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At least 1,243 records · Page 69

Integration of software tools for integrative modeling of biomolecular systems

Integrative modeling computes a model based on varied types of input information, be it from experiments or prior models. Often, a type of input information will be best handled by a specific modeling software package. In such a case, we desire to integrate our integrative modeling software package, Integrative Modeling Platform (IMP), with software specialized to the computational demands of the modeling problem at hand. After several attempts, however, we have concluded that even in collaboration with the software's developers, integration is either impractical or impossible. The reasons for the intractability of integration include software incompatibilities, differing modeling logic, the costs of collaboration, and academic incentives. In the integrative modeling software ecosystem, several large modeling packages exist with often redundant tools. So we reason, therefore, that the other development groups have similarly concluded that the benefit of integration does not justify the cost. As a result, modelers are often restricted to the set of tools within a single software package. The inability to integrate tools from distinct software negatively impacts the quality of the models and the efficiency of the modeling. As the complexity of modeling problems grows, we seek to galvanize developers and modelers to consider the long-term benefit that software interoperability yields. In this article, we formulate a demonstrative set of software standards for implementing a model search using tools from independent software packages and discuss our efforts to integrate IMP and the crystallography suite Phenix within the Bayesian modeling framework.

59 BASIC BIOLOGICAL SCIENCES↗

Boosting efficiency and reducing graph reliance: Basis adaptation integration in Bayesian multi-fidelity networks

The computational cost of high-fidelity numerical models makes outer-loop analysis, which requires repeated interrogation of the model such as uncertainty quantification, computationally demanding. Multi-fidelity methods, which construct a surrogate model using data from an ensemble of models of varying cost and accuracy, can substantially reduce the cost of outer-loop analysis. However, these methods can be difficult to apply when the model ensemble does not admit a clear hierarchy a priori and the correlations between models are low. Consequently, in this paper, we present a multi-fidelity method that leverages dimension reduction to enhance the correlation between models, thereby reducing the amount of data needed to train a surrogate from an unordered ensemble of models. Our method utilizes basis adaptation to build low-dimensional polynomial chaos expansions of each model and employs Multi-fidelity Networks to encode the relationships among models. We show that the resulting method exhibit two notable advantages over its counterpart: (1) enhanced accuracy (both reduced bias and variance); and (2) reduced dependency on the graph structure encoding relationships among models. We demonstrate the approach on an analytical test problem and a challenging finite element model for a spent nuclear fuel. Our method produces a surrogate model that is significantly more accurate than either a single-fidelity surrogate or a multi-fidelity surrogate constructed without basis adaptation.

42 ENGINEERING↗

Simulations and symmetries

ABSTRACT We investigate the range of applicability of a model for the real-space power spectrum based on N-body dynamics and a (quadratic) Lagrangian bias expansion. This combination uses the highly accurate particle displacements that can be efficiently achieved by modern N-body methods with a symmetries-based bias expansion which describes the clustering of any tracer on large scales. We show that at low redshifts, and for moderately biased tracers, the substitution of N-body-determined dynamics improves over an equivalent model using perturbation theory by more than a factor of two in scale, while at high redshifts and for highly biased tracers the gains are more modest. This hybrid approach lends itself well to emulation. By removing the need to identify haloes and subhaloes, and by not requiring any galaxy-formation-related parameters to be included, the emulation task is significantly simplified at the cost of modelling a more limited range in scale.

79 ASTRONOMY AND ASTROPHYSICS↗

Wind Tunnel Investigation of the Supersonic Stage Separation Aerodynamics of a Generic 0.0175-Scale Bimese Two-Stage-to-Orbit Reusable Launch Vehicle Configuration

