Numerical model of solid phase transformations governed by nucleation and growth: microstructure development during isothermal crystallization

A simple numerical model which calculates the kinetics of crystallization involving randomly distributed nucleation and isotropic growth is presented. The model can be applied to different thermal histories and no restrictions are imposed on the time and the temperature dependences of the nucleation and growth rates. We also develop an algorithm which evaluates the corresponding emerging grain-size distribution. The algorithm is easy to implement and particularly flexible, making it possible to simulate several experimental conditions. Its simplicity and minimal computer requirements allow high accuracy for two- and three-dimensional growth simulations. The algorithm is applied to explore the grain morphology development during isothermal treatments for several nucleation regimes. In particular, thermal nucleation, preexisting nuclei, and the combination of both nucleation mechanisms are analyzed. For the first two cases, the universal grain-size distribution is obtained. The high accuracy of the model is stated from its comparison to analytical predictions. Finally, the validity of the Kolmogorov-Johnson-Mehl-Avrami model SSSR, is verified for all the cases studied

The effect of thermal conductivity of RIM moulds in kinetics cure

Reaction Injection Moulding (RIM) is a moulding technology used for the production of large size and complex plastic parts. The RIM process is characterized essentially by the injection of a highly reactive chemical system (usually polyurethane) and fast cure, in a mould properly closed and thermally controlled. Several studies show that rapid manufacturing moulds obtained in epoxy resins for Thermoplastic Injection Moulding (TIM) affect the moulding process and the final properties of parts. The cycle time and mechanical properties of final parts are reduced, due to a low thermal conductivity of epoxy materials. In contrast, the low conductivity of materials usually applied for the rapid manufacturing of RIM moulds, increase the mechanical properties of final injected parts and reduce the cycle time. This study shows the effect of the rapid manufacturing moulds material during the RIM process. Several materials have been tested for rapid manufacturing of RIM moulds and the analysis of both, temperature profile of moulded parts during injection and the cure data experimentally obtained in a mixing and reaction cell, allow to determine and model the real effect of the mould material on the RIM process.

Uptake kinetics of metals by the earthworm Eisenia fetida exposed to field-contaminated soils

It is well known that earthworms can accumulate metals. However, most accumulation studies focus on Cd-, Cu-, Pb- or Zn-amended soils, additionally few studies consider accumulation kinetics. Here we model the accumulation kinetics of 18 elements by Eisenia fetida, exposed to 8 metal-contaminated and 2 uncontaminated soils. Tissue metal concentration was determined after 3, 7,14, 21, 28 and 42 days. Metal elimination rate was important in determining time to reach steady-state tissue metal concentration. Uptake flux to elimination rate ratios showed less variation and lower values for essential than for non-essential metals. In theory kinetic rate constants are dependent only on species and metal. Therefore it should be possible to predict steady-state tissue metal concentrations on the basis of very few measurements using the rate constants. However, our experiments show that it is difficult to extrapolate the accumulation kinetic constants derived using one soil to another. (C) 2009 Elsevier Ltd. All rights reserved.

The Wheal Jane wetlands model for bioremediation of acid mine drainage

Acid mine drainage (AMD) is a widespread environmental problem associated with both working and abandoned mining operations. As part of an overall strategy to determine a long-term treatment option for AMD, a pilot passive treatment plant was constructed in 1994 at Wheal Jane Mine in Cornwall, UK. The plant consists of three separate systems, each containing aerobic reed beds, anaerobic cell and rock filters, and represents the largest European experimental facility of its kind. The systems only differ by the type of pretreatment utilised to increase the pH of the influent minewater (pH <4): lime dosed (LD), anoxic limestone drain (ALD) and lime free (LF), which receives no form of pretreatment. Historical data (1994-1997) indicate median Fe reduction between 55% and 92%, sulphate removal in the range of 3-38% and removal of target metals (cadmium, copper and zinc) below detection limits, depending on pretreatment and flow rates through the system. A new model to simulate the processes and dynamics of the wetlands systems is described, as well as the application of the model to experimental data collected at the pilot plant. The model is process based, and utilises reaction kinetic approaches based on experimental microbial techniques rather than an equilibrium approach to metal precipitation. The model is dynamic and utilises numerical integration routines to solve a set of differential equations that describe the behaviour of 20 variables over the 17 pilot plant cells on a daily basis. The model outputs at each cell boundary are evaluated and compared with the measured data, and the model is demonstrated to provide a good representation of the complex behaviour of the wetland system for a wide range of variables. (C) 2004 Elsevier B.V/ All rights reserved.

