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At least 469 records · Page 26

Defining the scope for altering rice leaf anatomy to improve photosynthesis: a modelling approach

Summary Leaf structure plays an important role in photosynthesis. However, the causal relationship and the quantitative importance of any single structural parameter to the overall photosynthetic performance of a leaf remains open to debate. In this paper, we report on a mechanistic model, eLeaf, which successfully captures rice leaf photosynthetic performance under varying environmental conditions of light and CO 2 . We developed a 3D reaction‐diffusion model for leaf photosynthesis parameterised using a range of imaging data and biochemical measurements from plants grown under ambient and elevated CO 2 and then interrogated the model to quantify the importance of these elements. The model successfully captured leaf‐level photosynthetic performance in rice. Photosynthetic metabolism underpinned the majority of the increased carbon assimilation rate observed under elevated CO 2 levels, with a range of structural elements making positive and negative contributions. Mesophyll porosity could be varied without any major outcome on photosynthetic performance, providing a theoretical underpinning for experimental data. eLeaf allows quantitative analysis of the influence of morphological and biochemical properties on leaf photosynthesis. The analysis highlights a degree of leaf structural plasticity with respect to photosynthesis of significance in the context of attempts to improve crop photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗

First principles modeling of microscopic scintillation mechanisms using a Many-Body Green’s function approach (Final Report)

In 2010, we started the first lifecycle of a project on first principles modeling of microscopic unit processes that occur during scintillation in order to bring about a capability of formulating physics-based reaction-diffusion models that can predict scintillator light yield and explain their non-proportional response to the energy of incident ionizing radiation, with the hope that this will accelerate materials discovery that can mitigate this problem. During the ensuing years we focused on investigating from first principles the elementary quantum mechanical processes leading to polaron formation and exciton self-trapping in scintillators and identify the microscopic pathways leading to their transport. The effort to derive the master equation for carrier and exciton transport in realistic scintillators materials from first principles constitutes a challenge that requires an extensive background in various areas of computational physics. Previous theoretical investigations involved significant approximations and were limited in their scope. Most notably, the standard workhorse of the computational material scientist, density-functional theory, fails in describing the localized nature of self-trapped carriers as well as the electronic structure of rare-earth dopants. Advances in both algorithms and computational resources however, have rendered a comprehensive and accurate approach feasible. This has been amply demonstrated by the results produced by us during the first lifecycle of this project, which impressed upon the reviewers of the Independent Project Review: “The Review Team agreed, and commented that ’amazing and excellent progress had been made to date.’ The researchers tried and did improve the technology to advance the state of the art and show that it was adequate for the project.” In the following, we detail the progress achieved during each year of the project. We conclude by a final section where all our main achievements are summarized.

36 MATERIALS SCIENCE↗

Evaluation of Al3Mg2 precipitates and Mn-rich phase in aluminum-magnesium alloy based on scanning transmission electron microscopy imaging

Scanning transmission electron microscopy (STEM) and energy dispersive X-ray spectroscopy (EDS) were used to observe intergranular and intragranular -phase (Al3Mg2) formation and growth in as-received sample and long-term (~ 1 year) thermally treated samples of 5083-H131 alloy. Rod-shaped and equiaxed particles rich in Mn, Fe, and Cr were present in the as-received and heat treated samples. The -phase precipitated along grain boundaries as well as around and between preexisting Mn-Fe-Cr rich particles. The measured thickness of -phase along grain boundaries was lower than Zener Hillert diffusion model predicted value and the potential reasons were theoretically analyzed. Dislocation networks, grain boundaries, and different preexisting particles were observed to contribute to Mg diffusion and -phase precipitation.

Zhu, Yakun↗

Na ion dynamics in P2-Na x [Ni 1/3 Ti 2/3 ]O 2 : a combination of quasi-elastic neutron scattering and first-principles molecular dynamics study

In this work, the P2-type layered material Na 2/3 [Ni 1/3 Ti 2/3 ]O 2 was studied as a promising bi-functional electrode material for sodium-ion batteries. To assess the electrochemical performance of this material, we investigated the diffusion mechanism as well as ionic and electronic conductivity with a combination of experimental and computational techniques. The quasi-elastic neutron scattering (QENS) experiments and first-principles molecular dynamics (FPMD) simulations were performed to identify the diffusion mechanism. The QENS data showed that Na ion diffusion can be well described by the Singwi–Sjölander jump diffusion model, where the obtained mean jump length matched the distances between the neighboring edge-share and face-share Na sites. FPMD predicted diffusivity values similar to those from QENS. The computed composition dependence of ionic and electronic conductivity of Na x [Ni 1/3 Ti 2/3 ]O 2 suggested that electronic conductivity changes significantly when x deviates from 2/3 as the redox couple of Ni and Ti is activated, while the change of ionic conductivity with x is relatively small.

