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Fully consistent Eulerian Monte Carlo fields method for solving probability density function transport equations in turbulence modeling
The probability density function (PDF) transport equation method is a sophisticated model for the closure of turbulent mixing and turbulent reactive flows. An efficient solution approach for solving the PDF transport equation has been vital for the method to be widely used in applications. The Eulerian Monte Carlo fields (EMCF) method has been developed to solve the PDF transport equation efficiently for decades. A recent work by Wang et al. revealed a serious issue of the EMCF method for not being fully consistent with the PDF transport equation for which the method is designed to solve. This work advances the state of the art by introducing fully consistent EMCF methods for solving the PDF transport equation. The fully consistent EMCF formulations are derived for two different PDF equation forms. The consistency of the EMCF formulations is mathematically confirmed by examining the derived moment transport equations from the EMCF formulations and from the PDF transport equation. The method of manufactured solutions is employed to further verify the consistency and convergence of the different EMCF formulations numerically. The newly introduced EMCF formulations bring the EMCF method to full consistency with the PDF transport equations for the first time.
Advances on statistical/thermodynamical models for unpolarized structure functions
During the eights and nineties many statistical/thermodynamical models were proposed to describe the nucleons' structure functions and distribution of the quarks in the hadrons. Most of these models describe the compound quarks and gluons inside the nucleon as a Fermi / Bose gas respectively, confined in a MIT bag with continuous energy levels. Another models considers discrete spectrum. Some interesting features of the nucleons are obtained by these models, like the sea asymmetries {sup -}d/{sup -}u and {sup -}d-{sup -}u.
Call for Participation: Collaborative Benchmarking of Functional-Structural Root Architecture Models. The Case of Root Water Uptake
Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models, such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore, defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute toward improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.
Peculiarities of beta functions in sigma models
In this paper we consider perturbation theory in generic two-dimensional sigma models in the so-called first-order formalism, using the coordinate regularization approach. Our goal is to analyze the first-order formalism in application to β functions and compare its results with the standard geometric calculations. Already in the second loop, we observe deviations from the geometric results that cannot be explained by the regularization/renormalization scheme choices. Moreover, in certain cases the first-order calculations produce results that are not symmetric under the classical diffeomorphisms of the target space. Although we could not present the full solution to this remarkable phenomenon, we found some indirect arguments indicating that an anomaly similar to that established in supersymmetric Yang-Mills theory might manifest itself starting from the second loop. We discuss why the difference between two answers might be an infrared effect, similar to that in β functions in supersymmetric Yang-Mills theories.
Water balance model (WBM) v.1.0.0: a scalable gridded global hydrologic model with water-tracking functionality
Abstract. This paper describes the University of New Hampshire Water Balance Model, WBM, a process-based gridded global hydrologic model that simulates the land surface components of the global water cycle and includes water extraction for use in agriculture and domestic sectors. The WBM was first published in 1989; here, we describe the first fully open-source WBM version (v.1.0.0). Earlier descriptions of WBM methods provide the foundation for the most recent model version that is detailed here. We present an overview of the model functionality, utility, and evaluation of simulated global river discharge and irrigation water use. This new version adds a novel suite of water source tracking modules that enable the analysis of flow-path histories on water supply. A key feature of WBM v.1.0.0 is the ability to identify the partitioning of sources for each stock or flux within the model. Three different categories of tracking are available: (1) primary inputs of water to the surface of the terrestrial hydrologic cycle (liquid precipitation, snowmelt, glacier melt, and unsustainable groundwater); (2) water that has been extracted for human use and returned to the terrestrial hydrologic system; and (3) runoff originating from user-defined spatial land units. Such component tracking provides a more fully transparent model in that users can identify the underlying mechanisms generating the simulated behavior. We find that WBM v.1.0.0 simulates global river discharge and irrigation water withdrawals well, even with default parameter settings, and for the first time, we are able to show how the simulation arrives at these fluxes by using the novel tracking functions.
