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At least 523 records · Page 29

HIMMELI v1.0: HelsinkI Model of MEthane buiLd-up and emIssion for peatlands

Wetlands are one of the most significant natural sources of methane (CH 4 ) to the atmosphere. They emit CH 4 because decomposition of soil organic matter in waterlogged anoxic conditions produces CH 4 , in addition to carbon dioxide (CO 2 ). Production of CH 4 and how much of it escapes to the atmosphere depend on a multitude of environmental drivers. Models simulating the processes leading to CH 4 emissions are thus needed for upscaling observations to estimate present CH 4 emissions and for producing scenarios of future atmospheric CH 4 concentrations. Aiming at a CH 4 model that can be added to models describing peatland carbon cycling, we composed a model called HIMMELI that describes CH 4 build-up in and emissions from peatland soils. It is not a full peatland carbon cycle model but it requires the rate of anoxic soil respiration as input. Driven by soil temperature, leaf area index (LAI) of aerenchymatous peatland vegetation, and water table depth (WTD), it simulates the concentrations and transport of CH 4 , CO 2 , and oxygen (O 2 ) in a layered one-dimensional peat column. Here, we present the HIMMELI model structure and results of tests on the model sensitivity to the input data and to the description of the peat column (peat depth and layer thickness), and demonstrate that HIMMELI outputs realistic fluxes by comparing modeled and measured fluxes at two peatland sites. As HIMMELI describes only the CH 4 -related processes, not the full carbon cycle, our analysis revealed mechanisms and dependencies that may remain hidden when testing CH 4 models connected to complete peatland carbon models, which is usually the case. Our results indicated that (1) the model is flexible and robust and thus suitable for different environments; (2) the simulated CH 4 emissions largely depend on the prescribed rate of anoxic respiration; (3) the sensitivity of the total CH 4 emission to other input variables is mainly mediated via the concentrations of dissolved gases, in particular, the O 2 concentrations that affect the CH 4 production and oxidation rates; (4) with given input respiration, the peat column description does not significantly affect the simulated CH 4 emissions in this model version.

54 ENVIRONMENTAL SCIENCES↗

Process-level model evaluation: a snow and heat transfer metric

Land models require evaluation in order to understand results and guide future development. Examining functional relationships between model variables can provide insight into the ability of models to capture fundamental processes and aid in minimizing uncertainties or deficiencies in model forcing. This study quantifies the proficiency of land models to appropriately transfer heat from the soil through a snowpack to the atmosphere during the cooling season (Northern Hemisphere: October–March). Using the basic physics of heat diffusion, we investigate the relationship between seasonal amplitudes of soil versus air temperatures due to insulation from seasonal snow. Observations demonstrate the anticipated exponential relationship of attenuated soil temperature amplitude with increasing snow depth and indicate that the marginal influence of snow insulation diminishes beyond an effective snow depth of about 50 cm. A snow and heat transfer metric (SHTM) is developed to quantify model skill compared to observations. Land models within the CMIP5 experiment vary widely in SHTM scores, and deficiencies can often be traced to model structural weaknesses. The SHTM value for individual models is stable over 150 years of climate, 1850–2005, indicating that the metric is insensitive to climate forcing and can be used to evaluate each model's representation of the insulation process.

58 GEOSCIENCES↗

Constrained Block Nonlinear Neural Dynamical Models

Neural network modules conditioned by known priors can be effectively trained and combined to represent systems with nonlinear dynamics. This work explores a novel formulation for data-efficient learning of deep control-oriented nonlinear dynamical models by embedding local model structure and constraints. The proposed method consists of neural network blocks that represent input, state, and output dynamics with constraints placed on the network weights and system variables. For handling partially observable dynamical systems, we utilize a state observer neural network to estimate the states of the system's latent dynamics. We evaluate the performance of the proposed architecture and training methods on system identification tasks for three nonlinear systems: a continuous stirred tank reactor, a two tank interacting system, and an aerodynamics body. Models optimized with a few thousand system state observations accurately represent system dynamics in open loop simulation over thousands of time steps from a single set of initial conditions. Experimental results demonstrate an order of magnitude reduction in open-loop simulation mean squared error for our constrained, block-structured neural models when compared to traditional unstructured and unconstrained neural network models.