36 MATERIALS SCIENCE↗

Testing nonlocal models of electron thermal conduction for magnetic and inertial confinement fusion applications

Three models for nonlocal electron thermal transport are here compared against Vlasov-Fokker-Planck (VFP) codes to assess their accuracy in situations relevant to both inertial fusion hohlraums and tokamak scrape-off layers. The models tested are (i) a moment-based approach using an eigenvector integral closure (EIC) originally developed by Ji, Held, and Sovinec [Phys. Plasmas 16, 022312 (2009)]; (ii) the non-Fourier Landau-fluid (NFLF) model of Dimits, Joseph, and Umansky [Phys. Plasmas 21, 055907 (2014)]; and (iii) Schurtz, Nicolaï, and Busquet’s [Phys. Plasmas 7, 4238 (2000)] multigroup diffusion model (SNB). We find that while the EIC and NFLF models accurately predict the damping rate of a small-amplitude temperature perturbation (within 10% at moderate collisionalities), they overestimate the peak heat flow by as much as 35% and do not predict preheat in the more relevant case where there is a large temperature difference. The SNB model, however, agrees better with VFP results for the latter problem if care is taken with the definition of the mean free path. Additionally, we present for the first time a comparison of the SNB model against a VFP code for a hohlraum-relevant problem with inhomogeneous ionisation and show that the model overestimates the heat flow in the helium gas-fill by a factor of ∼2 despite predicting the peak heat flux to within 16%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Diffusion of Sn donors in β-Ga 2 O 3

Diffusion of the n-type dopant Sn in β-Ga 2 O 3 is studied using secondary-ion mass spectrometry combined with hybrid functional calculations. The diffusion of Sn from a Sn-doped bulk substrate with surface orientation (001) into an epitaxial layer is observed after heat treatments in the temperature range of 1050–1250 °C. Calculated formation energies of Sn-related and intrinsic defects show that the migration of Sn is mediated by Ga vacancies ( V Ga ) through the formation and dissociation of intermittent mobile V Ga Sn Ga complexes. The evolution of the Sn concentration vs depth profiles after heat treatments can be well described by a reaction–diffusion model. Using model parameters guided by the hybrid functional calculations, we extract a V Ga Sn Ga complex migration barrier of 3.0 ± 0.4 eV with a diffusion coefficient of 2 × 10 –1 cm 2 /s. The extracted migration barrier is consistent with our theoretical predictions using the nudged elastic band method, which shows migration barriers of 3.42, 3.15, and 3.37 eV for the [100], [010], and [001] directions, respectively.

36 MATERIALS SCIENCE↗

First-principles investigation of lanthanides diffusion in HCP zirconium via vacancy-mediated transport

The diffusion of lanthanide fission products plays an important role in the growth of the fuel-cladding chemical interaction (FCCI) region in metallic fuels. The use of a Zr interdiffusion barrier may mitigate the transport of lanthanides from the fuel to the cladding, but the efficacy of such a liner is not yet known. In this paper, the stability and vacancy-mediated diffusion of La, Ce, Pr, and Nd in hexagonal close-packed (HCP) Zr is investigated via density functional theory (DFT) calculations and self-consistent mean field (SCMF) analysis. DFT is used to calculate the formation, binding, and migration energies of vacancies and vacancy-solute pairs. The DFT energetics are used in the KineCluE code to calculate the Onsager transport coefficients. La is found to be the fastest diffusing species in HCP Zr and experiences an almost isotropic diffusion behavior. The other three species (Ce, Pr, and Nd) demonstrate anisotropic diffusion where the diffusion in the basal planes is significantly faster than that along the c-axis. Further, the calculated lanthanide diffusivities in HCP Zr are fitted to an Arrhenius relation and the activation energies and prefactors are reported for the first time. Furthermore, the vacancy drag and the segregation tendencies were analyzed using the calculated off-diagonal transport coefficients. According to our vacancy-mediated diffusion model, lanthanides are expected to be enriched at vacancy sinks at low temperatures, while at high temperatures, lanthanides are depleted at sinks and will preferably diffuse into the bulk. The enrichment/depletion transition temperature depends on the diffusion direction (basal or axial) and hence will be controlled by the grain texture and orientation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Tritium Formation and Mitigation in High Temperature Reactors

Tritium is a radiologically active isotope of hydrogen. It is formed in nuclear reactors by neutron absorption and ternary fission events and can subsequently escape into the environment. In order to prevent the tritium contamination of proposed reactor buildings and surrounding sites, this paper examines the root causes and potential solutions for the production of this radionuclide, including materials selection and inert gas sparging. A model is presented that can be used to predict permeation rates of hydrogen through metallic alloys at temperatures from 450–750°C. Results of the diffusion model are presented for one steady-state value of tritium production in the reactor.