Large eddy simulation of a reacting spray flame with multiple realizations under compression ignition engine conditions
An n-dodecane spray flame (Spray A from Engine Combustion Network) was simulated using a detailed combustion model along with a dynamic structure LES model to evaluate its performance at engine-relevant conditions and understand the transient behavior of this turbulent flame. The liquid spray was treated with a traditional Lagrangian method and the gas-phase reaction was modeled using a detailed combustion model. A 103-species skeletal mechanism was used for the n-dodecane chemical kinetic model. Significantly different flame structures and ignition processes are observed for the LES compared to those of RANS predictions. The LES data suggests that the first ignition initiates in lean mixture and propagates to rich mixture, and the main ignition happens in rich mixture, preferable less than 0.14 in mixture fraction space. LES was observed to have multiple ignition spots in the mixing layer simultaneously while the main ignition initiates in a clearly asymmetric fashion. The temporal flame development also indicates the flame stabilization mechanism is auto-ignition controlled and modulated by flame propagation. Soot predictions by LES present much better agreement with experiments compared to RANS both qualitatively and quantitatively. Multiple realizations for LES were performed to understand the realization to realization variation and to establish best practices for ensemble-averaging diesel spray flames. The relevance index analysis suggests that an average of 2 and 5 realizations can reach 99\% of similarity to the target average of 16 realizations on the temperature and mixture fraction fields, respectively. However, more realizations are necessary for OH and soot mass fraction due to their high fluctuations.
From model to crop: functional characterization of SPL8 in M. truncatula led to genetic improvement of biomass yield and abiotic stress tolerance in alfalfa
Biomass yield, salt tolerance and drought tolerance are important targets for alfalfa ( Medicago sativa L. ) improvement. Medicago truncatula has been developed into a model plant for alfalfa and other legumes. By screening a Tnt1 retrotransposon-tagged M. truncatula mutant population, we identified three mutants with enhanced branching. Branch development determines shoot architecture which affects important plant functions such as light acquisition, resource use and ultimately impacts biomass production. Molecular analyses revealed that the mutations were caused by Tnt1 insertions in the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8) gene. The M. truncatula spl8 mutants had increased biomass yield, while overexpression of SPL8 in M. truncatula suppressed branching and reduced biomass yield. Scanning electron microscopy (SEM) analysis showed that SPL8 inhibited branching by directly suppressing axillary bud formation. Based on the M. truncatula SPL8 sequence, alfalfa SPL8 (MsSPL8) was cloned and transgenic alfalfa plants were produced. MsSPL8 down-regulated or up-regulated alfalfa plants exhibited similar phenotypes to the M. truncatula mutants or overexpression lines, respectively. Specifically, the MsSPL8 down-regulated alfalfa plants showed up to 43% increase in biomass yield in the first harvest. The impact was even more prominent in the second harvest, with up to 86% increase in biomass production compared to the control. Furthermore, downregulation of MsSPL8 led to enhanced salt and drought tolerance in transgenic alfalfa. Results from this research offer a valuable approach to simultaneously improve biomass production and abiotic stress tolerance in legumes.
Towards a liana plant functional type for vegetation models
Lianas (woody climbers) are crucial components of tropical forests and they have been increasingly recognized to have profound effects on tropical forest carbon dynamics. Despite their importance, lianas' representation in vegetation models remains limited, partly due to the complexity of liana-tree dynamics and the diversity in liana life history strategies. This paper provides a comprehensive review of advances and challenges for mechanistically representing lianas in forest ecosystem models and a proposed path towards effectively representing lianas in these models. Defining a liana plant functional type is a significant challenge because of the high morphological and physiological diversity amongst liana species, and because of their structural association with trees. Here, we identify critical liana traits that likely should contribute to establishing a liana plant functional type, along with key processes to properly represent lianas in ecosystem models. Subsequently, we discuss a variety of possible liana implementation strategies with their associated strengths, limitations, computational costs and data requirements. A fundamental redesign of the tree-centric demographic vegetation models seems appropriate to accommodate the unique growth and competition strategies of lianas. We illustrate the potential of such models with a single-site case study where we disentangle putative mechanisms of liana increasing abundance. Furthermore, we underscore the critical need for comprehensive liana demographic and functional data (including long-term, physiological, and pantropical observations) for the qualitative implementation and evaluation in the proposed modeling efforts. Currently, there is a scarcity of liana data and the data that do exist have a neotropical bias. We finally introduce a new liana functional trait database that can centralize existing liana trait data, incentivize improved data gathering and thus facilitate model development and scientific analyses.
