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At least 1,117 records · Page 62

Functional Requirements Document for HALE UAS Operations in the NAS: Step 1. Version 3

The purpose of this Functional Requirements Document (FRD) is to compile the functional requirements needed to achieve the Access 5 Vision of "operating High Altitude, Long Endurance (HALE) Unmanned Aircraft Systems (UAS) routinely, safely, and reliably in the national airspace system (NAS)" for Step 1. These functional requirements could support the development of a minimum set of policies, procedures and standards by the Federal Aviation Administration (FAA) and various standards organizations. It is envisioned that this comprehensive body of work will enable the FAA to establish and approve regulations to govern safe operation of UAS in the NAS on a routine or daily "file and fly" basis. The approach used to derive the functional requirements found within this FRD was to decompose the operational requirements and objectives identified within the Access 5 Concept of Operations (CONOPS) into the functions needed to routinely and safely operate a HALE UAS in the NAS. As a result, four major functional areas evolved to enable routine and safe UAS operations for an on-demand basis in the NAS. These four major functions are: Aviate, Navigate, Communicate, and Avoid Hazards. All of the functional requirements within this document can be directly traceable to one of these four major functions. Some functions, however, are traceable to several, or even all, of these four major functions. These cross-cutting functional requirements support the "Command / Control: function as well as the "Manage Contingencies" function. The requirements associated to these high-level functions and all of their supporting low-level functions are addressed in subsequent sections of this document.

Source record↗

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introduced by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microscopically based energy density functionals for nuclei using the density matrix expansion. II. Full optimization and validation

Background: Energy density functional methods provide a generic framework to compute properties of atomic nuclei starting from models of nuclear potentials and the rules of quantum mechanics. Until now, the overwhelming majority of functionals have been constructed either from empirical nuclear potentials such as the Skyrme or Gogny forces, or from systematic gradient-like expansions in the spirit of the density functional theory for atoms. Purpose: In this study, we seek to obtain a usable form of the nuclear energy density functional that is rooted in the modern theory of nuclear forces. We thus consider a functional obtained from the density matrix expansion of local nuclear potentials from chiral effective field theory. We propose a parametrization of this functional carefully calibrated and validated on selected ground-state properties that is suitable for large-scale calculations of nuclear properties. Methods: Our energy functional comprises two main components. The first component is a non-local functional of the density and corresponds to the direct part (Hartree term) of the expectation value of local chiral potentials on a Slater determinant. Contributions to the mean field and the energy of this term are computed by expanding the spatial, finite-range components of the chiral potential onto Gaussian functions. The second component is a local functional of the density and is obtained by applying the density matrix expansion to the exchange part (Fock term) of the expectation value of the local chiral potential. We apply the UNEDF2 optimization protocol to determine the coupling constants of this energy functional. Results: We obtain a set of microscopically constrained functionals for local chiral potentials from leading order up to next-to-next-to-leading order with and without three-body forces and contributions from Δ excitations. These functionals are validated on the calculation of nuclear and neutron matter, nuclear mass tables, single-particle shell structure in closed-shell nuclei, and the fission barrier of 240 Pu . Quantitatively, they perform noticeably better than the more phenomenological Skyrme functionals. Conclusions: The inclusion of higher-order terms in the chiral perturbation expansion seems to produce a systematic improvement in predicting nuclear binding energies while the impact on other observables is not really significant. In conclusion, this result is especially promising since all the fits have been performed at the single-reference level of the energy density functional approach, where important collective correlations such as center-of-mass correction, rotational correction, or zero-point vibrational energies have not been taken into account yet.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

ABSTRACT Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for the control of natural and engineered systems. The discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28-day microcosm incubations to examine microbial community compositional and functional stability during plant litter decomposition. Using dissolved organic carbon (DOC) abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a “low DOC” phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as one solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. IMPORTANCE Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter–decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Ginzburg--Landau functionals in the large-graph limit

Ginzburg–Landau (GL) functionals on graphs, which are relaxations of graph-cut functionals on graphs, have yielded a variety of insights in image segmentation and graph clustering. In this paper, we study large-graph limits of GL functionals by taking a functional-analytic view of graphs as nonlocal kernels. For a graph Wn with n nodes, the corresponding graph GL functional GL W n ϵ is an energy for functions on Wn. We minimize GL functionals on sequences of growing graphs that converge to functions called graphons. For such sequences of graphs, we show that the graph GL functional Γ-converges to a continuous and nonlocal functional that we call the graphon GL functional. We investigate the sharp-interface limits of the graph GL and graphon GL functionals, and we relate these limits to a nonlocal total-variation (TV) functional. We express the limiting GL functional in terms of Young measures and thereby obtain a probabilistic interpretation of the minimization problem in the large-graph limit. Finally, to develop intuition about graphon GL functionals, we determine the GL minimizer for several example families of graphons.