42 ENGINEERING↗

Turbulence radiation coupling in boundary layers of heavy-duty diesel engines

The lack of accurate submodels for in-cylinder radiation and heat transfer has been identified as a key shortcoming in developing truly predictive, physics-based computational fluid dynamics (CFD) models that can be used to develop combustion systems for advanced high-efficiency, low-emissions engines. Recent measurements of wall layers in engines show discrepancies of up to 100% with respect to standard CFD boundary-layer models. And recent analysis of in-cylinder radiation based on the most recent spectral property databases and high-fidelity radiative transfer equation (RTE) solvers has shown that at operating pressures and exhaust-gas recirculation levels typical of modern heavy-duty compression-ignition engines, radiative emission can be as high as 40% of the wall heat losses, that molecular gas radiation (mainly CO2 and H2O) can be more important than soot radiation, and that a significant fraction of the emitted radiation can be reabsorbed before reaching the walls. That is, radiation not only contributes to heat losses, but also changes the in-cylinder temperature distribution, which in turn affects combustion and emissions. The goal of this research is to develop models that explicitly account for the potentially strong coupling between radiative and turbulent boundary layer heat transfer. For example, for optically thick conditions, a simple diffusion model might be formulated in terms of an absorption-coefficient-dependent turbulent Prandtl number.

Sircar, Arpan↗

Adaptive Sampling of Large Deviations

We introduce and test an algorithm that adaptively estimates large deviation functions characterizing the fluctuations of additive functionals of Markov processes in the long-time limit. These functions play an important role for predicting the probability and pathways of rare events in stochastic processes, as well as for understanding the physics of nonequilibrium systems driven in steady states by external forces and reservoirs. The algorithm uses methods from risk-sensitive and feedback control to estimate from a single trajectory a new process, called the driven process, known to be efficient for importance sampling. Its advantages compared to other simulation techniques, such as splitting or cloning, are discussed and illustrated with simple equilibrium and nonequilibrium diffusion models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Tritium Formation and Mitigation in High-Temperature Reactors

Tritium is a radiologically active isotope of hydrogen. It is formed in nuclear reactors by neutron absorption and ternary fission events and can subsequently escape into the environment. To prevent the tritium contamination of proposed reactor buildings and surrounding sites, this study examines the root causes and potential mitigation strategies for permeation of tritium (such as: materials selection, inert gas sparging, etc...). A model is presented that can be used to predict permeation rates of hydrogen through metallic alloys at temperatures from 450–750 degrees C. Results of the diffusion model are presented for a steady production of tritium

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Tritium Formation and Mitigation in High-Temperature Reactor Systems

Tritium is a radiologically active isotope of hydrogen. It is formed in nuclear reactors by neutron absorption and ternary fission events and can subsequently escape into the environment. To prevent the tritium contamination of proposed reactor buildings and surrounding sites, this study examines the root causes and potential mitigation strategies for permeation of tritium (such as: materials selection, inert gas sparging, etc...). A model is presented that can be used to predict permeation rates of hydrogen through metallic alloys at temperatures from 450–750 degrees C. Results of the diffusion model are presented for a steady production of tritium

42 ENGINEERING↗

Solution verification, goal-oriented adaptive methods for stochastic advection–diffusion problems

A goal-oriented analysis of linear, stochastic advection–diffusion models is presented which provides both a method for solution verification as well as a basis for improving results through adaptation of both the mesh and the way random variables are approximated. A class of model problems with random coefficients and source terms is cast in a variational setting. Specific quantities of interest are specified which are also random variables. A stochastic adjoint problem associated with the quantities of interest is formulated and a posteriori error estimates are derived. These are used to guide an adaptive algorithm which adjusts the sparse probabilistic grid so as to control the approximation error. Numerical examples are given to demonstrate the methodology for a specific model problem.

97 MATHEMATICS AND COMPUTING↗

BIPOLAR JETS LAUNCHED FROM ACCRETION DISKS. II. THE FORMATION OF ASYMMETRIC JETS AND COUNTER JETS

We investigate the jet launching from accretion disks, in particular the formation of intrinsically asymmetric jet/counter jet systems. We perform axisymmetric MHD simulations of the disk-jet structure on a bipolar computational domain covering both hemispheres. We apply various models such as asymmetric disks with (initially) different scale heights in each hemisphere, symmetric disks into which a local disturbance is injected, and jets launched into an asymmetric disk corona. We consider both a standard global magnetic diffusivity distribution and a novel local diffusivity model. Typical disk evolution first shows substantial disk warping and then results in asymmetric outflows with a 10%-30% mass flux difference. We find that the magnetic diffusivity profile is essential for establishing a long-term outflow asymmetry. We conclude that bipolar asymmetry in protostellar and extragalactic jets can indeed be generated intrinsically and maintained over a long time by disk asymmetries and the standard jet launching mechanism.