Cone model-based SEP event calculations for applications to multipoint observations

The problem of modeling solar energetic particle (SEP) events is important to both space weather research and forecasting, and yet it has seen relatively little progress. Most important SEP events are associated with coronal mass ejections (CMEs) that drive coronal and interplanetary shocks. These shocks can continuously produce accelerated particles from the ambient medium to well beyond 1 AU. This paper describes an effort to model real SEP events using a Center for Integrated Space weather Modeling (CISM) MHD solar wind simulation including a cone model of CMEs to initiate the related shocks. In addition to providing observation-inspired shock geometry and characteristics, this MHD simulation describes the time-dependent observer field line connections to the shock source. As a first approximation, we assume a shock jump-parameterized source strength and spectrum, and that scatter-free transport occurs outside of the shock source, thus emphasizing the role the shock evolution plays in determining the modeled SEP event profile. Three halo CME events on May 12, 1997, November 4, 1997 and December 13, 2006 are used to test the modeling approach. While challenges arise in the identification and characterization of the shocks in the MHD model results, this approach illustrates the importance to SEP event modeling of globally simulating the underlying heliospheric event. The results also suggest the potential utility of such a model for forcasting and for interpretation of separated multipoint measurements such as those expected from the STEREO mission.

A kinematically distorted flux rope model for magnetic clouds

Constant-α force-free magnetic flux rope models have proven to be a valuable first step toward understanding the global context of in situ observations of magnetic clouds. However, cylindrical symmetry is necessarily assumed when using such models, and it is apparent from both observations and modeling that magnetic clouds have highly noncircular cross sections. A number of approaches have been adopted to relax the circular cross section approximation: frequently, the cross-sectional shape is allowed to take an arbitrarily chosen shape (usually elliptical), increasing the number of free parameters that are fit between data and model. While a better “fit” may be achieved in terms of reducing the mean square error between the model and observed magnetic field time series, it is not always clear that this translates to a more accurate reconstruction of the global structure of the magnetic cloud. We develop a new, noncircular cross section flux rope model that is constrained by observations of CMEs/ICMEs and knowledge of the physical processes acting on the magnetic cloud: The magnetic cloud is assumed to initially take the form of a force-free flux rope in the low corona but to be subsequently deformed by a combination of axis-centered self-expansion and heliocentric radial expansion. The resulting analytical solution is validated by fitting to artificial time series produced by numerical MHD simulations of magnetic clouds and shown to accurately reproduce the global structure.

Use of a crop model ensemble to quantify CO2 stimulation of water-stressed and well-watered crops

Increased atmospheric concentrations of carbon dioxide (CO2) will benefit the yield of most crops. Two free air CO2 enrichment (FACE) meta-analyses have shown increases in yield of between 0 and 73% for C3 crops. Despite this large range, few crop modelling studies quantify the uncertainty inherent in the parameterisation of crop growth and development. We present a novel perturbed-parameter method of crop model simulation, which uses some constraints from observations, that does this. The model used is the groundnut (i.e. peanut; Arachis hypogaea L.) version of the general large-area model for annual crops (GLAM). The conclusions are of relevance to C3 crops in general. The increases in yield simulated by GLAM for doubled CO2 were between 16 and 62%. The difference in mean percentage increase between well-watered and water-stressed simulations was 6.8. These results were compared to FACE and controlled environment studies, and to sensitivity tests on two other crop models of differing levels of complexity: CROPGRO, and the groundnut model of Hammer et al. [Hammer, G.L., Sinclair, T.R., Boote, K.J., Wright, G.C., Meinke, H., Bell, M.J., 1995. A peanut simulation model. I. Model development and testing. Agron. J. 87, 1085-1093]. The relationship between CO2 and water stress in the experiments and in the models was examined. From a physiological perspective, water-stressed crops are expected to show greater CO2 stimulation than well-watered crops. This expectation has been cited in literature. However, this result is not seen consistently in either the FACE studies or in the crop models. In contrast, leaf-level models of assimilation do consistently show this result. An analysis of the evidence from these models and from the data suggests that scale (canopy versus leaf), model calibration, and model complexity are factors in determining the sign and magnitude of the interaction between CO2 and water stress. We conclude from our study that the statement that 'water-stressed crops show greater CO2 stimulation than well-watered crops' cannot be held to be universally true. We also conclude, preliminarily, that the relationship between water stress and assimilation varies with scale. Accordingly, we provide some suggestions on how studies of a similar nature, using crop models of a range of complexity, could contribute further to understanding the roles of model calibration, model complexity and scale. (C) 2008 Elsevier B.V. All rights reserved.

