Bayesian Model Calibration for Functional Data Using Elastic Alignment
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Shuler, Kurtis Woodfin↗
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Results for “functional modeling”
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Three Point Functions in Poisson Model
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Shelley, Alec [Stanford University]↗
Genome Extraction from Shotgun Metagenome Sequence Data
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).
Chivian, Dylan↗
Moab Desert Crust - Sample 4E
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).
Chivian, Dylan↗
A State Contingent Production Function Approach to Modeling Power System Disruptions from Variable Renewable Resources
Presents the results of a theoretical and empirical analysis conducted to estimate the impact of using variable renewable resources on the duration and frequency of customer reported power system disruptions.
Harker-Steele, Amanda↗
An Accurate, Affordable Density Functional Tight-Binding Model for Excited State Hydrocarbon Polymer Molecular Dynamics
We have developed a density functional tight-binding model for hydrocarbon excited state dynamics by referencing to high-level electronic structure theory and incorporating a many-body repulsive energy. We then validate our model against n-octane geometry optimizations, bond dissociation scans, and vibrational frequencies. Our model is approximately 10 3 times more efficient than hybrid time-dependent density functional theory calculations with comparable accuracy. In conclusion, our efforts enable longer timescale excited state simulations of photochemistry and scattering of incident radiation.
Chemical calculations↗
Regression models using shapes of functions as predictors
Functional variables are often used as predictors in regression problems. A commonly used parametric approach, called scalar-on-function regression, uses the $\mathbb L^2$ inner product to map functional predictors into scalar responses. This method can perform poorly when predictor functions contain undesired phase variability, causing phases to have disproportionately large influence on the response variable. One past solution has been to perform phase–amplitude separation (as a pre-processing step) and then use only the amplitudes in the regression model. In this paper, we propose a more integrated approach, termed elastic functional regression model (EFRM), where phase-separation is performed inside the regression model, rather than as a pre-processing step. This approach generalizes the notion of phase in functional data, and is based on the norm-preserving time warping of predictors. Due to its invariance properties, this representation provides robustness to predictor phase variability and results in improved predictions of the response variable over traditional models. We demonstrate this framework using a number of datasets involving gait signals, NMR data, and stock market prices.
97 MATHEMATICS AND COMPUTING↗
A Multi-Function AAA Algorithm Applied to Frequency-Dependent Line Modeling: Preprint
We present a new multi-input rational approximation algorithm (MIAAA) and illustrate its advantages respect to the popular Vector Fitting (VF) algorithm using examples of approximations of admittance matrices discussed in a very recent paper and by the creators of VF. We show that not only MIAAA outperforms VF in terms of achieving better accuracy using a smaller number of poles, but also has no numerical issues to achieve convergence. In contrast to VF, MIAA 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.
97 MATHEMATICS AND COMPUTING↗
Dry Deposition Methods Based on Turbulence Kinetic Energy: 1. Evaluation of Various Resistances and Sensitivity Studies Using a Single‐Point Model
Different functions are used to account for turbulence strength in the atmospheric boundary layer for different stability regimes. These functions are one of the sources for differences among different atmospheric models' predictions and associated biases. Also, turbulence strength is underrepresented in some of the resistance formulations. Here, to address these issues with dry deposition, firstly we take advantage of three‐dimensional (3‐D) turbulence information in estimating resistances by proposing and validating a 3‐D turbulence velocity scale that is relevant for different stability regimes of boundary layer. Secondly, we hypothesize and validate that friction velocity measured by 3‐D sonic anemometer can be effectively replaced by the new turbulence velocity scale multiplied by the von Karman constant. Finally, we (a) present a set of resistance formulations for ozone (O 3 ) based on the 3‐D turbulence velocity scale; (b) intercompare estimations of such resistances with those obtained using existing formulations; and, (c) evaluate simulated O 3 fluxes using a single‐point dry deposition model against long‐term observations of O 3 fluxes at the Harvard Forest (MA) site. Results indicate that the new resistance formulations work very well in simulating surface latent heat and O 3 fluxes when compared to respective existing formulations and measurements at a decadal time scale. Findings from this research may help to improve the capability of dry deposition schemes for better estimation of dry deposition fluxes and create opportunities for the development of a community dry deposition model for use in regional/global air quality models.