79 ASTRONOMY AND ASTROPHYSICS↗

Micro-Continuum Modeling of Nuclear Waste Glass Corrosion

The purpose of this contribution is to report on preliminary nano-continuum scale modeling of nuclear waste glass corrosion. The focus of the modeling is an experiment involving a French glass SON68 specimen leached for 25 years in a granitic environment (Guittonneau et al., 2011; Gin et al., 2011; Gin et al., 2013). The 25 year experiment carried out by French scientists offers a unique opportunity to examine the controls on the rate of nuclear glass corrosion under controlled experimental conditions using a borosilicate glass of the kind widely considered for nuclear waste storage. The long term experiment makes it possible to move beyond the initial rate stage, with direct measurements of the longer term, residual rates of corrosion. Important in this regard is whether the rate of corrosion shows a parabolic dependence on time, as would be expected from a conventional diffusion model in which the reaction products (amorphous silica-rich gel) create a diffusion barrier that grows in width over time, or whether the time dependence is linear (Guittonneau et al., 2011). A linear dependence on time would call into question the model of a Passive Reactive Interface (PRI) presented by Cailleteau et al. (2008), although it does not entirely preclude such a model if the interface maintains a constant width over time (forming at the leading edge next to the pristine glass and dissolving at the trailing edge). The leachate concentration measurements collected every 56 days over 25 years by Guittonneau et al. (2011) provide data to constrain the long term corrosion rate and its time dependence.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Constraining the Varied Response of Northern Hemisphere Winter Circulation Waviness to Climate Change

Abstract While a large latitudinal displacement of the westerly jet brings about disproportionate socioeconomic impacts over Northern Hemisphere midlatitude continents, it is not well understood as to whether the winter circulation will become wavier or less in response to climate change. Here, using observations and large ensembles of climate models, we show that changes in atmospheric waviness can be estimated from the optimal structures of the westerly jet for wavier circulation, which are obtained from an advection‐diffusion model. Thus, the changes in westerly jet structure in climate models under climate change provide a physical constraint on changes in atmospheric waviness, indicating that the North Atlantic wave activity will experience a robust decline in a warmer climate, while future North Pacific wave activity is obscured by model uncertainty rather than internal variability. These findings highlight the changes to jet stream structure as a constraint for regional circulation waviness in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

Generative Thermodynamic Computing

Here, we introduce a generative modeling framework for thermodynamic computing, in which structured data are synthesized from noise by the natural time evolution of a physical system governed by Langevin dynamics. While conventional diffusion models use neural networks to perform denoising, here the information needed to generate structure from noise is encoded by the dynamics of a thermodynamic system. Training proceeds by maximizing the probability with which the computer generates the reverse of a noising trajectory, which ensures that the computer generates data with minimal heat emission. We demonstrate this framework within a digital simulation of a thermodynamic computer. If realized in analog hardware, such a system would function as a generative model that produces structured samples without the need for artificially injected noise or active control of denoising.

Whitelam, Stephen [Lawrence Berkeley National Labo↗

Chemistry and Formation of the Beilby Layer During Polishing of Fused Silica Glass

The chemical characteristics and the proposed formation mechanisms of the modified surface layer (called the Beilby layer) on polished fused silica glasses are described. Fused silica glass samples were polished using different slurries, polyurethane pads, and at different rotation rates. The concentration profiles of several key contaminants, such as Ce, K, and H, were measured in the near surface layer of the polished samples using Secondary Ion Mass Spectroscopy (SIMS). The penetration of K, originating from KOH used for pH control during polishing, decreased with increase in polishing material removal rate. In contrast, penetration of the Ce and H increased with increase in polishing removal rate. In addition, Ce penetration was largely independent of the other polishing parameters (e.g., particle size distribution and the properties of the polishing pad). The resulting K concentration depth profiles are described using a two-step diffusion process: (1) steady-state moving boundary diffusion (due to material removal during polishing) followed by (2) simple diffusion during ambient postpolishing storage. Using known alkali metal diffusion coefficients in fused silica glass, this diffusion model predicts concentration profiles that are consistent with the measured data at various polishing material removal rates. On the other hand, the observed Ce profiles are inconsistent with diffusion based transport. Rather we propose that Ce penetration is governed by the ratio of Ce–O–Si and Si–O–Si hydrolysis rates; where this ratio increases with interface temperature (which increases with polishing material removal rate) resulting in greater Ce penetration into the Beilby layer. Calculated Ce surface concentrations using this mechanism are in good agreement to the observed change in measured Ce surface concentrations with polishing material removal rate. In conclusion, these new insights into the chemistry of the Beilby layer, combined together with details of the single particle removal function during polishing, are used to develop a more detailed and quantitative picture of the polishing process and the formation of the Beilby layer.

36 MATERIALS SCIENCE↗