Do we (need to) care about canopy radiation schemes in DGVMs? Caveats and potential impacts

Dynamic global vegetation models (DGVMs) are an essential part of current state-of-the-art Earth system models. In recent years, the complexity of DGVMs has increased by incorporating new important processes like, e.g., nutrient cycling and land cover dynamics, while biogeophysical processes like surface radiation have not been developed much further. Canopy radiation models are however very important for the estimation of absorption and reflected fluxes and are essential for a proper estimation of surface carbon, energy and water fluxes. The present study provides an overview of current implementations of canopy radiation schemes in a couple of state-of-the-art DGVMs and assesses their accuracy in simulating canopy absorption and reflection for a variety of different surface conditions. Systematic deviations in surface albedo and fractions of absorbed photosynthetic active radiation (faPAR) are identified and potential impacts are assessed. The results show clear deviations for both, absorbed and reflected, surface solar radiation fluxes. FaPAR is typically underestimated, which results in an underestimation of gross primary productivity (GPP) for the investigated cases. The deviation can be as large as 25% in extreme cases. Deviations in surface albedo range between −0.15 ≤ Δα ≤ 0.36, with a slight positive bias on the order of Δα ≈ 0.04. Potential radiative forcing caused by albedo deviations is estimated at −1.25 ≤ RF ≤ −0.8 (W m−2), caused by neglect of the diurnal cycle of surface albedo. The present study is the first one that provides an assessment of canopy RT schemes in different currently used DGVMs together with an assessment of the potential impact of the identified deviations. The paper illustrates that there is a general need to improve the canopy radiation schemes in DGVMs and provides different perspectives for their improvement

Folding and insertion thermodynamics of the transmembrane WALP peptide

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum---in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.Comment: 12 pages, 5 figure

Secondary Structure Transition and Critical Stress for a Model of Spider Silk Assembly

Spiders spin their silk from an aqueous solution to a solid fiber in ambient conditions. However, to date the assembly mechanism in the spider silk gland has not been satisfactorily explained. In this paper, we use molecular dynamics simulations to model N. clavipes MaSp1 dragline silk formation under shear flow and determine the secondary structure transitions leading to the experimentally observed fiber structures. While no experiments are performed on the silk fiber itself, insights from this polypeptide model can be transferred to the fiber scale. The novelty of this study lies in the calculation of the shear stress (300-700 MPa) required for fiber formation and identification of the amino acid residues involved in the transition. This is the first time that the shear stress has been quantified in connection with a secondary structure transition. By study of molecules containing varying numbers of contiguous MaSp1 repeats we identified the smallest molecule size that gives rise to a 'silk-like' structure contains six poly-alanine repeats. Through a probability analysis of the secondary structure we identify specific amino acids that transition from α-helix to β-sheet. In addition to portions of the poly-alanine section these amino acids include glycine, leucine and glutamine. Stability of β-sheet structures appears to arise from a close proximity in space of helices in the initial spidroin state. Our results are in agreement with the forces exerted by spiders in the silking process and the experimentally determined global secondary structure of spidroin and pulled MaSp1 silk. Our study emphasizes the role of shear in the assembly process of silk and can guide the design of microfluidic devices that attempt to mimic the natural spinning process and predict molecular requirements for the next generation of silk-based functional materials

Magnetisation of hole-doped CuO2 spin chains in Sr14-xCaxCu24O41

We report on magnetisation measurements of Sr14-xCaxCu24O41, with 0 <= x <= 12, in magnetic fields up to 16 T. The low temperature magnetic response of the CuO2 spin chains changes strongly upon doping. For x = 0, the ground state with nearly independent dimers is confirmed. Reduction of the number of holes in the chains through Ca-doping leads to an additional contribution to the magnetisation, which depends linearly on the magnetic field. Remarkably, the slope of this linear contribution increases with the Ca content. We argue that antiferromagnetic spin chains do not account for this behaviour but that the hole dynamics might be involved.Comment: In v2, spelling of author names has been change

Generalized Unitarity and Six-Dimensional Helicity

We combine the unitarity method with the six-dimensional helicity formalism of Cheung and O'Connell to construct loop-level scattering amplitudes. As a first example, we construct dimensionally regularized QCD one-loop four-point amplitudes. As a nontrivial multiloop example, we confirm that the recently constructed four-loop four-point amplitude of N=4 super-Yang-Mills theory, including nonplanar contributions, is valid for dimensions less than or equal to six. We comment on the connection of our approach to the recently discussed Higgs infrared regulator and on dual conformal properties in six dimensions.Comment: 38 pages, 7 figures, typos correcte

