Microfluidic simulation of a colonial diatom chain reveals oscillatory movement

Diatoms are single-celled organisms with rigid parts in relative motion at the micro- and nanometer length scales. Some diatom species form colonies comprising many cells. In this manuscript, the results of a two-dimensional finite element computer model are presented. This model was established to discover if diatom colonies start to exhibit some kind of »pumping« behaviour when subjected to water flow. To analyze this computationally, a model diatom colony with continuously repeated units of ten cells is investigated in a fluid dynamic simulation. In this first simple model, undisturbed fluid flow is allowed for between the single cells. The cells do not move actively, and are solely moved by the water. The initial fluid velocity is assumed between 0.01 m s–1 and 1 m s–1. Acomputational result that does not change anymore with time is called a steady state solution. Such a steady state solution is reached in all calculations performed. The steady state for a chain where initially all diatoms are spaced equally (equidistant spacing) has forces that encourage the formation of cell pairs with less distance between one another. These forces result from the flow of the surrounding fluid. The steady state for a chain with initially paired cells shows the opposite effect: the pairs tend to un-pair and head for the equidistant state again. The mutual change in forces between these two states, i.e., paired and unpaired formations, suggests that these two steady states lead into each other: The computer simulations suggest that a diatom colony subjected to water flow exhibits some kind of oscillatory movement. Such movement might facilitate nutrient uptake of the diatom colony

Transient one-dimensional fluid flow in high pressure applications for diesel-fuel

Künftige Abgasnormen wie EURO V I, JPNLT, US10 und US T4 erfordern eine Steigerung der Effizienz von Dieselmotoren. Der Verlauf der Einspritzrate des Dieselkraftstoffes während eines Brennzyklus spielt eine entscheidende Rolle für die Emission von CO, NOx und Russpartikeln. Um optimale Einspritzverlaufs- Formung zu bestimmen, bedarf es sowohl einer genauen Kenntnis der thermodynamischen Eigenschaften des Dieselkraftstoffes, als auch der sich ausbreitenden Wellen in den einzelnen Komponenten. Hier wird ein Simulationsmodell abgeleitet, das instationäre eindimensionale Strömungsvorgänge von Dieselkraftstoff berechnet. Das Modell besteht aus drei Komponenten, deren gemeinsame Grundlage eine Zustandsgleichung für flüssigen Dieselkraftstoff ist. Die Strömung in den Rohrleitungen wird eindimensional und reibunsfrei angenommen. Daher werden die Euler Gleichungen numerisch, mittels der Methode von Roe, gelöst. In einem Vorratsbehälter (Volumen) können die kinetischen Energien vernachlässigt und die Änderungen der inneren Energie mittels Massen- und Energiebilanz berechnet werden, unter Berücksichtigung von ein- und ausströmender Masse und Enthalpie, sowie der zeitlichen Änderung des Gesamtvolumens.Drosseln werden durch Druckverlustbeiwerte beschrieben. Außerdem werden Änderungen der Temperatur aufgrund des Joule-Thomson Effekts berücksichtigt. Die benötigten Zustandsgleichungen für flüssigen Diesel Kraftstoff werden aus Messungen von Dichte und isobarer Wärmekapazität hergeleitet. Um diese Zustandsgleichung zu testen, wurden daraus berechnete Werte für die Schallgeschwindigkeit mit Werten aus der Literatur verglichen. Um das Simulationsmodell auf die Fähigkeit Druckwellen, Verdünnungsfächer und Kontaktunstetigkeiten auflösen zu können zu überprüfen, werden die Ergebnisse eines Stoßrohrproblems gezeigt. Weiters werden die Änderungen von Dichte und Temperatur während der Kompression und Expansion in einer Kolbenpumpe gezeigt. Außerdem wurden zwei verschiedene Kombinationen von Komponenten ausgetestet. Zwei Volumina mit unterschiedlichen Anfangsbedingungen werden in einem Test mit einer Drossel und in einem anderen Test mit einer Leitung verbunden. Der zeitliche Verlauf der daraus resultierenden Ausgleichsvorgänge wird gezeigt.Die Arbeit soll helfen instationäre eindimensionale Strömungsvorgänge von flüssigem Diesel in modernen Einspritzsystemen, mit Betriebsdrücken bis zu 2500 bar und Temperaturen zwischen -10°C und 120°C, zu simulieren.Future emission laws like EURO V I, JPNLT, US 10 and US T4 require to increase the efficiency of diesel engines. Shaping the rate of diesel fuel injected into a cylinder during one combustion cycle has great influence on emission of CO, NOx and sooty particles. In order to determine an optimal rate shaping, knowledge of the thermodynamic behavior of diesel and of the pressure waves in the components of the injection system is needed. Here we deduce a simulation model, that calculates transient one-dimensional ow of diesel fuel. The model consists of three components, which are all based on the equations of state for liquid diesel fuel. The flow in the pipes is considered one-dimensional and inviscid. Thus the Euler equations are solved numerically using Roe's method. In a volume the kinetic energy can be neglected and the changes of internal energy are calculated by a mass and energy balance considering the in and out ow masses and their enthalpy and the change of volume with time, as well. A throttle will be described by a pressure loss coefficient.Changes of temperature due to the Joule-Thomson effect are also taken into account. Equations of state for liquid diesel Fuel have been derived from measured data for density and isobaric heat capacity. The equation of state is tested by comparing the predicted values for the speed of sound with measured data reported in the literature. To proof the ability of the simulation tool to resolve shock and rarefaction waves as well as contact discontinuities, the results for a shock tube test are shown. Further the change of density and temperature during compression and expansion in a piston pump is shown. Also the results for two volumes with different initial conditions, connected by a throttle in one test case and connected by a pipe in another test case, show different transient behavior. This work shall help simulating transient one dimensional flow of liquid diesel fuel in modern diesel injection systems, having operating pressures of up to 2500 bar and operating temperatures from 260 K to 393 K.4

