Remote Effects Modulating the Spin Equilibrium of the Resting State of Cytochrome P450cam –An Investigation Using Active Site Analogues

The crystal structure of the resting state of cytochrome P450cam (CYP101), a heme thiolate protein, shows a cluster of six water molecules in the substrate binding pocket, one of which is coordinating to iron(III) as sixth ligand. The resting state is low-spin and changes to high-spin when substrate camphor binds and H2O is removed. In contrast to the protein, previously synthesised enzyme models such as H2O[BOND]FeIII(porph)(ArS−) were shown to be purely high-spin. Iron(S−)porphyrins with different distal sites mimicking proposed remote effects have been prepared and studied by cw-EPR. The results indicate that the low-spin of the resting state of P450cam is due to the fact that the water molecule coordinating to iron has an OH−-like character because of hydrogen bonding and polarisation of the water cluster, respectively.

Reconstructing Arguments: Formalization and Reflective Equilibrium

Traditional logical reconstruction of arguments aims at assessing the validity of ordinary language arguments. It involves several tasks: extracting argumentations from texts, breaking up complex argumentations into individual arguments, framing arguments in standard form, as well as formalizing arguments and showing their validity with the help of a logical formalism. These tasks are guided by a multitude of partly antagonistic goals, they interact in various feedback loops, and they are intertwined with the development of theories of valid inference and adequate formalization. This paper explores how the method of reflective equilibrium can be used for modelling the complexity of such reconstructions and for justifying the various steps involved. The proposed approach is illustrated and tested in a detailed reconstruction of the beginning of Anselm’s De casu diaboli.

Computable Diagonalizations and Turing’s Cardinality Paradox

A. N. Turing’s 1936 concept of computability, computing machines, and computable binary digital sequences, is subject to Turing’s Cardinality Paradox. The paradox conjoins two opposed but comparably powerful lines of argument, supporting the propositions that the cardinality of dedicated Turing machines outputting all and only the computable binary digital sequences can only be denumerable, and yet must also be nondenumerable. Turing’s objections to a similar kind of diagonalization are answered, and the implications of the paradox for the concept of a Turing machine, computability, computable sequences, and Turing’s effort to prove the unsolvability of the Entscheidungsproblem, are explained in light of the paradox. A solution to Turing’s Cardinality Paradox is proposed, positing a higher geometrical dimensionality of machine symbol-editing information processing and storage media than is available to canonical Turing machine tapes. The suggestion is to add volume to Turing’s discrete two-dimensional machine tape squares, considering them instead as similarly ideally connected massive three-dimensional machine information cells. Three-dimensional computing machine symbol-editing information processing cells, as opposed to Turing’s two-dimensional machine tape squares, can take advantage of a denumerably infinite potential for parallel digital sequence computing, by which to accommodate denumerably infinitely many computable diagonalizations. A three-dimensional model of machine information storage and processing cells is recommended on independent grounds as better representing the biological realities of digital information processing isomorphisms in the three-dimensional neural networks of living computers.

Calibrating a CGE model with NTBs that Incorporates Standard Models of Modern Trade Theory

We propose a way to incorporate NTBs for the four workhorse models of the modern trade literature in computable general equilibrium models (CGEs). CGE models feature intermediate linkages and thus allow us to study global value chains (GVCs). We show that the Ethier-Krugman monopolistic competition model, the Melitz firm heterogeneity model and the Eaton and Kortum model can be defined as an Armington model with generalized marginal costs, generalized trade costs and a demand externality. As already known in the literature in both the Ethier-Krugman model and the Melitz model generalized marginal costs are a function of the amount of factor input bundles. In the Melitz model generalized marginal costs are also a function of the price of the factor input bundles. Lower factor prices raise the number of firms that can enter the market profitably (extensive margin), reducing generalized marginal costs of a representative firm. For the same reason the Melitz model features a demand externality: in a larger market more firms can enter. We implement the different models in a CGE setting with multiple sectors, intermediate linkages, non-homothetic preferences and detailed data on trade costs. We find the largest welfare effects from trade cost reductions in the Melitz model. We also employ the Melitz model to mimic changes in Non tariff Barriers (NTBs) with a fixed cost-character by analysing the effect of changes in fixed trade costs. While we work here with a model calibrated to the GTAP database, the methods developed can also be applied to CGE models based on the WIOD database.