Zhang, Edith↗

Enhancements to the SSME transfer function modeling code

This report details the results of a one year effort by Ohio University to apply the transfer function modeling and analysis tools developed under NASA Grant NAG8-167 (Irwin, 1992), (Bartholomew, 1992) to attempt the generation of Space Shuttle Main Engine High Pressure Turbopump transfer functions from time domain data. In addition, new enhancements to the transfer function modeling codes which enhance the code functionality are presented, along with some ideas for improved modeling methods and future work. Section 2 contains a review of the analytical background used to generate transfer functions with the SSME transfer function modeling software. Section 2.1 presents the 'ratio method' developed for obtaining models of systems that are subject to single unmeasured excitation sources and have two or more measured output signals. Since most of the models developed during the investigation use the Eigensystem Realization Algorithm (ERA) for model generation, Section 2.2 presents an introduction of ERA, and Section 2.3 describes how it can be used to model spectral quantities. Section 2.4 details the Residue Identification Algorithm (RID) including the use of Constrained Least Squares (CLS) and Total Least Squares (TLS). Most of this information can be found in the report (and is repeated for convenience). Section 3 chronicles the effort of applying the SSME transfer function modeling codes to the a51p394.dat and a51p1294.dat time data files to generate transfer functions from the unmeasured input to the 129.4 degree sensor output. Included are transfer function modeling attempts using five methods. The first method is a direct application of the SSME codes to the data files and the second method uses the underlying trends in the spectral density estimates to form transfer function models with less clustering of poles and zeros than the models obtained by the direct method. In the third approach, the time data is low pass filtered prior to the modeling process in an effort to filter out high frequency characteristics. The fourth method removes the presumed system excitation and its harmonics in order to investigate the effects of the excitation on the modeling process. The fifth method is an attempt to apply constrained RID to obtain better transfer functions through more accurate modeling over certain frequency ranges. Section 4 presents some new C main files which were created to round out the functionality of the existing SSME transfer function modeling code. It is now possible to go from time data to transfer function models using only the C codes; it is not necessary to rely on external software. The new C main files and instructions for their use are included. Section 5 presents current and future enhancements to the XPLOT graphics program which was delivered with the initial software. Several new features which have been added to the program are detailed in the first part of this section. The remainder of Section 5 then lists some possible features which may be added in the future. Section 6 contains the conclusion section of this report. Section 6.1 is an overview of the work including a summary and observations relating to finding transfer functions with the SSME code. Section 6.2 contains information relating to future work on the project.

Irwin, R. Dennis↗

An optimum approximation of n-point correlation functions of random heterogeneous material systems

An approximate solution for n-point correlation functions is developed in this study. In the approximate solution, weight functions are used to connect subsets of (n-1)-point correlation functions to estimate the full set of n-point correlation functions. In previous related studies, simple weight functions were introduced for the approximation of three and four-point correlation functions. In this work, the general framework of the weight functions is extended and derived to achieve optimum accuracy for approximate n-point correlation functions. Such approximation can be utilized to construct global n-point correlation functions for a system when there exist limited information about these functions in a subset of space. To verify its accuracy, the new formulation is used to approximate numerically three-point correlation functions from the set of two-point functions directly evaluated from a virtually generated isotropic heterogeneous microstructure representing a particulate composite system. Similarly, three-point functions are approximated for an anisotropic glass fiber/epoxy composite system and compared to their corresponding reference values calculated from an experimental dataset acquired by computational tomography. Results from both virtual and experimental studies confirm the accuracy of the new approximation. The new formulation can be utilized to attain a more accurate approximation to global n-point correlation functions for heterogeneous material systems with a hierarchy of length scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formalization of the functional analysis methodology to improve NPP I and C system design process - 244