Numerical Solution of 3D Poisson-Nernst-Planck Equations Coupled with Classical Density Functional Theory for Modeling Ion and Electron Transport in a Confined Environment
We have developed efficient numerical algorithms for the solution of 3D steady-state Poisson-Nernst-Planck equations (PNP) with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are discretized by finite difference scheme and solved iteratively by Gummel method with relaxation. The Nernst-Planck equations are transformed into Laplace equations through the Slotboom transformation. Algebraic multigrid method is then applied to efficiently solve the Poisson equation and the transformed Nernst-Planck equations. A novel strategy for calculating excess chemical potentials through fast Fourier transforms is proposed which reduces computational complexity from O(N2) to O(NlogN) where N is the number of grid points. Integrals involving Dirac delta function are evaluated directly by coordinate transformation which yields more accurate result compared to applying numerical quadrature to an approximated delta function. Numerical results for ion and electron transport in solid electrolyte for Li ion batteries are shown to be in good agreement with the experimental data and the results from previous studies.
Initial stages of ITO/Si interface formation: In situ x-ray photoelectron spectroscopy measurements upon magnetron sputtering and atomistic modelling using density functional theory
Initial stages of indium tin oxide (ITO) growth on a polished Si substrate upon magnetron sputtering were studied experimentally using in-situ x-ray photoelectron spectroscopy measurements. The presence of pure indium and tin, as well as Si bonded to oxygen at the ITO/Si interface were observed. The experimental observations were compared with several atomistic models of ITO/Si interfaces. A periodic model of the ITO/Si interface was constructed, giving detailed information about the local environment at the interface. Molecular dynamics based on density functional theory was performed, showing how metal-oxygen bonds are broken on behalf of silicon-oxygen bonds. These theoretical results support and provide an explanation for the present as well as previous ex-situ and in-situ experimental observations pointing to the creation of metallic In and Sn along with the growth of SiO{sub x} at the ITO/Si interface.
(U) Validation and Optimization of a 1-Dimensional Quasi-Isentropic Compression Model Using a Functionally Graded Material Flyer Plate
The fields studying highly compressed materials have been around for many years. These fields have given birth to better understandings of the solar fusion cycle and the liquid-metallic core of Jupiter. The highest pressures achieved have been at the National Ignition Facility (NIF) and more recently, the Z-Machine. One method to achieve higher levels of compression is to use quasi-isentropic (QI) compression. In practice, this means minimizing the amount of temperature increase of the target material. In their paper, J.H. Nguyen et. al. manufactured a functionally graded material (FGM) in order to help them achieve QI compression. The aim of the study described in this paper is to validate a 1-dimensional (1D) FLAG model that uses an FGM flyer to compress a copper (Cu) target. Once validated, the density/composition profile of the FGM is varied and optimized using Markov Chain Monte Carlo, specifically using a Metropolis-Hastings algorithm to find the optimal FGM profile that minimizes the temperature increase in the copper.
In Situ Raman Mapping of Si Island Electrodes and Stress Modeling as a Function of Lithiation and Size
Si is known for cracking and delamination during electrochemical cycling of a battery due to the large volume change associated with Li insertion and extraction. However, it has been found experimentally that patterned Si island electrodes that are 200 nm thick and less than 7 μm wide can deform in a purely elastic manner. Inspired by this, we performed in situ Raman stress characterization of model poly-crystalline Si island electrodes using an electrochemical cell coupled with an immersion objective lens and designed for a short working distance. A 5 μm wide Si island electrode showed a parabolic stress profile during lithiation, while for a 15 μm Si island electrode, a stress plateau in the center of the electrode was observed. A continuum model with coupled electro-chemo-mechanical (ECM) physics was established to understand the stress measurement. A qualitative agreement was reached between modeling and experimental data, and the critical size effect could be explained by the Li diffusive flux as governed by competition between the Li concentration and hydrostatic stress gradients. Below the critical size, the stress gradient drives Li toward the edges, where the electrode volume is free to expand, while above the critical size, the stress plateau inhibits Li diffusion to the edge and forces destructive stress relief by cracking. Furthermore, this work represents a promising methodology for in situ characterization of ECM coupling in battery electrodes, with suggestions provided for further improvement.