A wind tunnel investigation was conducted of the supersonic stage separation aerodynamics of a generic two-stage-to-orbit bimese wingbody configuration in the NASA Langley Research Center Unitary Plan Wind Tunnel. Proximity and isolated model testing was conducted at Mach numbers of 2.3, 3.0, and 4.5 and a unit Reynolds number of 2.0 million per foot using 0.0175-scale models of the Langley Glide-Back Booster concept designated as the orbiter and booster in belly-to-belly and back-to-belly configurations. Longitudinal forces and moments were obtained on both models and surface static pressure measurements were obtained on the orbiter model at 328 relative proximity locations and at relative angles of attack of 0 degrees and 5 degrees. The test results supported a larger effort to develop and validate experimental and computational tools applicable to the design and simulation of stage separation and abort procedures for reusable launch vehicles composed of multiple bodies, including winged bodies. An initial proof-of-concept experiment featuring low-cost uninstrumented models was conducted to verify an emerging automated model control system and new support system hardware, and to identify potential model and support system blockage and unsteady aerodynamics/model dynamics prior to committing to higher-fidelity instrumented models. This investigation led to upgrades in the facility stage separation hardware, calibration and testing techniques and capabilities, and data analysis and documentation methodologies that have been extended to the more recent NASA Constellation and Space Launch System crew and cargo launch vehicle programs. A virtual diagnostics interface methodology was used to facilitate the design of the stage separation support hardware, to position the models in the test section, and to define the experimental test space. Advances in the facility automated model positioning system established a foundation for the development of a continuous-sweep data acquisition technique that is responsible for significant productivity improvements to the current NASA Space Launch System test program. The automated model positioning capability was leveraged to conduct a companion statistically-designed stage separation experiment requiring randomization of the relative proximity positions of the orbiter and booster models. The respective zones of influence and interference effects of the orbiter and booster were identified from three-dimensional scatter plots, contour and influence maps, and two-dimensional plotting methods. The highly-nonlinear, shock-dominated aerodynamic characteristics of the orbiter and booster in the Unitary Plan Wind Tunnel exhibited good agreement with independent test data obtained in a NASA Marshall Space Flight Center wind tunnel and with computational fluid dynamics predictions using a compressible, three-dimensional flow solver and an inviscid, unstructured Cartesian method.

Erickson, Gary E.↗

Strategies for Automation of Model Tuning in Multifidelity Trajectory Uncertainty Propagation

Multi-model Monte Carlo methods are efficient strategies to perform forward uncertainty quantification studies in entry, descent, and landing (EDL) applications. These multi-model methods are based on the classical Monte Carlo estimator, but fuse predictions from several low-fidelity models to obtain estimators with greater precision given a prescribed computational budget. The effectiveness of these approaches relies on the magnitudes of correlations between the low-fidelity models and the high-fidelity model, as well as the relative computational costs of all models. Identifying and exploiting the best trade-off between correlation and cost, which ultimately depends on the selection of hyperparameters in the low-fidelity models, is a task often performed by hand or simply inspired by the deterministic understanding available for a specific application. This work extends a preliminary effort,

Marten Thompson↗

Towards large-scale calculations with State-Specific Multireference Coupled Cluster methods: Studies on dodecane, naphthynes, and polycarbenes

Multireference Coupled Cluster (MRCC) methods are essential for accurate descriptions of molecular systems that have nearly degenerate states. A number of these methods have been developed over the last three decades but their use has been hampered by their high computational cost. The development of highly scalableMRCC codes can significantly alleviate this problem. Our recent work on the parallelization of the Brillouin-Wigner MRCC implementation has clearly demonstrated that taking advantage of large computational resources can enable the MRCC calculations on chemically relevant molecules within practical time-to-solution and memory per core constraints. In this letter we report on a parallel implementation of the Mukherjee’s state-specific MRCC model with single and double excitations (MR MkCCSD). In particular the abstraction of a methyl-group from dodecane, the singlet-triplet splitting in naphthyne isomers, and the singlet-high-spin splitting in polycarbenes are considered as demonstrations of systems with significant multireference character and of challenging size that currently can be handled with the MR MkCCSD formalism.

74 ATOMIC AND MOLECULAR PHYSICS↗

plexosdb: A Modular Library for Programmatic PLEXOS Model Construction

plexosdb is a lightweight Python library for constructing PLEXOS models using a SQLite-backed data structure. It provides a clear, modular interface that maps relational data directly to model components. By leveraging SQLite and idiomatic Python, it enables fast iteration and reproducible workflows. The result is a performant, composable foundation for scalable PLEXOS model development.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Stochastic model for fatigue crack size and cost effective design decisions

This paper describes a methodology for making cost effective fatigue design decisions. The methodology is based on a probabilistic model for the stochastic process of fatigue crack growth with time. The development of a particular model for the stochastic process is also discussed in the paper. The model is based on the assumption of continuous time and discrete space of crack lengths. Statistical decision theory and the developed probabilistic model are used to develop the procedure for making fatigue design decisions on the basis of minimum expected cost or risk function and reliability bounds. Selections of initial flaw size distribution, NDT, repair threshold crack lengths, and inspection intervals are discussed.

