The logic of kinetic regulation in the thioredoxin system

<p>Abstract</p> <p>Background</p> <p>The thioredoxin system consisting of NADP(H), thioredoxin reductase and thioredoxin provides reducing equivalents to a large and diverse array of cellular processes. Despite a great deal of information on the kinetics of individual thioredoxin-dependent reactions, the kinetic regulation of this system as an integrated whole is not known. We address this by using kinetic modeling to identify and describe kinetic behavioral motifs found within the system.</p> <p>Results</p> <p>Analysis of a realistic computational model of the <it>Escherichia coli </it>thioredoxin system revealed several modes of kinetic regulation in the system. In keeping with published findings, the model showed that thioredoxin-dependent reactions were adaptable (i.e. changes to the thioredoxin system affected the kinetic profiles of these reactions). Further and in contrast to other systems-level descriptions, analysis of the model showed that apparently unrelated thioredoxin oxidation reactions can affect each other via their combined effects on the thioredoxin redox cycle. However, the scale of these effects depended on the kinetics of the individual thioredoxin oxidation reactions with some reactions more sensitive to changes in the thioredoxin cycle and others, such as the Tpx-dependent reduction of hydrogen peroxide, less sensitive to these changes. The coupling of the thioredoxin and Tpx redox cycles also allowed for ultrasensitive changes in the thioredoxin concentration in response to changes in the thioredoxin reductase concentration. We were able to describe the kinetic mechanisms underlying these behaviors precisely with analytical solutions and core models.</p> <p>Conclusions</p> <p>Using kinetic modeling we have revealed the logic that underlies the functional organization and kinetic behavior of the thioredoxin system. The thioredoxin redox cycle and associated reactions allows for a system that is adaptable, interconnected and able to display differential sensitivities to changes in this redox cycle. This work provides a theoretical, systems-biological basis for an experimental analysis of the thioredoxin system and its associated reactions.</p

Simulation study of phononic crystal structures

Thermoelectric materials are important in today’s society with a variety of applications. The material properties that determinate the efficiency of a thermoelectric device are mostly constants. In order to develop more efficient thermoelectric devices new materials and solutions need to be made. Minimizing the thermal conductivity in thermoelectric materials is of great interest to make them more effective.   One effective way of lowering the thermal conductivity is to introduce holes in the lattice and create a phononic crystal. The main focus of this master thesis has been on how to place these holes and to optimize the geometry to minimize thermal conductivity. The method used in this report is based solely on simulations, which were done using Comsol Multiphysics 5.2a. The results are compared to already published results. Different geometries are tested to see how it affects the thermal conductivity and to optimize the phononic crystal. The Maxwell-Eucken model is also used to see how porosity affects the thermal conductivity and to analyze what the lowering in thermal conductivity depends on.   The result showed a substantial reduction in thermal conductivity when creating a phononic crystal compared to bulk silicon. The simulated reduction compared to bulk silicon is up to 98.5% when introducing holes in the lattice, while Maxwell-Eucken only predicted a 74% reduction due to porosity.   The conclusion is that by creating holes in a periodical pattern, phonon dispersion will occur, which lower the thermal conduction significantly

Quartzene – A promising thermal insulator : Studies of thermal conductivity’s dependence of density and compression of Quartzene® in the form of powder.

The purpose of this project was to study Svenska Aerogel AB’s product Quartzene®, and develop its capacity as a thermal insulator. Quartzene® is a silica based mesoporous material developed by Svenska Aerogel AB, with properties similar to aerogels produced by the sol-gel process. In this report, the correlation between pore structure and thermal conductivity in the material has been studied using techniques, such as scanning electron microscopy, focused ion beam, finite element simulations and transient plane source. Its properties are interesting because of the expanding market of insulated vacuum panels; in which Svenska Aerogel AB wish to expand to. It was found that the pore sizes of M21-BU increased after compression, and the pore sizes of M4-0-2 decreased. The pore sizes of M21-BU became so large that the Knudsen effect is no longer of interest, and that could explain the different behaviors in thermal conductivity

Quartzene – A promising thermal insulator : Studies of thermal conductivity’s dependence of density and compression of Quartzene® in the form of powder.

The purpose of this project was to study Svenska Aerogel AB’s product Quartzene®, and develop its capacity as a thermal insulator. Quartzene® is a silica based mesoporous material developed by Svenska Aerogel AB, with properties similar to aerogels produced by the sol-gel process. In this report, the correlation between pore structure and thermal conductivity in the material has been studied using techniques, such as scanning electron microscopy, focused ion beam, finite element simulations and transient plane source. Its properties are interesting because of the expanding market of insulated vacuum panels; in which Svenska Aerogel AB wish to expand to. It was found that the pore sizes of M21-BU increased after compression, and the pore sizes of M4-0-2 decreased. The pore sizes of M21-BU became so large that the Knudsen effect is no longer of interest, and that could explain the different behaviors in thermal conductivity

Quartzene – A promising thermal insulator : Studies of thermal conductivity’s dependence of density and compression of Quartzene® in the form of powder.

The purpose of this project was to study Svenska Aerogel AB’s product Quartzene®, and develop its capacity as a thermal insulator. Quartzene® is a silica based mesoporous material developed by Svenska Aerogel AB, with properties similar to aerogels produced by the sol-gel process. In this report, the correlation between pore structure and thermal conductivity in the material has been studied using techniques, such as scanning electron microscopy, focused ion beam, finite element simulations and transient plane source. Its properties are interesting because of the expanding market of insulated vacuum panels; in which Svenska Aerogel AB wish to expand to. It was found that the pore sizes of M21-BU increased after compression, and the pore sizes of M4-0-2 decreased. The pore sizes of M21-BU became so large that the Knudsen effect is no longer of interest, and that could explain the different behaviors in thermal conductivity

Thin film metal sensors in fusion bonded glass chips for high-pressure microfluidics

High-pressure microfluidics offers fast analyses of thermodynamic parameters for compressed process solvents. However, microfluidic platforms handling highly compressible supercritical CO2 are difficult to control, and on-chip sensing would offer added control of the devices. Therefore, there is a need to integrate sensors into highly pressure tolerant glass chips. In this paper, thin film Pt sensors were embedded in shallow etched trenches in a glass wafer that was bonded with another glass wafer having microfluidic channels. The devices having sensors integrated into the flow channels sustained pressures up to 220 bar, typical for the operation of supercritical CO2. No leakage from the devices could be found. Integrated temperature sensors were capable of measuring local decompression cooling effects and integrated calorimetric sensors measured flow velocities over the range 0.5-13.8 mm/s. By this, a better control of high-pressure microfluidic platforms has been achieved.Part financed through Swedish Agency for the Innovation System, Vinnova, through the Centre for Natural Disaster Science (CNDS)</p

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

non present