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements

To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced ∼0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide

Constraints on the vital effect in coccolithophore and dinoflagellate calcite by oxygen isotopic modification of seawater

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 141 (2014): 612-627, doi:10.1016/j.gca.2014.05.002.In this study, we show that there are independent controls of 18O/16O and 13C/12C fractionation in coccolithophore and dinoflagellate calcite due to the contrasting kinetics of each isotope system. We demonstrate that the direction and magnitude of the oxygen isotope fractionation with respect to equilibrium is related to the balance between calcification rate and the replenishment of the internal pool of dissolved inorganic carbon (DIC). As such, in fast growing cells, such as those of Emiliania huxleyi and Gephyrocapsa oceanica (forming the so-called “heavy group”), calcification of the internal carbon pool occurs faster than complete isotopic re-adjustment of the internal DIC pool with H2O molecules. Hence, coccoliths reflect the heavy oxygen isotope signature of the CO2 overprinting the whole DIC pool. Conversely, in large and slow growing cells, such as Coccolithus pelagicus ssp. braarudii, complete re-equilibration is achieved due to limited influx of CO2 leading to coccoliths that are precipitated in conditions close to isotopic equilibrium (“equilibrium group”). Species exhibiting the most negative oxygen isotope composition, such as Calcidiscus leptoporus (“light group”), precipitate coccolith under increased pH in the coccolith vesicle, as previously documented by the “carbonate ion effect”. We suggest that, for the carbon isotope system, any observed deviation from isotopic equilibrium is only “apparent”, as the carbon isotopic composition in coccolith calcite is controlled by a Rayleigh fractionation originating from preferential incorporation of 12C into organic matter. Therefore, species with low PIC/POC ratios as E. huxleyi and G. oceanica are shifted towards positive carbon isotope values as a result of predominant carbon fixation into the organic matter. By contrast, cells with higher PIC/POC as C. braarudii and C. leptoporus maintain, to some extent, the original negative isotopic composition of the CO2. The calcareous dinoflagellate Thoracosphaera heimii exhibits different behaviour for both isotopic systems, in particular with respect to its very negative carbon isotope composition, owing to coeval intra and extracellular biomineralisation in this group. In this study, we also investigate the sensitivity of 18O/16O fractionation to varying ambient oxygen isotope composition of the medium for inorganic, coccolithophore, and dinoflagellate calcite precipitated under controlled laboratory conditions. The varying responses of different taxa to increased oxygen isotope composition of the growth medium may point to a potential bias in sea surface temperature reconstructions that are based on the oxygen isotopic compositions of sedimentary calcite, especially during times of changing seawater oxygen isotopic composition. Overall, this study represent an important step towards establishing a mechanistic understanding of the “vital effect” in coccolith and dinoflagellate calcite, and provides valuable information for interpreting the geochemistry of the calcareous nannofossils in the sedimentary record, at both monospecific and interspecies levels.MH is grateful to the Natural Environment Research Council (NERC) for funding through Postdoctoral Fellowship (NE/H015523/1). TJH is supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Doherty Foundation. REMR was supported through European Research Council (ERC) grant SP2-GA-2008-200915

Robustness Of Baryon Acoustic Oscillation Constraints For Early-Universe Modifications Of ΛCDM Cosmology

Baryon acoustic oscillations (BAO) provide a robust standard ruler and can be used to constrain the expansion history of the Universe at low redshift. Standard BAO analyses return a model-independent measurement of the expansion rate and the comoving angular diameter distance as a function of redshift, normalized by the sound horizon at radiation drag. However, this methodology relies on anisotropic distance distortions of a fixed, precomputed template (obtained in a given fiducial cosmology) in order to fit the observations. Therefore, it may be possible that extensions to the consensus ΛCDM add contributions to the BAO feature that cannot be captured by the template fitting. We perform mock BAO fits to power spectra computed assuming cosmological models that modify the growth of perturbations prior to recombination in order to test the robustness of the standard BAO analysis. We find no significant bias in the BAO analysis for the models under study (ΛCDM with a free effective number of relativistic species, early dark energy, and a model with interactions between neutrinos and a fraction of the dark matter), even for cases that do not provide a good fit to Planck measurements of the cosmic microwave background power spectra. This result supports the use of the standard BAO analysis and its measurements to perform cosmological parameter inference and to constrain exotic models. In addition, we provide a methodology to reproduce our study for different models and surveys, as well as discuss different options to handle eventual biases in the BAO measurements