Construction and analysis of a modular model of caspase activation in apoptosis

<p>Abstract</p> <p>Background</p> <p>A key physiological mechanism employed by multicellular organisms is apoptosis, or programmed cell death. Apoptosis is triggered by the activation of caspases in response to both extracellular (extrinsic) and intracellular (intrinsic) signals. The extrinsic and intrinsic pathways are characterized by the formation of the death-inducing signaling complex (DISC) and the apoptosome, respectively; both the DISC and the apoptosome are oligomers with complex formation dynamics. Additionally, the extrinsic and intrinsic pathways are coupled through the mitochondrial apoptosis-induced channel via the Bcl-2 family of proteins.</p> <p>Results</p> <p>A model of caspase activation is constructed and analyzed. The apoptosis signaling network is simplified through modularization methodologies and equilibrium abstractions for three functional modules. The mathematical model is composed of a system of ordinary differential equations which is numerically solved. Multiple linear regression analysis investigates the role of each module and reduced models are constructed to identify key contributions of the extrinsic and intrinsic pathways in triggering apoptosis for different cell lines.</p> <p>Conclusion</p> <p>Through linear regression techniques, we identified the feedbacks, dissociation of complexes, and negative regulators as the key components in apoptosis. The analysis and reduced models for our model formulation reveal that the chosen cell lines predominately exhibit strong extrinsic caspase, typical of type I cell, behavior. Furthermore, under the simplified model framework, the selected cells lines exhibit different modes by which caspase activation may occur. Finally the proposed modularized model of apoptosis may generalize behavior for additional cells and tissues, specifically identifying and predicting components responsible for the transition from type I to type II cell behavior.</p

HORIZONTAL PRODUCER WELLS IN INSITU COMBUSTION (ISC) PROCESSES

A simple 3-D physical model has been developed to investigate the use of horizontal producer wells in in situ combustion processes. The semi-scaled 3-D model was a rectangular box with 40 cm by 40 cm by 10 cm dimensions. Dry in situ combustion experiments were conducted with three different well configurations: (1) a vertical injector and horizontal producer, (2) a vertical injector and two horizontal producers, and (3) injector and producer, both vertical. A matrix of 60 thermocouples was used to obtain temperature profile information, in the vertical and horizontal mid-planes. Most experiments were conducted with sandpacks containing a high saturation of heavy crude oil So(i) congruent-to 0.80. For each horizontal well configuration, the effect of oxygen flux and oxygen enrichment (21% and 3.5% oxygen) was investigated

Computation of instantaneous fuel consumption for the determination of combustion efficiency with special reference to coal briquette size

This study comprises of the computation of instantaneous fuel consumptions as a straight means for the interpretation of combustion-related characteristics of coal. The model relies on the determination of the extent of combustion by the calculated fuel combustion amounts at specific instants in order to examine the oxidation behavior and possible influences governed by any variable of interest. In this context, coal briquettes prepared by varying dimensions with and without a volume constraint were evaluated and instantaneous fuel consumptions corresponding to the determined instants were computed for comparison rather than introducing the model with a single experiment. Thus, the influences imposed by the enlargement of the briquette volume as well as by the variations in the compactness of briquettes on the effectiveness and efficiency of combustion reactions were dealt. The applicability of the model was checked by the trends revealed from the view of reaction kinetics in terms of activation energies. At the end of the study, the results deduced on the grounds of instantaneous fuel consumption values were seen to have been in full confirmation by those related to reaction kinetics, showing the applicability of the model in reflecting the particular cases during a combustion reaction

Combustion characteristics of coal briquettes. 1. Thermal features

In this study, the influence of some of the most important briquetting parameters on the combustion and thermal properties of coal briquettes were studied in detail. For this purpose, briquettes with various organic (molasses, sulfide liquor, carboxyl methyl cellulose, Peridur XC3, and Peridur C10) and inorganic agents (cement and bentonite) were prepared, to be combusted in a reaction cell that was complemented with a continuous gas analyzer unit. Furthermore, using the binding agent that provided the most favorable thermal features, the effect of the binder quantity, as well as the amount of water addition, was successfully determined with fractions of 5%, 10%, and 15%. The influence of the relevant variables on the thermal behavior of the coal briquettes were expressed and investigated, using the effluent gas analysis method, by considering (i) the changes in the amounts of evolved CO and CO2 and consumed O-2 gases, as a function of temperature and time; (ii) the O-2 peak temperatures and times; and (iii) the residue that remained at the end of each run. The binder type, as well as the amount of binder agent and water addition, had a significant effect on the thermal behavior and combustion efficiency of the coal briquettes