Skomski, Elliott↗

BioRT-Flux-PIHM v1.0: a biogeochemical reactive transport model at the watershed scale

Watersheds are the fundamental Earth surface functioning units that connect the land to aquatic systems. Many watershed-scale models represent hydrological processes but not biogeochemical reactive transport processes. This has limited our capability to understand and predict solute export, water chemistry and quality, and Earth system response to changing climate and anthropogenic conditions. Here we present a recently developed BioRT-Flux-PIHM (BioRT hereafter) v1.0, a watershed-scale biogeochemical reactive transport model. The model augments the previously developed RT-Flux-PIHM that integrates land-surface interactions, surface hydrology, and abiotic geochemical reactions. It enables the simulation of (1) shallow and deep-water partitioning to represent surface runoff, shallow soil water, and deeper groundwater and of (2) biotic processes including plant uptake, soil respiration, and nutrient transformation. The reactive transport part of the code has been verified against the widely used reactive transport code CrunchTope. BioRT-Flux-PIHM v1.0 has recently been applied in multiple watersheds under diverse climate, vegetation, and geological conditions. This paper briefly introduces the governing equations and model structure with a focus on new aspects of the model. It also showcases one hydrology example that simulates shallow and deep-water interactions and two biogeochemical examples relevant to nitrate and dissolved organic carbon (DOC). These examples are illustrated in two simulation modes of complexity. One is the spatially lumped mode (i.e., two land cells connected by one river segment) that focuses on processes and average behavior of a watershed. Another is the spatially distributed mode (i.e., hundreds of cells) that includes details of topography, land cover, and soil properties. Whereas the spatially lumped mode represents averaged properties and processes and temporal variations, the spatially distributed mode can be used to understand the impacts of spatial structure and identify hot spots of biogeochemical reactions. The model can be used to mechanistically understand coupled hydrological and biogeochemical processes under gradients of climate, vegetation, geology, and land use conditions.

54 ENVIRONMENTAL SCIENCES↗

Diffusion Paths for Interstitial Impurities in Different Polymorphic Modifications of Niobium Silicide Nb{sub 5}Si{sub 3}

Structural models of the α, β, and γ modifications of Nb{sub 5}Si{sub 3} silicides, which are used as a reinforcing phase in composites obtained in situ based on the Nb‒Si system, have been constructed by computer simulation methods. A geometric analysis of unit cells is performed using the H-poisk program to estimate the voids existing in the structures. The results of measuring the number of voids and their sizes are reported. A conclusion about possible diffusion paths of interstitial boron, carbon, nitrogen and oxygen atoms is drawn based on the calculation results, and the solubility of these impurities in the structure of each Nb{sub 5}Si{sub 3} modification is estimated.

36 MATERIALS SCIENCE↗

HRTEM, SAED and XRD investigations of RE{sub 4}O{sub 4}[AsO{sub 4}]Cl (RE = La, Pr, Nd, Sm, Eu, Gd)

Graphical abstract: The new compounds RE{sub 4}O{sub 4}[AsO{sub 4}]Cl (RE = La, Pr, Nd, Sm, Eu, Gd) were synthesised by solid state reaction via a salt flux route and investigated by HRTEM, SAED, and single crystal X-ray diffraction. - Highlights: • We discovered the series of RE{sub 4}O{sub 4}[AsO{sub 4}]Cl (RE = La, Pr, Nd, Sm, Eu, Gd) compounds. • The RE{sub 4}O{sub 4}[AsO{sub 4}]Cl single crystals were grown using NaCl/KCl flux. • The RE{sub 4}O{sub 4}[AsO{sub 4}]Cl structures were solved using single crystal X-ray diffraction data. • The layered RE{sub 4}O{sub 4}[AsO{sub 4}]Cl compounds were further characterized using HRTEM and SAED. • We observed an alternation of ordered-[RE{sub 4}O{sub 4}]{sup 4+} and disordered-[ClAsO{sub 4}]{sup 4–} layers. - Abstract: The new compounds RE{sub 4}O{sub 4}[AsO{sub 4}]Cl (RE = La, Pr, Nd, Sm, Eu, Gd) were synthesised by solid state reaction via a salt flux route and investigated by HRTEM, SAED, and single crystal X-ray diffraction. The samples crystallise with a tetragonal cell, space group P4{sub 2}/mnm and Z = 2. Their crystal structure consists of an alternation of [RE{sub 4}O{sub 4}]{sup 4+} and [ClAsO{sub 4}]{sup 4–} layers. The [RE{sub 4}O{sub 4}]{sup 4+} layer contains ORE{sub 4/4} tetrahedra which share common edges. The anions AsO{sub 4}{sup 3–} and Cl{sup –} are located between these layers in disordered manner. SAED and HRTEM experiments confirmed this structural model and enabled us to propose an ordered model for the [ClAsO{sub 4}]{sup 4–} layers.