Functional analysis is a universal methodology, which is able to support NPP and I and C design process. The paper proposes an approach to combining the functional analysis process and I and C design process into a single I and C functional design process. Operation of a system is considered as a set of functions providing not only the achievement of goal, but also keeping material and energy balances. A notation for graphical representation of semantic network (hierarchy of functions) describing a system is suggested. This network includes four levels, namely functional goals, abstract functions level, process functions level, and equipment level. The elements of the hierarchy are connected by three kinds of relationships, namely: parent-child, main-support, and cause-consequence. Then the semantic network (hierarchy) of functions is converted into a functional network which looks as a directed graph. This graph is used for development of control algorithm and for building of instrumentation and control functions hierarchy. Farther analysis of process functions reveals a set of criteria indicating real-time status and effectiveness of functions. The criteria are used for allocation of instruments and actuators. The process of functional analysis and design is illustrated in application to a simple heat generation system. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Solute-solvent cavity and bridge functions. I. Varying size of the solute

In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios—up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from simulation results in the investigated temperature and density ranges. We also find that the behavior of the indirect and cavity correlation functions is non-monotonous within the hard-core region, but the latter can be successfully approximated by mean-field theory if the solute-solvent interaction energy is divided into repulsive and attractive contribution, according to Weeks-Chandler-Andersen theory. Furthermore, in spite of the non-monotonous behavior of logarithm of the cavity function and the indirect correlation function, their difference, i.e., the bridge function remains constant within the hard-core region. Such behavior of the bridge and indirect correlation functions at small distances and for small values of indirect correlation function is well known from the Duh-Haymet plots, where the non-unique relationship results in loops of the bridge function vs. indirect correlation function graphs. We show that the same pathological behavior appears also when distance is small and indirect correlation function is large. We further show that the unique functional behavior of the bridge function can be established when bridge is represented as a function of the renormalized, repulsive indirect correlation function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy Density Functional for Nuclei and Neutron Stars

Background: Recent observational data on neutron star masses and radii provide stringent constraints on the equation of state of neutron rich matter [ Annu. Rev. Nucl. Part. Sci. 62 485 (2012)]. Purpose: We aim to develop a nuclear energy density functional that can be simultaneously applied to finite nuclei and neutron stars. Methods: We use the self-consistent nuclear density functional theory (DFT) with Skyrme energy density functionals and covariance analysis to assess correlations between observables for finite nuclei and neutron stars. In a first step two energy functionals a high density energy functional giving reasonable neutron properties, and a low density functional fitted to nuclear properties are matched. In a second step, we optimize a new functional using exactly the same protocol as in earlier studies pertaining to nuclei but now including neutron star data. This allows direct comparisons of performance of the new functional relative to the standard one. Results: The new functional TOV-min yields results for nuclear bulk properties (energy, rms radius, diffraction radius, and surface thickness) that are of the same quality as those obtained with the established Skyrme functionals, including SV-min. When comparing SV-min and TOV-min, isoscalar nuclear matter indicators vary slightly while isovector properties are changed considerably. We discuss neutron skins, dipole polarizability, separation energies of the heaviest elements, and proton and neutron drip lines. We confirm a correlation between the neutron skin of 208Pb and the neutron star radius. Conclusions: We demonstrate that standard energy density functionals optimized to nuclear data do not carry information on the expected maximum neutron star mass, and that predictions can only be made within an extremely broad uncertainty band. For atomic nuclei, the new functional TOV-min performs at least as well as the standard nuclear functionals, but it also reproduces expected neutron star data within assumed error bands. This functional is expected to yield more reliable predictions in the region of very neutron rich heavy nuclei.

Erler, J.↗

SU-C-BRA-06: Developing Clinical and Quantitative Guidelines for a 4DCT-Ventilation Functional Avoidance Clinical Trial

