors were enough to explain the variability seen in the data. The statistical analysis showed that the positive and negative effects of the five chemical supplements and their combinations were directly translated into an increase or decrease in time required to attain stationary phase and the population size at which the stationary phase started. The stochastic ecological model proved to be useful, as it effectively explained and summarized the uncertainty seen in the recorded growth curves. Our findings have broad implications for both basic and applied research and illustrate how stochastic mathematical modeling coupled with rigorous statistical methods can be of great assistance in understanding basic processes in microbial ecology.

Edetic Acid↗

PubMed1998

Comparison between the polymerization behavior of a new bone cement and a commercial one: modeling and in vitro analysis.

The polymerization behavior of a new bone cement based on poly(ethylmethacrylate), hydroxyapatite powder and n-butylmethacrylate monomer and a commercial cement have been studied. Polymerization kinetics were analyzed by means of differential scanning calorimetry (DSC). DSC data have been used to evaluate a phenomenological model describing the cure kinetics of this new bone cement. The kinetic model coupled with the energy balance was then used to obtain temperature and degree of conversion profiles in the bone-cement-prosthesis system, under non-isothermal conditions, as function of initial temperature and thickness of the cement. Material properties, boundary and initial conditions and the kinetic behavior were the input data for the numerically solved heat-transfer model. The modeling results have been compared with in vitro results.

Journal Article↗