Surface-Enhanced Raman Spectroscopy for biomedical diagnostics and imaging

The final publication is available via https://doi.org/10.3233/BSI-120034.Surface-enhanced Raman spectroscopy (SERS) is an analytical technique exploiting plasmonic effects that enhance sensitivity significantly, compared to conventional Raman spectroscopy. Progress in nanotechnology led to new fabrication methods for nanostructures and nanoparticles over the last decade. Besides increased comprehension of mechanisms that cause the signal enhancement, computational methods have been developed to tailor analyte-specific nanostructures efficiently. The ability to control the size, shape, and material of surfaces has facilitated the widespread application of SERS in biomedical analytics and clinical diagnostics. In this review, a brief excerpt of such SERS applications is shown, with special focus on cancer diagnostics, glucose detection and in vivo imaging applications. Simulation techniques are discussed to show that electro-dynamic theory can be used to predict the characteristics of nanostructure arrangements. Different fabrication methods, such as nanoparticle synthesis, their immobilization and lithographic methods are reviewed in brief

Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

In this short summary we summarize some of the latest developments in vibrational spectroscopic tools applied for the sensing of (small) molecules and biomolecules in a label-free mode of operation. We first introduce various concepts for the enhancement of InfraRed spectroscopic techniques, including the principles of Attenuated Total Reflection InfraRed (ATR-IR), (phase-modulated) InfraRed Reflection Absorption Spectroscopy (IRRAS/PM-IRRAS), and Surface Enhanced Infrared Reflection Absorption Spectroscopy (SEIRAS). Particular attention is put on the use of novel nanostructured substrates that allow for the excitation of propagating and localized surface plasmon modes aimed at operating additional enhancement mechanisms. This is then be complemented by the description of the latest development in Surface- and Tip-Enhanced Raman Spectroscopies, again with an emphasis on the detection of small molecules or bioanalytes