Purpose: 4DCT-ventilation is an exciting new imaging modality that uses 4DCTs to calculate lung ventilation. Because 4DCTs are acquired as part of routine care, calculating 4DCT-ventilation allows for lung function evaluation without additional cost or inconvenience to the patient. Development of a clinical trial is underway at our institution to use 4DCT-ventilation for thoracic functional avoidance with the idea that preferential sparing of functional lung regions can decrease pulmonary toxicity. The purpose of our work was to develop the practical aspects of a 4DCT-ventilation functional avoidance clinical trial including: 1.assessing patient eligibility 2.developing trial inclusion criteria and 3.developing treatment planning and dose-function evaluation strategies. Methods: 96 stage III lung cancer patients from 2 institutions were retrospectively reviewed. 4DCT-ventilation maps were calculated using the patient’s 4DCTs, deformable image registrations, and a density-change-based algorithm. To assess patient eligibility and develop trial inclusion criteria we used an observer-based binary end point noting the presence or absence of a ventilation defect and developed an algorithm based on the percent ventilation in each lung third. Functional avoidance planning integrating 4DCT-ventilation was performed using rapid-arc and compared to the patient’s clinically used plan. Results: Investigator-determined clinical ventilation defects were present in 69% of patients. Our regional/lung-thirds ventilation algorithm identified that 59% of patients have lung functional profiles suitable for functional avoidance. Compared to the clinical plan, functional avoidance planning was able to reduce the mean dose to functional lung by 2 Gy while delivering comparable target coverage and cord/heart doses. Conclusions: 4DCT-ventilation functional avoidance clinical trials have great potential to reduce toxicity, and our data suggest that 59% of lung cancer patients have lung function profiles suitable for functional avoidance. Our study used a retrospective evaluation of a large lung cancer patient database to develop the practical aspects of a 4DCT-ventilation functional avoidance clinical trial. (R.C., E.C., T.G.), NIH Research Scientist Development Award K01-CA181292 (R.C.), and State of Colorado Advanced Industries Accelerator Grant (Y.V.)

60 APPLIED LIFE SCIENCES↗

Generalized Functions for the Fractional Calculus

Previous papers have used two important functions for the solution of fractional order differential equations, the Mittag-Leffler functionE(sub q)[at(exp q)](1903a, 1903b, 1905), and the F-function F(sub q)[a,t] of Hartley & Lorenzo (1998). These functions provided direct solution and important understanding for the fundamental linear fractional order differential equation and for the related initial value problem (Hartley and Lorenzo, 1999). This paper examines related functions and their Laplace transforms. Presented for consideration are two generalized functions, the R-function and the G-function, useful in analysis and as a basis for computation in the fractional calculus. The R-function is unique in that it contains all of the derivatives and integrals of the F-function. The R-function also returns itself on qth order differ-integration. An example application of the R-function is provided. A further generalization of the R-function, called the G-function brings in the effects of repeated and partially repeated fractional poles.

Lorenzo, Carl F.↗

The Functional Breakdown Structure (FBS) and Its Relationship to Life Cycle Cost

The Functional Breakdown Structure (FBS) is a structured, modular breakdown of every function that must be addressed to perform a generic mission. It is also usable for any subset of the mission. Unlike a Work Breakdown Structure (WBS), the FBS is a function-oriented tree, not a product-oriented tree. The FBS details not products, but operations or activities that should be performed. The FBS is not tied to any particular architectural implementation because it is a listing of the needed functions, not the elements, of the architecture. The FBS for Space Transportation Systems provides a universal hierarchy of required functions, which include ground and space operations as well as infrastructure - it provides total visibility of the entire mission. By approaching the systems engineering problem from the functional view, instead of the element or hardware view, the SPST has created an exhaustive list of potential requirements which the architecture designers can use to evaluate the completeness of their designs. This is a new approach that will provide full accountability of all functions required to perform the planned mission. It serves as a giant check list to be sure that no functions are omitted, especially in the early architectural design phase. A significant characteristic of a FBS is that if architecture options are compared using this approach, then any missing or redundant elements of each option will be ' identified. Consequently, valid Life Cycle Costs (LCC) comparisons can be made. For example, one architecture option might not need a particular function while another option does. One option may have individual elements to perform each of three functions while another option needs only one element to perform the three functions. Once an architecture has been selected, the FBS will serve as a guide in development of the work breakdown structure, provide visibility of those technologies that need to be further developed to perform required functions, and help identify the personnel skills required to develop and operate the architecture. It also wifi allow the systems engineering activities to totally integrate each discipline to the maximum extent possible and optimize at the total system level, thus avoiding optimizing at the element level (stove-piping). In addition, it furnishes a framework that wifi help prevent over or under specifying requirements because all functions are identified and all elements are aligned to functions.