Retention of SO2 emission of coal combustion by using lime in briquetting

In this study, the effect of lime on control of SO2 emissions was investigated by briquetting of coal particles with various lime contents. The influence of the added lime was determined not only from the view of its contribution to environmental aspects but also in terms of effects on the thermal features and reaction kinetics of coal. The extent of improvement was determined by detailed sulfur analysis. Thermal qualification and reaction kinetics of the coal briquettes with varying lime contents were performed by evolved gas analysis and its complementing kinetic model based on Arrhenius principles. At the end of experiments, utilization of lime was seen to contribute considerably to desulfurization process. However, lime addition had an adverse effect both on the effectiveness of combustion and the liability of the coal briquettes to oxidize

Influence of coal briquette size on the combustion kinetics

In this study, the effects of one of the most important parameters in coal briquetting process, the briquette size, on the combustion behaviour of coal briquettes were determined from the view of combustion kinetics, i.e. their liability to ignite and combust. Effect of size on the combustion kinetics was treated by two different approaches. The first one consists of combustion kinetics experiments with briquettes of increasing sizes, thus of expanding volumes. In the second phase, briquette dimensions were alternated by keeping the briquette volume fixed. The influences of the concerned parameters were investigated through effluent gas analysis method and interpreted by an Arrhenius kinetic model relying on the changes in the amounts of evolved carbon oxides and consumed 02 gas as a function of temperature and time at three different pressure levels, 25, 50 and 75 psig. At the end of experiments, the activation energy and Arrhenius constant for each run were calculated and the distinct variations in the activation energy values showed that the liability of the coal briquettes to ignite and the efficiency and effectiveness of the combustion reaction were considerably affected both by the size enlargement and dimension variation on a constant volume basis

Combustion characteristics of coal briquettes. 2. Reaction kinetics

This study comprises the influence of the major briquetting parameters, such as binder type and amount of binder and water addition, on the combustion kinetics of the coal briquettes. In this manner, briquettes that have been prepared with different organic agents (molasses, carboxyl methyl cellulose, Peridur XC3, Peridur C10, and sulfide liquor) and inorganic agents (cement and bentonite) were combusted in a reaction cell assembly that operated in coordination with a continuous gas analyzer. Moreover, not only was the addition amount of the binder providing the most favorable reaction kinetics with the lowest activation energy varied, but the quantity of the water added was also varied with fractions of 5%, 10%, and 15% (by mass), to determine the possible effect of variations in binder and water quantities. The influence of the parameters of concern on the combustion kinetics of the coal briquettes was investigated using the effluent gas analysis method and was interpreted by an Arrhenius kinetic model that operated on the basis of the changes in the amounts of CO and CO2 that were evolved and the amount Of O-2 gases that were consumed, as a function of temperature and time at three different pressure levels: 25, 50, and 75 psig. At the end of experiments, the activation energy and Arrhenius constant for each run were calculated, and it was observed that the liability of the coal briquettes to ignite and the efficiency and effectiveness of the combustion reaction were considerably affected both by the binder type used and by the amount of binding agent and water addition

Beneficiation of Himmetoglu oil shale by flotation as a solid fuel substitute. Part 2. Process optimization by a statistical approach

The effects of the important flotation parameters on the cleaning process of the Himmetoglu oil shale from Turkey were investigated. The individual and multiple interaction effects of conditioning time, flotation time, pulp density, particle size, and frother dosage were determined using statistical analysis and factorial design of experiments. The influence of these parameters on the cleaning performance were evaluated in terms of ash yield, calorific value, and combustible recovery of the concentrates. XRD studies were also carried out to view the variations in the organic and inorganic content of the concentrates. Optimum parameter conditions, which provided the most effective cleaning, were determined by the applied model. It was seen that all parameters affected the flotation performance with varying degrees of significance. At optimum conditions, flotation performance increased and the ash yield of the concentrate decreased to 16.81% with 84.10% combustible recovery, and the calorific value increased to 5564.02 kcal/kg. XRD spectra revealed that the extent of mineral matter removal depended on the flotation performance, and the inorganic matter was effectively removed at optimum conditions