Hanagud, S.↗

DEVELOPMENT AND APPLICATION OF RISK ANALYSIS TOOLKIT FOR PLANT RESOURCE OPTIMIZATION

This paper presents the development of methods and tools that are being designed to optimize plant operations (e.g., maintenance/replacement schedules and optimal maintenance postures for plant components) in a manner that is more cost effective than current approaches and makes better use of available component health and cost data. These methods include both data- and model-based optimization methods. Model-based optimization methods directly include reliability and cost models to determine an optimal plant operational strategy. We consider gradient-based and evolutionary (based on genetic algorithms) optimization methods. The second class of methods target more specific use cases (e.g., project schedule optimization) and are not based on reliability models directly, but they require specific component reliability and cost data. This class of methods is based on variants of the knapsack problem with an aim to determine an optimal project schedule that maximizes the overall NPV. This paper also presents multi-objective methods designed to identify an optimal maintenance posture based on a Pareto frontier analysis. Rather than dictating the “right” tradeoff (i.e., identify the absolute best posture), we show how it is possible to perform a trade space exploration approach (i.e., identify value and costs of several postures and let the analysis account for desired value and cost metrics). This is performed by identifying maintenance postures that maximize value (e.g., system availability) and minimize operational costs, i.e., the Pareto frontier in a value-cost trade space. For all these methods we present detailed applicative examples that show their validity from a decision-making perspective.

97 - MATHEMATICS AND COMPUTING↗

A technoeconomic analysis of poly- and single-crystalline NMCxyz from material synthesis to battery pack design

A process model was developed for estimating the cost of manufacturing lithium nickel manganese cobalt oxide (LiNi x Mn y Co z O 2 , NMCxyz), the main cathode active material in lithium-ion batteries used for electric vehicles in the United States. The model was used to estimate the prices of NMC622, NMC811, and NMC955 with poly- and single-crystalline morphologies. The Battery Performance and Cost Model (BatPaC) was used to translate the NMC prices into battery pack prices. A decrease in cobalt content from NMC622 (20% Co) to NMC955 (5% Ni) decreases the material price by $\$$0.85/kg (−3%) due to a decrease in the cost of battery materials, which account for >60% of the total price. NMC622 only produce cheaper packs if the nickel sulfate cost is > 4 × its baseline, indicating higher nickel materials will lower pack cost under normal market conditions. Single-crystalline materials are $\$$2/kg (+8%) more expensive than their polycrystalline counterparts due to higher manufacturing costs from longer, hotter calcinations in less densely packed saggars. This increases the pack price by ∼$\$$3/kWh, assuming identical electrochemical properties. In conclusion, the single-crystalline materials could yield cheaper packs if cycled to higher upper cutoff voltages (i.e., 4.35 to 4.43 V for the single-crystalline material vs. 4.25 V for their polycrystalline counterparts).

Cost modeling↗

Four equation k-omega based turbulence model with algebraic flux for supercritical flows