DeHoff, Bryan↗

Goal-Function Tree Modeling for Systems Engineering and Fault Management

The draft NASA Fault Management (FM) Handbook (2012) states that Fault Management (FM) is a "part of systems engineering", and that it "demands a system-level perspective" (NASAHDBK- 1002, 7). What, exactly, is the relationship between systems engineering and FM? To NASA, systems engineering (SE) is "the art and science of developing an operable system capable of meeting requirements within often opposed constraints" (NASA/SP-2007-6105, 3). Systems engineering starts with the elucidation and development of requirements, which set the goals that the system is to achieve. To achieve these goals, the systems engineer typically defines functions, and the functions in turn are the basis for design trades to determine the best means to perform the functions. System Health Management (SHM), by contrast, defines "the capabilities of a system that preserve the system's ability to function as intended" (Johnson et al., 2011, 3). Fault Management, in turn, is the operational subset of SHM, which detects current or future failures, and takes operational measures to prevent or respond to these failures. Failure, in turn, is the "unacceptable performance of intended function." (Johnson 2011, 605) Thus the relationship of SE to FM is that SE defines the functions and the design to perform those functions to meet system goals and requirements, while FM detects the inability to perform those functions and takes action. SHM and FM are in essence "the dark side" of SE. For every function to be performed (SE), there is the possibility that it is not successfully performed (SHM); FM defines the means to operationally detect and respond to this lack of success. We can also describe this in terms of goals: for every goal to be achieved, there is the possibility that it is not achieved; FM defines the means to operationally detect and respond to this inability to achieve the goal. This brief description of relationships between SE, SHM, and FM provide hints to a modeling approach to provide formal connectivity between the nominal (SE), and off-nominal (SHM and FM) aspects of functions and designs. This paper describes a formal modeling approach to the initial phases of the development process that integrates the nominal and off-nominal perspectives in a model that unites SE goals and functions of with the failure to achieve goals and functions (SHM/FM). This methodology and corresponding model, known as a Goal-Function Tree (GFT), provides a means to represent, decompose, and elaborate system goals and functions in a rigorous manner that connects directly to design through use of state variables that translate natural language requirements and goals into logical-physical state language. The state variable-based approach also provides the means to directly connect FM to the design, by specifying the range in which state variables must be controlled to achieve goals, and conversely, the failures that exist if system behavior go out-of-range. This in turn allows for the systems engineers and SHM/FM engineers to determine which state variables to monitor, and what action(s) to take should the system fail to achieve that goal. In sum, the GFT representation provides a unified approach to early-phase SE and FM development. This representation and methodology has been successfully developed and implemented using Systems Modeling Language (SysML) on the NASA Space Launch System (SLS) Program. It enabled early design trade studies of failure detection coverage to ensure complete detection coverage of all crew-threatening failures. The representation maps directly both to FM algorithm designs, and to failure scenario definitions needed for design analysis and testing. The GFT representation provided the basis for mapping of abort triggers into scenarios, both needed for initial, and successful quantitative analyses of abort effectiveness (detection and response to crew-threatening events).

Patterson, Jonathan D.↗

Trade-offs among restored ecosystem functions are context-dependent in Mediterranean-type regions

Global biodiversity hotspots, including Mediterranean-type ecosystems worldwide, are highly threatened by global change that alters biodiversity, ecosystem functions, and services. Some restoration activities enhance ecosystem functions by reintroducing plant species based on known relationships between plant traits and ecosystem processes. Achieving multiple functions across different site conditions, however, requires understanding how abiotic factors like climate and soil, along with plant assemblages, influence ecosystem functions, including their trade-offs and synergies. We used the ModEST ecosystem simulation model, which integrates carbon, water, and nutrient processes with plant traits, to assess the relationships between restored plant assemblages and ecosystem functions in Mediterranean-type climates and soils. We investigated whether maximised carbon increment, water use efficiency, and nitrogen use efficiency, along with their trade-offs and synergies, varied across different abiotic contexts. Further, we asked whether assemblages that maximised functions varied across environments and among these functions. We found that maximised ecosystem carbon increment and nitrogen use efficiency occurred under moist, warm conditions, while water use efficiency peaked under drier conditions. Generally, the assemblage that maximised one function differed from those for other maximised functions. Synergies were rare, except between water and nitrogen use efficiencies in loam soils across most climates. Trade-offs among maximised functions were common, varying in strength with abiotic context and plant assemblages, and were more pronounced in sandy loam soils compared to clay-rich soils. Our findings suggest that due to variation in abiotic conditions within and across Mediterranean-type regions at the global scale, site-specific plant assemblages are required to maximise ecosystem functions. Thus, lessons from a single site cannot be transferred to another site, even where the same plant functional types are available for restoration. Our simulation results offer valuable insights into potential ecosystem performance under specific abiotic conditions following restoration with particular plant functional types, thereby informing local restoration efforts.