54 ENVIRONMENTAL SCIENCES↗
A Green's Function Wind Turbine Induction Model That Incorporates Complex Inflow Conditions
ABSTRACT In this work, we develop a new analytical turbine induction model that can incorporate complex inflow conditions including cases where the wind velocity and temperature profiles can vary as functions of height. This induction model is derived from the linearized Navier–Stokes and leads to a second‐order ODE that can be solved using a Green's function formulation. The corresponding Green's function for several configurations are found including the infinite domain, semi‐infinite domain with ground plane, and a power law velocity inflow profile. The results of this approach are then compared with simulations of the turbine induction field using the AMR‐Wind CFD solver with a uniformly loaded actuator disk model. These comparisons show that the Green's function approach captures the centerline blockage, three‐dimensional blockage flow field, and streamwise velocity slow down, with very good agreement for lower thrust conditions and at larger distances away from rotor disk. The effects of shear on the turbine blockage were also compared using a power law inflow profile, and we show that this approach matches the CFD predictions for the cases considered.
17 WIND ENERGY↗
On the Stability Analysis of Astrophysical Cooling Functions
To model the temperature evolution of optically thin astrophysical environments at MHD scales, radiative and collisional cooling rates are typically either pretabulated or fit into a functional form and then input into MHD codes as a radiative loss function. Thermal balance requires estimates of the analogous heating rates, which are harder to calculate, and due to uncertainties in the underlying dissipative heating processes these rates are often simply parameterized. The resulting net cooling function defines an equilibrium curve that varies with density and temperature. Such cooling functions can make the gas prone to thermal instability (TI), which will cause departures from equilibrium. There has been no systematic study of thermally unstable parameter space for nonequilibrium states. Motivated by our recent finding that there is a related linear instability, catastrophic cooling instability, that can dominate over TI, here we carry out such a study. We show that Balbus instability criteria for TI can be used to define a critical cooling rate, Λ c , that permits a nonequilibrium analysis of cooling functions through the mapping of TI zones. We furthermore illustrate how thermal conduction modifies the shape of TI zones. Upon applying a Λ c -based stability analysis to coronal loop simulations, we find that loops undergoing periodic episodes of coronal rain formation are linearly unstable to catastrophic cooling instability, while TI is stabilized by thermal conduction.
79 ASTRONOMY AND ASTROPHYSICS↗
Spectroscopy outperforms leaf trait relationships for predicting photosynthetic capacity across different forest types
Leaf trait relationships are widely used to predict ecosystem function in Terrestrial Biosphere Models (TBMs), in which leaf maximum carboxylation capacity (V c,max ), an important trait for modelling photosynthesis, can be inferred from other easier- to-measure traits. However, whether trait-V c,max relationships are robust across different forest types remains unclear. Here we used measurements of leaf traits, including one morphological trait (leaf mass per area), three biochemical traits (leaf water content, area-based leaf nitrogen content, and leaf chlorophyll content), one physiological trait (V c,max ), as well as leaf reflectance spectra, and explored their relationships within and across three contrasting forest types in China. We found weak and forest type-specific relationships between V c,max and the four morphological and biochemical traits (R 2 ≤ 0.15), indicated by significantly changing slopes and intercepts across forest types. In contrast, reflectance spectroscopy effectively collapsed the differences in the trait-V c,max relationships across three forest biomes into a single robust model for V c,max (R 2 = 0.77), and also accurately estimated the four traits (R 2 = 0.75-0.94). Furthermore, these findings challenge the traditional use of empirical trait-V c,max relationships in TBMs for estimating terrestrial plant photosynthesis, but also highlight spectroscopy as an efficient alternative for characterizing V c,max and multi-trait variability, with critical insights into ecosystem modeling and functional trait ecology.
54 ENVIRONMENTAL SCIENCES↗
SOHIP Abel Transform and Onion Peeling Model Module
This software provides tools for analyzing and modeling physical systems using mathematical transforms and layered models. It includes (1) functions for performing the Abel transform, which is used to relate measurements of bending angles to properties such as refractive index and radius in a medium. The code can compute bending angles from input profiles and also reconstruct these profiles from observed data; (2) the functions for modeling systems with multiple layers using an onion-peeling approach, allowing users to simulate and analyze the behavior of layered materials or structures. These capabilities are useful for researchers and engineers working in fields such as optics, atmospheric science, and materials analysis, enabling them to interpret and model data from experiments or simulations relates to refraction in spherical symmetric medium.