Non-tariff barriers, integration and the transatlantic economy

We examine the potential impact of TTIP through trade-cost reductions, applying a mix of econometric and computational methods to develop estimates of the benefits (and costs) for the EU, United States, and third countries. Econometric results point to an approximate 80% growth in bilateral trade with an ambitious trade agreement. However, at the same time, computable general equilibrium (CGE) estimates highlight distributional impacts across countries and factors not evident from econometrics alone. Translated through our CGE framework, while bilateral trade increases roughly 80%, there is a fall of about 2.5% in trade with the rest of the world in our central case. The estimated gains in annual consumption range between 1% and 2.25% for the United States and EU, respectively. A purely discriminatory agreement would harm most countries outside the agreement, while the direction of third-country effects hinges critically on whether NTB reductions end up being discriminatory or not. Within the United States and EU, while labour gains across skill categories, the impact on farmers is mixed.

Helium in solubility equilibrium with quartz and porefluids in rocks - a new approach in hydrology

Quartz crystals in sandstones at depths of 1200 m–1400 m below the surface appear to reach a solubility equilibrium with the 4He-concentration in the surrounding pore- or groundwater after some time. A rather high 4Heconcentration of 4.5x10E-3 cc STP 4He/cm3 of water measured in a groundwater sample would for instance maintain a He pressure of 0.47 atm in a related volume. This value is equal within analytical error to the pressure deduced from the measured helium content of the quartz and its internal helium-accessible volume. To determine this volume, quartz crystals of 0.1 to 1 mm were separated from sandstones and exposed to a helium gas pressure of 32 atm at a temperature of 290°C for up to 2 months. By crushing, melting or isothermal heating the helium was then extracted from the helium saturated samples. Avolume on the order of 0.1% of the crystal volume is only accessible to helium atoms but not to argon atoms or water molecules. By monitoring the diffusive loss of He from the crystals at 350°C an effective diffusion constant on the order of 10E-9 cm2/s is estimated. Extrapolation to the temperature of 70°C in the sediments at a depth of 1400 m gives a typical time of about 100 000 years to reach equilibrium between helium in porewaters and the internal He-accessible volume of quartz crystals. In a geologic situation with stagnant pore- or groundwaters in sediments it therefore appears to be possible with this new method to deduce a 4He depth profile for porewaters in impermeable rocks based on their mineral record.

Barium isotope fractionation during witherite (BaCO3) dissolution, precipitation and at equilibrium

This study examines the behavior of Ba isotope fractionation between witherite and fluid during mineral dissolution, precipitation and at chemical equilibrium. Experiments were performed in batch reactors at 25 oC in 10-2 M NaCl solution where the pH was adjusted by continuous bubbling of a water saturated gas phase of CO2 or atmospheric air. During witherite dissolution no Ba isotope fractionation was observed between solid and fluid. In contrast, during witherite precipitation, caused by a pH increase, a preferential uptake of the lighter 134Ba isotopomer in the solid phase was observed. In this case, the isotope fractionation factor αwitherite-fluid is calculated to be 0.99993 ± 0.00004 (or Δ137/134Bawitherite-fluid ≈ -0.07 ± 0.04 ‰, 2sd). The most interesting feature of this study, however, is that after the attainment of chemical equilibrium, the Ba isotope composition of the aqueous phase is progressively becoming lighter, indicating a continuous exchange of Ba2+ ions between witherite and fluid. Mass balance calculations indicate that the detachment of Ba from the solid is not only restricted to the outer surface layer of the solid, but affects several (~7 unit cells) subsurface layers of the crystal. This observation comes in excellent agreement with the concept of a dynamic system at chemical equilibrium in a mineral-fluid system, denoting that the time required for the achievement of isotopic equilibrium in the witherite-fluid system is longer compared to that observed for chemical equilibrium. Overall, these results indicate that the isotopic composition of Ba bearing carbonates in natural environments may be altered due to changes in fluid composition without a net dissolution/precipitation to be observed.