54 ENVIRONMENTAL SCIENCES↗

Localizing Holes as Polarons and Predicting Band Gaps, Defect Levels, and Delithiation Energies of Solid-State Materials with a Local Exchange-Correlation Functional

Here, we assess the performance of seven exchange–correlation functionals (some with and some without a Hubbard U correction) for their ability (i) to predict band gaps of silicon, diamond, and Li-ion battery cathode materials, (ii) to localize hole polarons and predict delithiation energies in Li-ion battery cathode materials, and (iii) to predict transition levels of charge carriers of doped silicon and diamond. Both local and hybrid exchange–correlation functionals were tested. The local functionals tend to underestimate band gaps and delocalize polarons. The hybrid functionals very often give a good description of both properties, but they may not be practical for calculations involving large unit cells, large ensembles, or dynamics, and therefore a local functional with a Hubbard U correction is often used (giving the method called DFT+U), where the value of a parameter U is adjusted according to the system and the property being investigated. Keeping in mind the importance of computational cost and the undesirability of having to adjust an empirical parameter for each system or property of interest, we recently developed a local functional, namely HLE17, to try to accurately predict band gaps and excitation energies, and we validated it using mostly main-group solids and molecules. Here we test the performance of HLE17 for its ability to predict band gaps and localize polarons in other solid-state materials, and we compare its performance to that of popular local functionals (PBE, PBEsol, and TPSS), a range-separated hybrid functional with screened exchange (HSE06), and DFT+U. We find that HLE17 predicts more accurate band gaps than other local functionals and can localize holes as polarons, which other local functionals usually fail to do, and for a number of cases it is comparable in performance quality to Hubbard-corrected functionals without the need for system-specific parametrization and to hybrid functionals without the high cost. Because HLE17 does not predict accurate lattice constants, we use the single-point method of quantum chemistry, where the geometry is optimized with one functional and the band gap is calculated with HLE17, or we perform calculations with the lattice constants obtained by TPSS and both the fractional intracell coordinates and the electronic structure obtained by HLE17 (a new method denoted HLE17\\TPSS). In particular, we performed calculations by HLE17//TPSS, HLE17//HSE06, HLE17//DFT+U, and HLE17\\TPSS, and these methods usually agree well with each other and give values similar to experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Frequency-dependent dielectric function of semiconductors with application to physisorption

Furthermore, the dielectric function is one of the most important quantities that describes the electrical and optical properties of solids. Accurate modeling of the frequency-dependent dielectric function has great significance in the study of the long-range van der Waals (vdW) interaction for solids and adsorption. In this work we calculate the frequency-dependent dielectric functions of semiconductors and insulators using the GW method with and without exciton effects, as well as efficient semilocal density functional theory (DFT), and compare these calculations with a model frequency-dependent dielectric function. We find that for semiconductors with moderate band gaps, the model dielectric functions, GW values, and DFT calculations all agree well with each other. However, for insulators with strong exciton effects, the model dielectric functions have a better agreement with accurate GW values than the DFT calculations, particularly in high-frequency region. To understand this, we repeat the DFT calculations with scissors correction, by shifting the DFT Kohn-Sham energy levels to match the experimental band gap. We find that scissors correction only moderately improves the DFT dielectric function in the low-frequency region. Based on the dielectric functions calculated with different methods, we make a comparative study by applying these dielectric functions to calculate the vdW coefficients (C3 and C5) for adsorption of rare-gas atoms on a variety of surfaces. We find that the vdW coefficients obtained with the nearly free electron gas-based model dielectric function agree quite well with those obtained from the GW dielectric function, in particular for adsorption on semiconductors, leading to an overall error of less than 7% for C 3 and 5% for C 5 . This demonstrates the reliability of the model dielectric function for the study of physisorption.

36 MATERIALS SCIENCE↗

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.

59 BASIC BIOLOGICAL SCIENCES↗