Approaches and tools to manipulate the carbonate chemistry

Although the chemistry of ocean acidifi cation is very well understood (see chapter 1), its impact on marine organisms and ecosystems remains poorly known. The biological response to ocean acidifi cation is a recent field of research, the fi rst purposeful experiments have only been carried out as late as the 1980s (Agegian, 1985) and most were not performed until the late 1990s. The potentially dire consequences of ocean acidifi cation have attracted the interest of scientists and students with a limited knowledge of the carbonate chemistry and its experimental manipulation. Perturbation experiments are one of the key approaches used to investigate the biological response to elevated p(CO2). Such experiments are based on measurements of physiological or metabolic processes in organisms and communities exposed to seawater with normal and altered carbonate chemistry. The basics of the carbonate chemistry must be understood to perform meaningful CO2 perturbation experiments (see chapter 1). Briefl y, the marine carbonate system considers € CO2 ∗(aq) [the sum of CO2 and H2CO3], € HCO3 −, € CO3 2−, H+, € OH− , and several weak acid-base systems of which borate-boric acid (€ B(OH)4 − , B(OH)3) is the most important. As discussed by Dickson (chapter 1), if two components of the carbonate chemistry are known, all the other components can be calculated for seawater with typical nutrient concentrations at given temperature, salinity, and pressure. One of the possible pairs is of particular interest because both components can be measured with precision, accuracy, and are conservative in the sense that their concentrations do not change with temperature or pressure. Dissolved inorganic carbon (DIC) is the sum of all dissolved inorganic carbon species while total alkalinity (AT) equals € [HCO3 − ] + 2 € [CO3 2− ] + € [B(OH)4 − ] + € [OH− ] - [H+] + minor components, and refl ects the excess of proton acceptors over proton donors with respect to a zero level of protons (see chapter 1 for a detailed defi nition). AT is determined by the titration of seawater with a strong acid and thus can also be regarded as a measure of the buffering capacity. Any changes in any single component of the carbonate system will lead to changes in several, if not all, other components. In other words, it is not possible to vary a single component of the carbonate system while keeping all other components constant. This interdependency in the carbonate system is important to consider when performing CO2 perturbation experiments. To adjust seawater to different p(CO2) levels, the carbonate system can be manipulated in various ways that usually involve changes in AT or DIC. The goal of this chapter is (1) to examine the benefi ts and drawbacks of various manipulation methods used to date and (2) to provide a simple software package to assist the design of perturbation experiments

On the recombination in high-order harmonic generation in molecules

We show that the dependence of high-order harmonic generation (HHG) on the molecular orientation can be understood within a theoretical treatment that does not involve the strong field of the laser. The results for H_2 show excellent agreement with time-dependent strong field calculations for model molecules, and this motivates a prediction for the orientation dependence of HHG from the N_2 3s_g valence orbital. For both molecules, we find that the polarization of recombination photons is influenced by the molecular orientation. The variations are particularly pronounced for the N_2 valence orbital, which can be explained by the presence of atomic p-orbitals.Comment: 6 pages 7 figure

Dynamics of photo-activated Coulomb complexes

Intense light with frequencies above typical atomic or molecular ionization potentials as provided by free-electron lasers couples many photons into extended targets such as clusters and biomolecules. This implies, in contrast to traditional multi-photon ionization, multiple single-photon absorption. Thereby, many electrons are removed from their bound states and either released or trapped if the target charge has become sufficiently large. We develop a simple model for this photo activation to study electron migration and interaction. It satisfies scaling relations which help to relate quite different scenarios. To understand this type of multi-electron dynamics on very short time scales is vital for assessing the radiation damage inflicted by that type of radiation and to pave the way for coherent diffraction imaging of single molecules.Comment: 14 pages, 6 figures, 1 tabl

Clusters under strong VUV pulses: A quantum-classical hybrid-description incorporating plasma effects

The quantum-classical hybrid-description of rare-gas clusters interacting with intense light pulses which we have developed is described in detail. Much emphasis is put on the treatment of screening electrons in the cluster which set the time scale for the evolution of the system and form the link between electrons strongly bound to ions and quasi-free plasma electrons in the cluster. As an example we discuss the dynamics of an Ar147 cluster exposed to a short VUV laser pulse of 20eV photon energy.Comment: 8 pages, 9 figure

Effects of precipitation uncertainty on discharge calculations for main river basins

