Accelerated stochastic simulation of the stiff enzyme-substrate reaction

The enzyme-catalyzed conversion of a substrate into a product is a common reaction motif in cellular chemical systems. In the three reactions that comprise this process, the intermediate enzyme-substrate complex is usually much more likely to decay into its original constituents than to produce a product molecule. This condition makes the reaction set mathematically "stiff." We show here how the simulation of this stiff reaction set can be dramatically speeded up relative to the standard stochastic simulation algorithm (SSA) by using a recently introduced procedure called the slow-scale SSA. The speedup occurs because the slow-scale SSA explicitly simulates only the relatively rare conversion reactions, skipping over occurrences of the other two less interesting but much more frequent reactions. We describe, explain, and illustrate this simulation procedure for the isolated enzyme-substrate reaction set, and then we show how the procedure extends to the more typical case in which the enzyme-substrate reactions occur together with other reactions and species. Finally, we explain the connection between this slow-scale SSA approach and the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] formula, which has long been used in deterministic chemical kinetics to describe the enzyme-substrate reaction.     

Zur Bestimmung des Schwefelgehaltes in Gasen, besonders in Koksofengas

Zusammenfassung Auf Grund vergleichender Versuche über die Volumenänderungen von Gasen beim Durchleiten durch alkalische H₂O₂-Lösungen verschiedener Konzentration wurde eine Arbeitsvorschrift festgelegt, nach der bei einer Gasgeschwindigkeit von 0,2l/min. innerhalb rund 2 Stunden eine titrimetrische, unter Berücksichtigung der Volumenänderung für Betriebsverhältnisse genaue S-Bestimmung auszuführen ist, wobei aller anorganischer und organischer S mit Ausnahme des dem Thiophen entstammenden Schwefels erfasst wird und infolge des verhältnismäßig grossen Volumens (20l) auch eine genügende Durchschnittsgaszusammensetzung gewährleistet ist.     

Komplexbildung und Extraktion von Molybdän(VI) mit zweizähnigen Liganden

Coordination and Extraction of Molybdenum(VI) with Bidentate Ligands A series of bidentate ligands as well as their thio derivatives from the groups of 8-quinolinols, β-diketones, acylpyrazolones, and N-acyl-phenylhydroxylamines was studied for the ability to extract molybdenum(VI) from heptamolybdate. The extraction principally runs only in acidic medium, sulfur-containing extractants having no advantage. The composition of the complexes was determined by the isolation of compounds in the solid state and also by the interpretation of distribution data.     

Über Rosmarin und Rosmarinsäure

Rosmarinic acid, a tan from Lamiaceae, is found in rosemary and many other plants such as thyme, painted nettle, savory, sage, oregano, or lemon balm, from which it has been isolated here. It is a caffeic acid ester and a chiral, aromatic natural product. Rosmarinic acid tastes bitter, which may be attractive for rosemary as spice. Due to the catechol subunit the acid is an antioxidant. Using rosmarinic acid as a cure is possible due to manyfold physiological effects which are still under investigation. The rosmarinic acid biosynthesis pathway was completely elucidated at the painted nettle. This led to attempts to produce the acid biotechnologically by plant cell cultures in high yields. The preparation of a spectroscopically pure sample is challenging. All analytical spectra were recorded and are reproduced and interpreted either in the main part or in the supporting information.     

A Monte Carlo simulation study of lipid bilayer formation on hydrophilic substrates from vesicle solutions

A general lattice Monte Carlo model is used for simulating the formation of supported lipid bilayers (SLBs) from vesicle solutions. The model, based on a previously published paper, consists of adsorption, decomposition, and lateral diffusion steps, and is derived from fundamental physical interactions and mass transport principles. The Monte Carlo simulation results are fit to experimental data at different vesicle bulk concentrations. A sensitivity analysis reveals that the process strongly depends on the bulk concentration C(0), adsorption rate constant K, and all vesicle radii parameters. A measure of "quality of coverage" is proposed. By this measure, the quality of the formed bilayers is found to increase with vesicle bulk concentration.     

An algorithm for simulation of electrochemical systems with surface–bulk coupling strategies

In Buoni and Petzold (2007) [13] we described a new algorithm for simulation of electrochemical systems on two-dimensional irregular, time-dependent domains. Here we show how to extend the algorithm to three dimensions. We demonstrate our three-dimensional algorithm by simulating copper electrodeposition into a via structure. This problem poses challenges for the coupling of the dilute electrolyte (bulk) model to the surface dynamics model, which involves a complex network of reactions. To handle this coupling, we introduce a new and highly effective semi-implicit method.     

Gas-phase reactions of charged phenyl radicals with neutral biomolecules evaporated by laser-induced acoustic desorption

A generally applicable method for the study of phenyl radicals' reactions with neutral biomolecules in the gas phase is demonstrated. Neutral biomolecules were evaporated into a Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR) by means of laser-induced acoustic desorption (LIAD) and subsequently reacted with trapped charged phenyl radicals. The structural integrity of the evaporated alanylalanine molecules was verified by reaction with dichlorophosphenium ions. Examination of the reactions of charged phenyl radicals with alanylalanine and thymidine evaporated via LIAD revealed hydrogen atom abstraction for both alanylalanine and thymidine as well as an addition/elimination product for the reaction with thymidine. These reactions are consistent with the results obtained by others in solution. Further, a previously unstudied reaction of the nucleotide of thymine (T1) with charged phenyl radical was found to yield analogous products as the reaction with thymidine.     

Chemical properties of a para-benzyne

5,8-Didehydroisoquinolinium ion, a para benzyne analogue, was generated in a Fourier transform ion cyclotron resonance mass spectrometer, and its reactivity toward various neutral reagents was examined. A direct comparison of the reaction kinetics of the para benzyne, a meta isomer, and analogous monoradicals, indicates that the para benzyne is a poorer electrophile but a more reactive radical than its meta isomer.     

Method comparison study on soot-selective techniques

In a long-term field study at two locations with different air pollution levels several soot-selective measurement techniques were compared with a thermochemical method which measures non-extractable carbon (NEC) detecting the evolved CO₂ by means of coulometric titration. The attenuation measurement technique (aethalometer) and the aerosol photoemission method showed good correlations to NEC for concentrations ranging from 1.6g/m³ to 40.8g/m³. The specific mass absorption coefficient of black carbon with respect to NEC varied between 8.4m²/g and 13.7m²/g with respect to the measurement sites, but the value was found to remain constant at each site independent of seasonal or meteorological variations. The ratio of photoelectric signal to NEC varied between 16 fA·(g/m³)^–1 and 33 fA·(g/m³)^–1 depending on the age of the aerosol. The diurnal variations of that ratio showed strong similarities to the traffic patterns. Additionally a slight temperature dependence of this ratio was found for the aged aerosol with a proportionality factor of – 0.35 fA·(K·g/m³)^–1. With the reflectance measurement technique (smoke shade method) reliable NEC determination was not possible for NEC concentrations 5 g/m³.     

Die Bestimmung des Sulfatgehaltes von Chromaten und Dichromaten

Zusammenfassung Es wird eine neue Methode zur Bestimmung von Sulfat in Anwesenheit eines großen Überschusses von Chromat bzw. Dichromat gegeben, die schnell und unkompliziert ist. Durch Anwendung von konz. Überchlorsäure wird das störende Chromat als Chromsäureanhydrid abgetrennt und im Filtrat nach Neutralisation und schwachem Ansäuern das Sulfat wie üblich als Bariumsulfat bestimmt. Sehr geringe Sulfatmengen können nephelometrisch ermittelt werden.