A continuum receptor model of hepatic lipoprotein metabolism

A mathematical model describing the uptake of low density lipoprotein (LDL) and very low density lipoprotein (VLDL) particles by a single hepatocyte cell is formulated and solved. The model includes a description of the dynamic change in receptor density on the surface of the cell due to the binding and dissociation of the lipoprotein particles, the subsequent internalisation of bound particles, receptors and unbound receptors, the recycling of receptors to the cell surface, cholesterol dependent de novo receptor formation by the cell and the effect that particle uptake has on the cell's overall cholesterol content. The effect that blocking access to LDL receptors by VLDL, or internalisation of VLDL particles containing different amounts of apolipoprotein E (we will refer to these particles as VLDL-2 and VLDL-3) has on LDL uptake is explored. By comparison with experimental data we find that measures of cell cholesterol content are important in differentiating between the mechanisms by which VLDL is thought to inhibit LDL uptake. We extend our work to show that in the presence of both types of VLDL particle (VLDL-2 and VLDL-3), measuring relative LDL uptake does not allow differentiation between the results of blocking and internalisation of each VLDL particle to be made. Instead by considering the intracellular cholesterol content it is found that internalisation of VLDL-2 and VLDL-3 leads to the highest intracellular cholesterol concentration. A sensitivity analysis of the model reveals that binding, unbinding and internalisation rates, the fraction of receptors recycled and the rate at which the cholesterol dependent free receptors are created by the cell have important implications for the overall uptake dynamics of either VLDL or LDL particles and subsequent intracellular cholesterol concentration. (C) 2008 Elsevier Ltd. All rights reserved.

Efficient and accurate experimental design for enzyme kinetics: Bayesian studies reveal a systematic approach

In areas such as drug development, clinical diagnosis and biotechnology research, acquiring details about the kinetic parameters of enzymes is crucial. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. We demonstrate that a Bayesian approach (the use of prior knowledge) can produce major gains quantifiable in terms of information, productivity and accuracy of each experiment. Developing the use of Bayesian Utility functions, we have used a systematic method to identify the optimum experimental designs for a number of kinetic model data sets. This has enabled the identification of trends between kinetic model types, sets of design rules and the key conclusion that such designs should be based on some prior knowledge of K-M and/or the kinetic model. We suggest an optimal and iterative method for selecting features of the design such as the substrate range, number of measurements and choice of intermediate points. The final design collects data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. (C) 2003 Elsevier Science B.V. All rights reserved.

A pressure-jump time-resolved x-ray diffraction study of cubic-cubic transition kinetics in monoolein

In the past two decades, the geometric pathways involved in the transformations between inverse bicontinuous cubic phases in amphiphilic systems have been extensively theoretically modeled. However, little experimental data exists on the cubic-cubic transformation in pure lipid systems. We have used pressure-jump time-resolved X-ray diffraction to investigate the transition between the gyroid Q(II)(G) and double-diamond Q(II)(D) phases in mixtures of 1-monoolein in 30 wt% water. We find for this system that the cubic-cubic transition occurs without any detectable intermediate structures. In addition, we have determined the kinetics of the transition, in both the forward and reverse directions, as a function of pressure-jump amplitude, temperature, and water content. A recently developed model allows (at least in principle) the calculation of the activation energy for lipid phase transitions from such data. The analysis is applicable only if kinetic reproducibility is achieved, at least within one sample, and achievement of such kinetic reproducibility is shown here, by carrying out prolonged pressure-cycling. The rate of transformation shows clear and consistent trends with pressure-jump amplitude, temperature, and water content, all of which are shown to be in agreement with the effect of the shift in the position of the cubic-cubic phase boundary following a change in the thermodynamic parameters.