This study quantifies the uncertainty in discharge calculations caused by uncertainty in precipitation input for 294 river basins worldwide. Seven global gridded precipitation datasets are compared at river basin scale in terms of mean annual and seasonal precipitation. The representation of seasonality is similar in all datasets, but the uncertainty in mean annual precipitation is large, especially in mountainous, arctic, and small basins. The average precipitation uncertainty in a basin is 30%, but there are strong differences between basins. The effect of this precipitation uncertainty on mean annual and seasonal discharge was assessed using the uncalibrated dynamic global vegetation and hydrology model Lund-Potsdam-Jena managed land (LPJmL), yielding even larger uncertainties in discharge (average 90%). For 95 basins (out of 213 basins for which measurements were available) calibration of model parameters is problematic because the observed discharge falls within the uncertainty of the simulated discharge. A method is presented to account for precipitation uncertainty in discharge simulations

ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes

Motivation Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we focused on new pairs of interacting proteins for several model organisms based solely on sequence-based prediction methods. Results We extracted reliable experimental data about which proteins interact (binary) for eight diverse model organisms from public databases, namely from Escherichia coli, Schizosaccharomyces pombe, Plasmodium falciparum, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and for the previously used Homo sapiens and Saccharomyces cerevisiae. Those data were the base to develop a PPI prediction method for each model organism. The method used evolutionary information through a profile-kernel Support Vector Machine (SVM). With the resulting eight models, we predicted all possible protein pairs in each organism and made the top predictions available through a web application. Almost all of the PPIs made available were predicted between proteins that have not been observed in any interaction, in particular for less well-studied organisms. Thus, our work complements existing resources and is particularly helpful for designing experiments because of its uniqueness. Experimental annotations and computational predictions are strongly influenced by the fact that some proteins have many partners and others few. To optimize machine learning, recent methods explicitly ignored such a network-structure and rely either on domain knowledge or sequence-only methods. Our approach is independent of domain-knowledge and leverages evolutionary information. The database interface representing our results is accessible from https://rostlab.org/services/ppipair/. The data can also be downloaded from https://figshare.com/collections/ProfPPI-DB/4141784

Energy bunching in soft recollisions revealed with long-wavelength few-cycle pulses

Soft recollisions are laser-driven distant collisions of an electron with its parent ion. Such collisions may cause an energy bunching, since electrons with different initial drift momenta can acquire impacts, which exactly counterbalance these differences. The bunching generates a series of peaks in the photo-electron spectrum. We will show that this series could be uncovered peak-by-peak experimentally by means of phase-stabilized few-cycle pulses with increasing duration.Comment: 8 pages, 3 figure

The impact of iron limitation on the physiology of the Antarctic diatom Chaetoceros simplex

Iron availability strongly governs the growth of Southern Ocean phytoplankton. To investigate how iron limitation affects photosynthesis as well as the uptake of carbon and iron in the Antarctic diatom Chaetoceros simplex, a combination of chlorophyll a fluorescence measurements and radiotracer incubations in the presence and absence of chemical inhibitors was conducted. Iron limitation in C. simplex led to a decline in growth rates, photochemical efficiency and structural changes in photosystem II (PSII), including a reorganisation of photosynthetic units in PSII and an increase in size of the functional absorption cross section of PSII. Iron-limited cells further exhibited a reduced plastoquinone pool and decreased photosynthetic electron transport rate, while non-photochemical quenching and relative xanthophyll pigment content were strongly increased, suggesting a photoprotective response. Additionally, iron limitation resulted in a strong decline in carbon fixation and thus the particulate organic carbon quotas. Inhibitor studies demonstrated that, independent of the iron supply, carbon fixation was dependent on internal, but not on extracellular carbonic anhydrase activity. Orthovanadate more strongly inhibited iron uptake in iron-limited cells, indicating that P-type ATPase transporters are involved in iron uptake. The stronger reduction in iron uptake by ascorbate in iron-limited cells suggests that the re-oxidation of iron is required before it can be taken up and further supports the presence of a high-affinity iron transport pathway. The measured changes to photosystem architecture and shifts in carbon and iron uptake strategies in C. simplex as a result of iron limitation provide evidence for a complex interaction of these processes to balance the iron requirements for photosynthesis and carbon demand for sustained growth in iron-limited waters. © 2014 The Author(s)

The totally asymmetric exclusion process with generalized update

We consider the totally asymmetric exclusion process in discrete time with generalized updating rules. We introduce a control parameter into the interaction between particles. Two particular values of the parameter correspond to known parallel and sequential updates. In the whole range of its values the interaction varies from repulsive to attractive. In the latter case the particle flow demonstrates an apparent jamming tendency not typical for the known updates. We solve the master equation for $N$ particles on the infinite lattice by the Bethe ansatz. The non-stationary solution for arbitrary initial conditions is obtained in a closed determinant form.Comment: 11 pages, 3 figure