Hydrocarbon and nuclear fuels will contribute substantially to the growing global energy portfolio for some time to come. At the same time atmospheric carbon levels and economic concerns are increasingly shaping the power generation environment. Supercritical fluid technologies are being investigated to address both concerns. For example, direct fired supercritical CO 2 power cycles offer key advantages for carbon capture and thermal efficiency. Additionally, the supercritical water reactor Generation IV nuclear reactor allows higher power densities and more efficient operation than current pressurized or boiling water reactors. As these technologies are developed, a need exists for accurate, yet cost-effective modeling and simulation solutions to assist with design and safety calculations. Supercritical fluid properties are strongly dependent on temperature which results in a number of unique flow features. Among these features are the complex buoyancy and buoyancy-turbulence interaction behaviors exhibited by supercritical flows that are not found in liquid or gas flows. Therefore, standard turbulence models with current model coefficient values are not likely to be applicable to supercritical fluid flows. The subject of this paper is efficient modeling and simulation of supercritical flows to support nascent technologies growing to maturation and operational deployment. We present a framework for developing Reynolds-Averaged Navier-Stokes turbulence models specifically equipped for the challenges of supercritical flows. A novel formulation of the algebraic heat flux model of the buoyancy production of turbulence term is used with a traditional shear stress transport model. To produce a new turbulence model for supercritical channel flows, the empirical coefficients of the resulting four equation model were calculated from data previously published by other authors regarding upward supercritical flow through heated pipes. The presented SST k t - ω t approach was validated against heated tube experiments to show predictive capabilities in moderate flow conditions, where buoyancy effects are important but not dominating of inertial effects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A Gaussian process autoregressive model capturing microstructure evolution paths in a Ni–Mo–Nb alloy

Additive manufacturing is increasingly being employed to produce components of complex geometries in structural alloys because of the expected energy savings associated with the near-net-shape capability and the ability to build in novel internal features that are not possible with many conventional manufacturing approaches. However, because of the extreme thermal conditions encountered, the non-equilibrium microstructures produced during powder bed-based additive manufacturing processes must be subjected to custom post-heat treatment processes to recover the target mechanical properties. Phase-field models and simulation techniques have matured to a state where the microstructure evolution paths, and the morphologies of the resulting precipitate phases can be predicted reasonably accurately, considering alloy-specific thermodynamic and kinetic aspects of the nucleation and growth processes. However, phase-field simulations are computationally intensive, which precludes the ability to apply the simulations directly to the length scale of the entire component. Therefore, it is highly desirable to develop low-computational-cost surrogate models that effectively capture the physics at the microstructural length scale, while facilitating the design of optimized processing conditions resulting in location-specific targeted microstructures at the component scale. The work presented here demonstrates the application of the materials knowledge system framework to develop a surrogate model that effectively captures the microstructural path during annealing of a Ni–Mo–Nb alloy containing different Mo and Nb compositions known to segregate during solidification under additive manufacturing conditions. Specifically, the surrogate model built in this work is based on a Gaussian process autoregressive model informed by statistical representation of simulated microstructures using two-point correlations and dimensionality reduction through principal component analysis. In conclusion, this surrogate model is shown to capture the bifurcation of the microstructural path during precipitation, which yields a microstructure dominated by the $\gamma^{\prime\prime}$ phase at high Nb concentrations and the $\delta$ phase at low Nb concentrations.

36 MATERIALS SCIENCE↗

Identification of blind geothermal resources in Surprise Valley, CA, using publicly available groundwater well water quality data

Geothermal resource exploration is generally limited to areas with surface expressions of thermal activity (fumaroles and hot springs), or relies on expensive geophysical exploration techniques. The hidden subsurface distribution of geothermal fluids has been identified using a free and publicly available water quality dataset from agricultural and domestic water wells in Surprise Valley, northeastern California. Thermally evolved waters in Surprise Valley have element ratios that vary in response to Ca carbonate and Mg silicate mineral precipitation, and have elevated total dissolved solids (TDS). The arid climate in Surprise Valley leads to surface water evaporation in a closed basin, producing high TDS Na-Cl-CO 3 -SO 4 brines in three ephemeral alkali lakes and in shallow groundwater under elevated soil CO 2 conditions. Evaporated fluids in Surprise Valley follow a chemical divide that leads to Ca carbonate and Mg silicate mineral precipitation. Plots of dissolved element ratios can be used to distinguish groundwater affected by evaporation from water affected by thermal water-rock interaction, however it is challenging to select components for plotting that best illustrate different fluid evolution mechanisms. Here, we use a principal component analysis of centered log-ratio transformed data, coupled with geochemical models of fluid evaporation and thermal mixing pathways, to identify components to plot that distinguish between groundwater samples influenced by evaporation from those influenced by thermal processes. We find that groundwater samples with a thermal signature come from wells that define a coherent, linear geographical distribution that closely matches the location of known and inferred faults. Finally, modification of the general approach employed here provides promise for identifying blind geothermal resources in other locations, by applying low-cost geochemical modeling and statistical techniques to areas where large groundwater quality geochemical datasets are available.