A DFT study of free radicals formed from artemisinin and related compounds

Ab initio calculations using density functional theory have shown that the reactions that occur between artemisinin, 1, a cyclic trioxane active against malaria, and some metal ions and complexes lead to a series of radicals which are probably responsible for its therapeutic activity. In particular it has been shown that the interaction of Fe(H) with artemisinin causes the O-O bond to be broken as indeed does Fe(III) and Cu(I), while Zn(II) does not. Calculations were carried out with Fe(II) in several different forms including the bare ion, [Fe(H2O)(5)](2+) and [FeP(Im)] (P, porphyrin; Im, imadazole) and similar results were obtained. The resulting oxygen-based radicals are readily converted to more stable carbon-based radicals and/or. stable products. Similar radicals and products are also formed from two simple model trioxanes 2 and 3 that show little or no therapeutic action against malaria although some subtle differences were obtained. This suggests that the scaffold surrounding the pharmacophore may be involved in molecular recognition events allowing efficient uptake of this trioxane warhead into the parasite. (C) 2004 Elsevier B.V. All rights reserved.

A theoretical adaptive model of thermal comfort – Adaptive Predicted Mean Vote (aPMV)

This paper presents in detail a theoretical adaptive model of thermal comfort based on the “Black Box” theory, taking into account factors such as culture, climate, social, psychological and behavioural adaptations, which have an impact on the senses used to detect thermal comfort. The model is called the Adaptive Predicted Mean Vote (aPMV) model. The aPMV model explains, by applying the cybernetics concept, the phenomena that the Predicted Mean Vote (PMV) is greater than the Actual Mean Vote (AMV) in free-running buildings, which has been revealed by many researchers in field studies. An Adaptive coefficient (λ) representing the adaptive factors that affect the sense of thermal comfort has been proposed. The empirical coefficients in warm and cool conditions for the Chongqing area in China have been derived by applying the least square method to the monitored onsite environmental data and the thermal comfort survey results.

Effect of fecal water on an in vitro model of colonic mucosal barrier function

Fecal water (FW) has been shown to exert, in cultured cells, cytotoxic and genotoxic effects that have implications for colorectal cancer (CRC) risk. We have investigated a further biological activity of FW, namely, the ability to affect gap junctions in CACO2 cell monolayers as an index of mucosal barrier function, which is known to be disrupted in cancer. FW samples fi-om healthy, free-living, European subjects that were divided into two broad age groups, adult (40 +/- 9.7 yr; n = 53) and elderly (76 +/- 7.5 yr; n = 55) were tested for effects on gap junction using the transepithelial resistance (TER) assay. Overall, treatment of CACO2 cells with FW samples fi-om adults increased TER (+ 4 %), whereas FW from elderly subjects decreased TER (-5%); the difference between the two groups was significant (P < 0.05). We also measured several components of FW potentially associated with modulation of TER, namely, short-chain fatty acid (SCFA) and ammonia. SCFAs (propionic, acetic, and n-butyric) were significantly lower in the elderly population (-30%, -35%, and -21%, respectively, all P pound 0.01). We consider that FW modulation of in vitro epithelial barrier function is a potentially useful noninvasive biomarker, but it requires further validation to establish its relationship to CRC risk.

Measurement of acrylamide and its precursors in potato, wheat, and rye model systems

The relationship between acrylamide and its precursors, namely, free asparagine and reducing sugars, was studied in cakes made from potato flake, wholemeal wheat, and wholemeal rye, cooked at 180 degreesC, from 5 to 60 min. Between 5 and 20 min, major losses of asparagine, water, and total reducing sugars were accompanied by large increases in acrylamide, which maximized in all three products between 25 and 30 min, followed by a slow linear reduction. Acrylamide formation did not occur to a large degree until the moisture contents of the cakes fell below 5%. Linear relationships were observed for acrylamide formation with the residual levels of asparagine and reducing sugars for all three food materials.

Modelling the uptake and growth kinetics of Penicillium glabrum in a tannic acid-containing solid-state fermentation for tannase production

A mathematical growth model for the batch solid-state fermentation process for fungal tannase production was developed and tested experimentally. The unstructured model describes the uptake and growth kinetics of Penicillium glabrum in an impregnated polyurethane foam substrate system. In general, good agreement between the experimental data and model simulations was obtained. Biomass, tannase and spore production are described by logistic kinetics with a time delay between biomass production and tannase and spore formation. Possible induction mechanisms for the latter are proposed. Hydrolysis of tannic acid, the main carbon source in the substrate system, is reasonably well described with Michaelis-Menten kinetics with time-varying enzyme concentration but a more complex reaction mechanism is suspected. The metabolism of gallic acid, a tannase-hydrolysis product of tannic acid, was shown to be growth limiting during the main growth phase. (c) 2004 Elsevier Ltd. All rights reserved.