Xu, Shuang [Lawrence Livermore National Laboratory↗
IMPLEMENTATION OF TURBULENCE MODELING FOR THE COUPLED GRIFFIN-PRONGHORN SIMULATION OF THE MOLTEN SALT FAST REACTOR FOR THE VIRTUAL TEST BED
In support of the Virtual Test Bed (VTB) repository, the Molten Salt Fast Reactor (MSFR) concept is modeled using MOOSE-based tools, notably Griffin and Pronghorn, employing newly implemented initial turbulence models and standard wall functions. The models are adapted to Pronghorn’s spirit of a multidimensional coarse-mesh intermediate fidelity code. Multiphysics simulations of a 2D axisymmetric model of an MSFR are carried out to study the coupling between the different physics.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
First-order formalism for β functions in bosonic sigma models from supersymmetry breaking
We consider the renormalization group flow equation for the two-dimensional sigma models with the Kähler target space. The first-order formulation allows us to treat perturbations in these models as current-current deformations. We demonstrate, however, that the conventional first-order formalism misses certain anomalies in the measure, and should be amended. We reconcile beta functions obtained within the conformal perturbation theory for the current-current deformations with traditional “geometric” results obtained in the background field methods, in this way resolving the peculiarities pointed out in O. Gamayun et al. [Peculiarities of beta functions in sigma models, J. High Energy Phys. 10 (2023) 097]. The result is achieved by the supersymmetric completion of the first-order sigma model.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Numerical fluid dynamics for FRG flow equations: Zero-dimensional QFTs as numerical test cases. I. The O ( N ) model
The functional renormalization group (FRG) approach is a powerful tool for studies of a large variety of systems, ranging from statistical physics over the theory of the strong interaction to gravity. The practical application of this approach relies on the derivation of so-called flow equations, which describe the change of the quantum effective action under the variation of a coarse-graining parameter. In the present work, we discuss in detail a novel approach to solve such flow equations. This approach relies on the fact that RG equations can be rewritten such that they exhibit similarities with the conservation laws of fluid dynamics. This observation can be exploited in different ways. First of all, we show that this allows to employ powerful numerical techniques developed in the context of fluid dynamics to solve RG equations. In particular, it allows us to reliably treat the emergence of nonanalytic behavior in the RG flow of the effective action as it is expected to occur in studies of, e.g., spontaneous symmetry breaking. Second, the analogy between RG equations and fluid dynamics offers the opportunity to gain novel insights into RG flows and their interpretation in general, including the irreversibility of RG flows. Further, we work out this connection in practice by applying it to zero-dimensional quantum-field theoretical models. The generalization to higher-dimensional models is also discussed. Our findings are expected to help improving future FRG studies of quantum field theories in higher dimensions both on a qualitative and quantitative level.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Atmospheric Feedbacks Reverse the Sensitivity of Modeled Photosynthesis to Stomatal Function
Stomata mediate fluxes of carbon and water between terrestrial plants and the atmosphere. These fluxes are governed by stomatal function and can be modulated in many Earth system models by an empirical parameter within the calculation of stomatal conductance, the stomatal slope (𝑔 1𝑀 ). Intuitively, 𝑔 1𝑀 represents the marginal water cost of carbon, relating it to the emergent plant property of water use efficiency. Observations show that 𝑔 1𝑀 can range widely across and within plant types in varying environments, and this distribution of 𝑔 1𝑀 is not captured within Earth system models which represent each plant type with a single 𝑔 1𝑀 value. Here we examine how 𝑔 1𝑀 influences photosynthesis using coupled Earth system model simulations by perturbing 𝑔 1𝑀 to observed 5th and 95th percentiles for each plant type. We find that high 𝑔 1𝑀 reduces photosynthesis nearly everywhere, while low 𝑔 1𝑀 has regionally dependent responses. Under fixed atmospheric conditions, low 𝑔 1𝑀 increases photosynthesis in the Amazon and central North America but decreases photosynthesis in boreal Canada. These responses reverse when the atmosphere responds interactively due to spatially differing sensitivity to increases in temperature and vapor pressure deficit. Choice of 𝑔 1𝑀 also influences photosynthetic response to changes in atmospheric carbon dioxide (CO 2 ), with lower and higher 𝑔1𝑀 modifying total global response to elevated 2x preindustrial CO 2 by +6.4% and −9.6%, respectively. Our work demonstrates that atmospheric feedbacks are critical for determining the photosynthetic response to 𝑔 1𝑀 assumptions and some regions are particularly sensitive to choice of 𝑔 1𝑀 .
Liu, Amy X. [University of Washington, Seattle, WA↗