15 GEOTHERMAL ENERGY↗

Cost optimization in low volume VLSI circuits

The relationship of integrated circuit (IC) cost to electronic system cost is developed using models for integrated circuit cost which are based on design/fabrication approach. Emphasis is on understanding the relationship between cost and volume for custom circuits suitable for NASA applications. In this report, reliability is a major consideration in the models developed. Results are given for several typical IC designs using off the shelf, full custom, and semicustom IC's with single and double level metallization.

Cook, K. B., Jr.↗

Designing Iowa Agricultural Landscapes to Improve Environmental Co-Benefits of Bioenergy Production

Cellulosic bioenergy feedstocks are needed to improve carbon (C) management while provisioning biomass for bioproducts and biofuel. The transition to increased cellulosic biomass production can be guided by land management plans designed to improve economic, environmental, and ecological performance. We constructed a sustainability model to compare landscape designs for biofuel production from corn (Zea mays L.) stover and switchgrass (Panicum virgatum L.) in central Iowa, USA. We used the model to compare environmental and socioeconomic outcomes associated with four landscape management strategies, with and without cellulosic biomass markets. We evaluated (1) a fuelshed area containing over 1.2 million ha (3 million acres) of corn and soybean (Glycine max (L.) Merr.) within 80 km (50 miles) of a commercial-scale cellulosic biorefinery in Nevada, Iowa, and (2) the South Fork watershed containing over 72,000 ha (178,000 acres) of these row crops within eight north central Iowa HUC-12 (hydrologic unit code) watersheds. At both landscape scales, we found that it is possible to achieve multiple environmental and socioeconomic benefits concomitantly with cellulosic biomass production by strategically collecting corn stover and converting the 10% of the lowest-profitability row crop land to perennial switchgrass. Potential benefits from landscape design include increased biodiversity, soil and water quality improvements, increased soil carbon sequestration for climate change mitigation, and reduced fertilizer use and cost. Our model results showed that increasing benefits can accrue when complementary conservation practices (e.g., reduced tillage, use of a rye cover crop) are combined and integrated throughout a fuelshed or watershed area. We conclude that ecologically based landscape designs offer valuable insights about costs and benefits of land management alternatives, with relevance for achieving stakeholder goals.

54 ENVIRONMENTAL SCIENCES↗

Estimating the Cost of Doing a Cost Estimate

This article provides a model for estimating the cost required to do a cost estimate...Our earlier work provided data for high technology projects. This article adds data from the construction industry which validates the model over a wider range of technology.

Cost cost estimating budgets budget estimating pro↗

A cost-benefit analysis of landfill mining and material recycling in China

Highlights: • Assessing the economic feasibility of landfill mining. • We applied a cost-benefit analysis model for landfill mining. • Four material cycling and energy recovery scenarios were designed. • We used net present value to evaluate the cost-benefit efficiency. - Abstract: Landfill mining is an environmentally-friendly technology that combines the concepts of material recycling and sustainable waste management, and it has received a great deal of worldwide attention because of its significant environmental and economic potential in material recycling, energy recovery, land reclamation and pollution prevention. This work applied a cost-benefit analysis model for assessing the economic feasibility, which is important for promoting landfill mining. The model includes eight indicators of costs and nine indicators of benefits. Four landfill mining scenarios were designed and analyzed based on field data. The economic feasibility of landfill mining was then evaluated by the indicator of net present value (NPV). According to our case study of a typical old landfill mining project in China (Yingchun landfill), rental of excavation and hauling equipment, waste processing and material transportation were the top three costs of landfill mining, accounting for 88.2% of the total cost, and the average cost per unit of stored waste was 12.7 USD ton{sup −1}. The top three benefits of landfill mining were electricity generation by incineration, land reclamation and recycling soil-like materials. The NPV analysis of the four different scenarios indicated that the Yingchun landfill mining project could obtain a net positive benefit varying from 1.92 million USD to 16.63 million USD. However, the NPV was sensitive to the mode of land reuse, the availability of energy recovery facilities and the possibility of obtaining financial support by avoiding post-closure care.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