36 MATERIALS SCIENCE↗

The role of chemical structure on the magnetic and electronic properties of Co{sub 2}FeAl{sub 0.5}Si{sub 0.5}/Si(111) interface

We show that Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film deposited on Si(111) has a single crystal structure and twin related epitaxial relationship with the substrate. Sub-nanometer electron energy loss spectroscopy shows that in a narrow interface region there is a mutual inter-diffusion dominated by Si and Co. Atomic resolution aberration-corrected scanning transmission electron microscopy reveals that the film has B2 ordering. The film lattice structure is unaltered even at the interface due to the substitutional nature of the intermixing. First-principles calculations performed using structural models based on the aberration corrected electron microscopy show that the increased Si incorporation in the film leads to a gradual decrease of the magnetic moment as well as significant spin-polarization reduction. These effects can have significant detrimental role on the spin injection from the Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film into the Si substrate, besides the structural integrity of this junction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Neutrino-induced reactions and neutrino scattering with nuclei in low and high neutrino energy

We reviewed present status regarding theoretical approaches for neutrino-induced reactions and neutrino scattering. With a short introduction of relevant data, our recent calculations by distorted-wave Born approximation (DWBA) for quasielastic region are presented for MiniBooNE data. We also discussed that one step-process estimated by the DWBA is comparable to the two-step process, which has been usually used in the neutrino-nucleosynthesis. For much higher energy neutrino data, such as NOMAD data, elementary process approach was shown to be useful instead of using complicated nuclear models. But, in the low energy region, detailed nuclear structure model, such as QRPA and shell model, turn out to be inescapable to explain the reaction data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Generating a debris model for a structure

A computer generates a computer model based on the output data of a finite element analysis (FEA) performed on a structure that has experienced a break up event. The output data is processed to generate a debris model. The debris model comprises data defining the structure, as well as any fragments or pieces of debris caused by forces exerted on the structure during the break up event. The debris model can then be utilized as input data to generate other computer models.

Laverty, Richard Rion↗

Microstructure and magnetic properties of ultrathin FePt granular films

FePt granular films with grain size smaller than 10 nm are promising candidates for storage media used in the next generation heat-assisted magnetic recording technology. However, FePt films show degraded magnetic properties when the grain size is reduced to this scale, which cannot be explained solely by the finite size theory. In this study, we explored the structural cause of property degradation by employing advanced electron microscopy and atomistic modeling. Structural features unique to the nanostructured FePt granular films at significantly reduced grain sizes of 2~8 nm were studied by high-resolution scanning transmission electron microscopy with geometric aberrations corrected up to the third order. Two critical structural parameters, the threshold grain size corresponding to the upper size limit of the FePt grains with zero chemical ordering and the sub-nanometer thin interfacial impurity at grain boundaries, were identified. A new atomistic model was developed to correlate these structural characteristics with key magnetic properties such as Curie temperature, saturation magnetization, magnetocrystalline anisotropy, and their grain-to-grain variation. The model shows good agreement with the experimental magnetic data and explains the gap in magnetic properties between the bulk and nanostructured FePt.