Application of Gaussian Process Modeling to Analysis of Functional Unreliability
This paper applies Gaussian Process (GP) modeling to analysis of the functional unreliability of a “passive system.” GPs have been used widely in many ways [1]. The present application uses a GP for emulation of a system simulation code. Such an emulator can be applied in several distinct ways, discussed below. All applications illustrated in this paper have precedents in the literature; the present paper is an application of GP technology to a problem that was originally analyzed [2] using neural networks (NN), and later [3, 4] by a method called “Alternating Conditional Expectations” (ACE). This exercise enables a multifaceted comparison of both the processes and the results. Given knowledge of the range of possible values of key system variables, one could, in principle, quantify functional unreliability by sampling from their joint probability distribution, and performing a system simulation for each sample to determine whether the function succeeded for that particular setting of the variables. Using previously available system simulation codes, such an approach is generally impractical for a plant-scale problem. It has long been recognized, however, that a well-trained code emulator or surrogate could be used in a sampling process to quantify certain performance metrics, even for plant-scale problems. “Response surfaces” were used for this many years ago. But response surfaces are at their best for smoothly varying functions; in regions of parameter space where key system performance metrics may behave in complex ways, or even exhibit discontinuities, response surfaces are not the best available tool. This consideration was one of several that drove the work in [2]. In the present paper, (1) the original quantification of functional unreliability using NN [2], and later ACE [3], is reprised using GP; (2) additional information provided by the GP about uncertainty in the limit surface, generally unavailable in other representations, is discussed; (3) a simple forensic exercise is performed, analogous to the inverse problem of code calibration, but with an accident management spin: given an observation about containment pressure, what can we say about the system variables? References 1. For an introduction to GPs, see (for example) Gaussian Processes for Machine Learning, C. E. Rasmussen and C. K. I. Williams (MIT, 2006). 2. Reliability Quantification of Advanced Reactor Passive Safety Systems, J. J. Vandenkieboom, PhD Thesis (University of Michigan, 1996). 3. Z. Cui, J. C. Lee, J. J. Vandenkieboom, and R. W. Youngblood, “Unreliability Quantification of a Containment Cooling System through ACE and ANN Algorithms,” Trans. Am. Nucl. Soc. 85, 178 (2001). 4. Risk and Safety Analysis of Nuclear Systems, J. C. Lee and N. J. McCormick (Wiley, 2011). See especially §11.2.4.
A Multi-Function AAA Algorithm Applied to Frequency Dependent Line Modeling
Modeling of power distribution system components that are valid for a wide range of frequencies are crucial for highly accurate modeling of electromagnetic transient (EMT) events. This has recently become of interest due to the improvements needed for the resilient operation of distribution systems. Vector fitting (VF) is a very popular and commonly used algorithm for wide band representations of power system components in EMT simulations. In this research, we present a new multi-input rational approximation algorithm (MIAAA) and illustrate its advantages with respect to VF using examples of approximations of admittance matrices discussed in the literature. We show that MIAAA not only outperforms VF in terms of achieving better accuracy using lesser number of poles, but also has no numerical issues achieving convergence. In contrast to VF, MIAAA is not sensitive to the location of input sample points and it does not require good estimates for the location of the desired approximation poles. The novelty of this research work is the use of recent mathematical results to solve existing challenges in distribution system modeling and to develop rational approximations for power system models that intend to be optimal in terms of accuracy and performance.