A kinetic model of proton transport in a multi-redox centre protein: cytochrome coxidase

The final publication is available via https://doi.org/10.3184/146867812X13558465325118We use chemical reaction kinetics to explore the stepwise electron and proton transfer reactions of cytochrome c oxidase (CcO) from R. sphaeroides. Proton transport coupled to electron transport (ET) is investigated in terms of a sequence of protonation-dependent second-order redox reactions. Thereby, we assume fixed rather than shifting dissociation constants of the redox sites. Proton transport can thus be simulated particularly when separate proton uptake and release sites are assumed rather than the same proton pump site for every ET step. In order to test these assumptions, we make use of a model system introduced earlier, which allows us to study direct ET of redox enzymes by electrochemistry. A four-electron transfer model of CcO had been developed before, according to which electrons are transferred from the electrode to CuA. Thereafter, electrons are transferred along the sequence heme a, heme a3 and CuB. In the present investigation, we consider protonation equilibria of the oxidised and reduced species for each of the four centres. Moreover, we add oxygen/H2O as the terminal (fifth) redox couple including protonation of reduced oxygen to water. Finally we arrive at a kinetic model comprising five protonation-dependent redox couples. The results from the simulations are compared with experimental data obtained in the absence and presence of oxygen. As a result, we can show that proton transport can be modelled in terms of protonation-dependent redox kinetics

Time-Resolved Surface-Enhanced IR-Absorption Spectroscopy of Direct Electron Transfer to Cytochrome c Oxidase from R. sphaeroides

The final publication is available via https://doi.org/10.1016/j.bpj.2013.10.037.Time-resolved surface-enhanced IR-absorption spectroscopy triggered by electrochemical modulation has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. Single bands isolated from a broad band in the amide I region using phase-sensitive detection were attributed to different redox centers. Their absorbances changing on the millisecond timescale could be fitted to a model based on protonation-dependent chemical reaction kinetics established previously. Substantial conformational changes of secondary structures coupled to redox transitions were revealed

Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface

The heme protein cytochrome c adsorbed to a two-layer gold surface modified with a self-assembled monolayer of 2-mercaptoethanol was analyzed using a two-dimensional (2D) heterospectral correlation analysis that combined surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise increasing electric potentials were applied to alter the redox state of the protein and to induce conformational changes within the protein backbone. We demonstrate herein that 2D heterospectral correlation analysis is a particularly suitable and useful technique for the study of heme-containing proteins as the two spectroscopies address different portions of the protein. Thus, by correlating SERS and SEIRAS data in a 2D plot, we can obtain a deeper understanding of the conformational changes occurring at the redox center and in the supporting protein backbone during the electron transfer process. The correlation analyses are complemented by molecular dynamics calculations to explore the intramolecular interactions.ASTAR (Agency for Sci., Tech. and Research, S’pore)Accepted versio

Two-Dimensional Heterospectral Correlation Analysis of the Redox-Induced Conformational Transition in Cytochrome <i>c</i> Using Surface-Enhanced Raman and Infrared Absorption Spectroscopies on a Two-Layer Gold Surface

The heme protein cytochrome <i>c</i> adsorbed to a two-layer gold surface modified with a self-assembled monolayer of 2-mercaptoethanol was analyzed using a two-dimensional (2D) heterospectral correlation analysis that combined surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise increasing electric potentials were applied to alter the redox state of the protein and to induce conformational changes within the protein backbone. We demonstrate herein that 2D heterospectral correlation analysis is a particularly suitable and useful technique for the study of heme-containing proteins as the two spectroscopies address different portions of the protein. Thus, by correlating SERS and SEIRAS data in a 2D plot, we can obtain a deeper understanding of the conformational changes occurring at the redox center and in the supporting protein backbone during the electron transfer process. The correlation analyses are complemented by molecular dynamics calculations to explore the intramolecular interactions