36 MATERIALS SCIENCE↗

Ultra-flexible framework breathing in response to dehydration in liskeardite, [(Al,Fe){sub 16}(AsO{sub 4}){sub 9}(OH){sub 21}(H{sub 2}O){sub 11}]·26H{sub 2}O, a natural open-framework compound

Dehydration of the natural open-framework compound, liskeardite, [(Al,Fe){sub 16}(AsO{sub 4}){sub 9}(OH){sub 21}(H{sub 2}O){sub 11}]·26H{sub 2}O, is accompanied by a change in the sign of the thermal expansion from positive to negative above room temperature, and at ~100 °C the structure undergoes a dramatic 2D contraction by co-operative rotation of heteropolyhedral columns that constitute the framework walls. Monoclinic liskeardite, I112 with a≈b≈24.7 Å, c ≈7.8 Å and β≈90° is transformed to a tetragonal phase, I-4 with a≈20.6 Å, c ≈7.7 Å. The associated 30% decrease in volume is unprecedented in inorganic microporous compounds. The flexibility of the contraction is related to the double-hinged nature of the column rotations about [001]. Octahedra in adjacent columns are interconnected by corner-sharing with the two pairs of anions forming opposing edges of AsO{sub 4} tetrahedra, so a double-hinged rotation mechanism operates. Thermal analysis and mass spectroscopic results for liskeardite show that the phase transition at ~100 °C is related to removal of the channel water. The tetragonal phase shows exceptionally large NTE behaviour. Over the temperature range 148–178 the NTE along a and b is close to linear with a magnitude of the order of −900×10{sup −6} °C{sup −1}. The contraction along the channel direction is smaller but still appreciable at −200×10{sup −6} °C{sup −1}. - Graphical abstract: Structure of the collapsed liskeardite framework, formed on dehydration above 100 °C. - Highlights: • The thermal expansion of the mineral liskeardite changes + to − above ambient. • Dehydration at 100 °C results in a record reversible 30% volume reduction. • In situ synchrotron XRD has led to a structural model for the dehydrated phase. • Framework breathing flexibility is attributed to a double-hinge rotation mechanism. • The dehydrated phase shows unprecedented -ve expansion for inorganic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Well-Defined Nanoparticle Electrocatalysts for the Refinement of Theory

The relationship between experiment and theory in electrocatalysis is one of profound importance. Until fairly recently, the principal role of theory in this field was interpreting experimental results. Over the course of the past decade (roughly the period covered by this review), however, that has begun to change, with theory now frequently leading the design of electrocatalytic materials. Though rewarding, this has not been a particularly easy union. For one thing, experimentalists and theorists have to come to grips with the fact that they rely on different models. Theorists make predictions based on individual, perfect structural models, while experimentalists work with more complex and heterogeneous ensembles of electrocatalysts. As discussed in this review, computational capabilities have improved in recent years, so that theory is better represented by the structures that experimentalists are able to prepare. Likewise, synthetic chemists are able to make ever more complex electrocatalysts with high levels of control, which provide a more extensive palette of materials for testing theory. Finally, the goal of this review is to highlight research from the last ~10 years that focuses on carefully controlled electrocatalytic experiments which, in combination with theoretical predictions, bring us closer to bridging the gap between real catalysts and computational models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unexpected structural softening of interstitial boron solid solution WB{sub 3+x}

Using first-principles calculations, we reveal an unexpected structural softening in a recently proposed WB{sub 3+x} structural model that tries to explain the X-ray diffraction, high resolution TEM, pressure dependence of the normalized lattice c/a ratio, and hardness experimental results of the synthesized tungsten boride compounds with a nominal composition WB{sub 4}. We show that the interstitial boron in WB{sub 3+x}, which was proposed to strengthen the covalent bonding network, unexpectedly weakens the atomic bonding, resulting in a large reduction of its indentation strength to well below that of WB{sub 3}. This is in direct contradiction to the experimental results showing that synthesized WB{sub 4} is harder than WB{sub 3}. The unusual structural softening is attributed to the unique three-center covalent bonding formed by the interstitial boron atoms that can easily deform under indentation. Our results show that the proposed interstitial boron solid solution WB{sub 3+x} structure is incompatible with experimental results, which calls for further investigations to determine the crystal structure of the synthesized WB{sub 4}.