Approaching periodic systems in ensemble density functional theory via finite one-dimensional models
Ensemble density functional theory (EDFT) is a generalization of ground-state DFT, which is based on an exact formal theory of finite collections of a system's ground and excited states. EDFT in various forms has been shown to improve the accuracy of calculated energy level differences in isolated model systems, atoms, and molecules, but it is not yet clear how EDFT could be used to calculate band gaps for periodic systems. We extend the application of EDFT toward periodic systems by estimating the thermodynamic limit with increasingly large finite one-dimensional 'particle in a box' systems, which approach the uniform electron gas (UEG). Using ensemble-generalized Hartree and local spin density approximation exchange-correlation functionals, we find that corrections go to zero in the infinite limit, as expected for a metallic system. However, there is a correction to the effective mass, with results comparable to other calculations on 1D, 2D, and 3D UEGs, which indicates promise for non-trivial results from EDFT on periodic systems.
Bond length and electric current oscillation of long linear carbon chains: Density functional theory, MpB model, and quantum spin transport studies
Carbon linear atomic chains attached to graphene have experimentally been produced. Motivated by these results, we study the nature of the carbon bonds in these nanowires and how it affects their electrical properties. In the present study we investigate chains with different numbers of atoms and we observe that nanowires with odd number of atoms present a distinct behavior than the ones with even numbers. Using graphene nanoribbons as leads, we identify differences in the quantum transport of the chains with the consequence that even and odd numbered chains have low and high electrical conduction, respectively. We also noted a dependence of current with the wire size. We study this unexpected behavior using a combination of first principles calculations and simple models based on chemical bond theory. From our studies, the electrons of carbon nanowires present a quasi-free electron behavior and this explains qualitatively the high electrical conduction and the bond lengths with unexpected values for the case of odd nanowires. Our study also allows the understanding of the electric conduction dependence with the number of atoms and their parity in the chain. In the case of odd number chains a proposed π-bond (MpB) model describes unsaturated carbons that introduce a mobile π-bond that changes dramatically the structure and transport properties of these wires. Our results indicate that the nature of bonds plays the main role in the oscillation of quantum electrical conduction for chains with even and odd number of atoms and also that nanowires bonded to graphene nanoribbons behave as a quasi-free electron system, suggesting that this behavior is general and it could also remain if the chains are bonded to other materials.
MUTZ-3 derived Langerhans cells in human skin equivalents show differential migration and phenotypic plasticity after allergen or irritant exposure
After allergen or irritant exposure, Langerhans cells (LC) undergo phenotypic changes and exit the epidermis. In this study we describe the unique ability of MUTZ-3 derived Langerhans cells (MUTZ-LC) to display similar phenotypic plasticity as their primary counterparts when incorporated into a physiologically relevant full-thickness skin equivalent model (SE-LC). We describe differences and similarities in the mechanisms regulating LC migration and plasticity upon allergen or irritant exposure. The skin equivalent consisted of a reconstructed epidermis containing primary differentiated keratinocytes and CD1a{sup +} MUTZ-LC on a primary fibroblast-populated dermis. Skin equivalents were exposed to a panel of allergens and irritants. Topical exposure to sub-toxic concentrations of allergens (nickel sulfate, resorcinol, cinnamaldehyde) and irritants (Triton X-100, SDS, Tween 80) resulted in LC migration out of the epidermis and into the dermis. Neutralizing antibody to CXCL12 blocked allergen-induced migration, whereas anti-CCL5 blocked irritant-induced migration. In contrast to allergen exposure, irritant exposure resulted in cells within the dermis becoming CD1a{sup −}/CD14{sup +}/CD68{sup +} which is characteristic of a phenotypic switch of MUTZ-LC to a macrophage-like cell in the dermis. This phenotypic switch was blocked with anti-IL-10. Mechanisms previously identified as being involved in LC activation and migration in native human skin could thus be reproduced in the in vitro constructed skin equivalent model containing functional LC. This model therefore provides a unique and relevant research tool to study human LC biology in situ under controlled in vitro conditions, and will provide a powerful tool for hazard identification, testing novel therapeutics and identifying new drug targets. - Highlights: • MUTZ-3 derived Langerhans cells integrated into skin equivalents are fully functional. • Anti-CXCL12 blocks allergen-induced MUTZ-LC migration. • Anti-CCL5 blocks irritant-induced MUTZ-LC migration. • Irritant mediated MUTZ-LC trans-differentiation to macrophage-like cell in dermis. • Trans-differentiation of MUTZ-LC is IL-10 dependent.