36 MATERIALS SCIENCE↗

Biophysical studies and modelling indicate the binding preference of TAZ WW domain for LATS1 PPxY motif

Highlights: • TAZ WW domain preferentially binds to the second PPxY motif of LATS1. • Modelled structure of TAZ WW-PPxY2 is stable and adopts the typical WW fold. • Binding site residues, L143 and T150 reduce the binding affinity of TAZ WW domain. The Hippo tumor suppressor pathway is an important regulator of cell proliferation and apoptosis, and signal transduction occurs through phosphorylation of the effector protein TAZ by the serine/threonine kinase LATS1/2. Here, we report the biophysical and computational studies to characterize the interaction between TAZ and LATS1/2 through WW domain-PPxY motif binding. We show that the TAZ WW domain exhibits a binding preference for the second of the two PPxY motifs of LATS1 in vitro. We modelled the structure of the domain in complex with LATS1 PPxY2 peptide and, through molecular dynamics simulations, show that WW domain-PPxY2 complex is stable with some flexibility in the peptide region. Next, we predict and verify that L143 and T150 of the WW domain are important for TAZ binding with the PPxY2 peptide using mutational and isothermal titration calorimetric studies. Furthermore, we suggest that the electrostatic potential of charged residues within the binding pocket may influence the ligand affinity among otherwise highly similar WW domains.

60 APPLIED LIFE SCIENCES↗

Anisotropic In distribution in InGaN core-shell nanowires

In this work, we investigate the local atomic structure of defect-free homogeneous and self-organized core-shell structure nanowires by means of X-ray Absorption Fine Structure (XAFS) Spectroscopy at the In L{sub III} and K edges and Multiwavelength Anomalous Diffraction. The results are interpreted by comparison of the experimental data with X-ray absorption calculations carried out with ab initio structural models. Extended-XAFS data analysis at In K-edge shows an anisotropic In distribution in the second nearest neighbors pointing out to a deviation from randomness in In distribution for the core-shell sample.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Syntheses, structures, and ionic conductivities of perovskite-structured lithium–strontium–aluminum/gallium–tantalum-oxides

The ionic conductivities of new perovskite-structured lithium–strontium–aluminum/gallium–tantalum oxides were investigated. Solid solutions of the new perovskite oxides, (Li{sub x}Sr{sub 1−x})(Al{sub (1−x)/2}Ta{sub (1+x)/2})O{sub 3} and (Li{sub x}Sr{sub 1−x})(Ga{sub (1−x)/2}Ta{sub (1+x)/2})O{sub 3}, were synthesized using a ball-milled-assisted solid-state method. The partial substitution of the smaller Ga{sup +3} for Ta{sup +5} resulted in new compositions, the structures of which were determined by neutron diffraction measurements using a cubic perovskite structural model with the Pm−3m space group. Vacancies were introduced into the Sr(Li) sites by the formation of solid solutions with compositions (Li{sub x}Sr{sub 1−x−y}☐{sub y})(Ga{sub [(1−x)/2]−y}Ta{sub [(1+x)/2]+y})O{sub 3}, where the composition range of 0≤y≤0.20 was examined for x=0.2 and 0.25. The highest conductivity, 1.85×10{sup −3} S cm{sup −1} at 250 °C, was obtained for (Li{sub 0.25}Sr{sub 0.625}☐{sub 0.125})(Ga{sub 0.25}Ta{sub 0.75})O{sub 3} (x=0.25, y=0.125). Enhanced ionic conductivities were achieved by the introduction of vacancies at the A-sites. - Graphical abstract: Novel lithium-conducting oxides with the cubic perovskite structure (Li{sub x}Sr{sub 1−x−y}☐{sub y})(Ga{sub [(1−x)/2]−y}Ta{sub [(1+x)/2]+y})O{sub 3} provide a specific solid-solution region with various x and y values, exhibiting the highest ionic conductivity (1.85 S cm{sup −1} at 250 °C) for (Li{sub 0.25}Sr{sub 0.625}☐{sub 0.125})(Ga{sub 0.25}Ta{sub 0.75})O{sub 3} (x=0.25, y=0.125 in (Li{sub x}Sr{sub 1−x−y}☐{sub y})(Ga{sub [(1−x)/2]−y}Ta{sub [(1+x)/2]+y})O{sub 3}). The vacancies (☐) introduced into the A-sites contribute to the enhancement of lithium diffusion in the perovskite structure because of the enlargement of the bottleneck size and suppression of the interaction between lithium and oxygen. - Highlights: • The perovskite-structured novel Li–Sr–Al/Ga–Ta oxides were investigated. • The Ga cation offers a larger bottleneck by increasing the B−O bond length. • The greater conductivity was observed upon Ga-containing perovskite. • The ionic conductivity was improved by the introduction of vacancies into A-site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