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DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Temporal mismatches in flight activity patterns between Pipistrellus kuhlii and Prays oleae in olive farms: Implications for biocontrol services potential

Abstract Biocontrol services are widely recognized to provide key incentives for bat conservation. However, we have virtually no information on whether and how disruptions in bat‐mediated biocontrol services are driven by mismatches between the temporal activity patterns of insectivorous bats and insect pests. We investigated the temporal relationship between the nightly activity patterns of the common pipistrelle bat ( Pipistrellus kuhlii ) and the olive fruit moth ( Prays oleae ). Temporal mismatches between species pairs were estimated as the time difference (expressed as a percentage of the night) at which P. kuhlii and P. oleae reached 50% of their abundance. The study was carried out during spring, summer, and fall between 2017 and 2019 in 60 olive farms representing increasing levels of structural simplification (as a surrogate of agricultural intensification). Olive farms were classified as exhibiting high (i.e. HIGH olive farms; n = 27), intermediate (MID; n = 18), and low (LOW; n = 15) structural complexity. Temporal mismatches between the activity levels of P. kuhlii and P. oleae varied between seasons and types of olive farms, being comparatively lower in summer than in spring and fall. Furthermore, summer was the only season in which temporal mismatches between species pairs differed between types of olive farms, with higher temporal mismatches found in LOW than in HIGH and MID olive farms. Overall, our work demonstrates the existence of temporal mismatches between the nightly activity patterns of P. kuhlii and P. oleae . Furthermore, it demonstrates that the structural simplification of olive farms increases temporal mismatches between species pairs, particularly in summer when bat‐mediated biocontrol services are most needed. Synthesis and applications . Future research should consider mismatches between the temporal activity patterns of insectivorous bats and insect pests. Otherwise, the actual impact of agricultural intensification on bat‐mediated biocontrol services as well as the economic impact of their loss on the agriculture industry might be underestimated. To enhance biocontrol services, we propose increasing the availability of suitable roosting and foraging sites as well as conserving areas of remnant native woodland and scattered hollow‐bearing trees.

Herrera, José M.↗

DOE OSTI2021

A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure

In this work, cascading transmission line failures are studied through a dynamical model of the power system operating under fixed conditions. The power grid is modeled as a stochastic dynamical system where first-principles electromechanical dynamics are excited by small Gaussian disturbances in demand and generation around a specified operating point. In this context, a single line failure is interpreted in a large deviation context as a first escape event across a surface in phase space defined by line security constraints. The resulting system of stochastic differential equations admits a transverse decomposition of the drift, which leads to considerable simplification in evaluating the quasipotential (rate function) and, consequently, computation of exit rates. Tractable expressions for the rate of transmission line failure in a restricted network are derived from large deviation theory arguments and validated against numerical simulations. Extensions to realistic settings are considered, and individual line failure models are aggregated into a Markov model of cascading failure inspired by chemical kinetics. Cascades are generated by traversing a graph composed of weighted edges representing transitions to degraded network topologies. Numerical results indicate that the Markov model can produce cascades with qualitative power-law properties similar to those observed in empirical cascades.

Kinetic Monte Carlo, rare events, Cascading Failur↗

DOE OSTI2024

Estimates of Southern Hemispheric Gravity Wave Momentum Fluxes across Observations, Reanalyses, and Kilometer-Scale Numerical Weather Prediction Model

Abstract Gravity waves (GWs) are among the key drivers of the meridional overturning circulation in the mesosphere and upper stratosphere. Their representation in climate models suffers from insufficient resolution and limited observational constraints on their parameterizations. This obscures assessments of middle atmospheric circulation changes in a changing climate. This study presents a comprehensive analysis of stratospheric GW activity above and downstream of the Andes from 1 to 15 August 2019, with special focus on GW representation ranging from an unprecedented kilometer-scale global forecast model (1.4 km ECMWF IFS), ground-based Rayleigh lidar (CORAL) observations, modern reanalysis (ERA5), to a coarse-resolution climate model (EMAC). Resolved vertical flux of zonal GW momentum (GWMF) is found to be stronger by a factor of at least 2–2.5 in IFS compared to ERA5. Compared to resolved GWMF in IFS, parameterizations in ERA5 and EMAC continue to inaccurately generate excessive GWMF poleward of 60°S, yielding prominent differences between resolved and parameterized GWMFs. A like-to-like validation of GW profiles in IFS and ERA5 reveals similar wave structures. Still, even at ∼1 km resolution, the resolved waves in IFS are weaker than those observed by lidar. Further, GWMF estimates across datasets reveal that temperature-based proxies, based on midfrequency approximations for linear GWs, overestimate GWMF due to simplifications and uncertainties in GW wavelength estimation from data. Overall, the analysis provides GWMF benchmarks for parameterization validation and calls for three-dimensional GW parameterizations, better upper-boundary treatment, and vertical resolution increases commensurate with increases in horizontal resolution in models, for a more realistic GW analysis. Significance Statement Gravity wave–induced momentum forcing forms a key component of the middle atmospheric circulation. However, complete knowledge of gravity waves, their atmospheric effects, and their long-term trends are obscured due to limited global observations, and the inability of current climate models to fully resolve them. This study combines a kilometer-scale forecast model, modern reanalysis, and a coarse-resolution climate model to first compare the resolved and parameterized momentum fluxes by gravity waves generated over the Andes, and then evaluate the fluxes using a state-of-the-art ground-based Rayleigh lidar. Our analysis reveals shortcomings in current model parameterizations of gravity waves in the middle atmosphere and highlights the sensitivity of the estimated flux to the formulation used.

Meteorology & Atmospheric Sciences↗

DOE OSTI2026

Data for Impact of Vertical and Seasonal Variation in Leaf Traits on Simulating Soybean Canopy Photosynthesis via 1D and 3D Modeling

Accurate modeling of photosynthesis is crucial for predicting crop productivity and quantifying the carbon cycle in agroecosystems. Leaf traits are essential inputs for modeling canopy photosynthesis. Yet, many existing models still use fixed plant functional type (PTF)-based values to parameterize leaf traits under a big-leaf or two-big-leaf assumption, neglecting their vertical profiles and seasonal changes. This simplification may introduce significant uncertainties in estimating gross primary productivity (GPP). In this study, we simulated soybean GPP and tested the effects of vertical and seasonal variation in three key leaf photosynthetic traits: the maximum carboxylation rate at 25 °C (Vcmax25), leaf chlorophyll content (LCC), and leaf mass per area (LMA) in the 1D-SCOPE and 3D-Helios models. Weekly field measurements were conducted during the growing season of 2024 to support the simulation. We designed ten leaf trait parameterization schemes by incorporating different combinations of vertical profiles and seasonal changes, while assuming homogeneous canopy architecture in both models. Our results revealed that Vcmax25 vertical and seasonal variation had the strongest influence on simulated GPP in both 1D and 3D models, while LCC and LMA effects were minimal. Particularly, the scheme with an empirically parameterized Vcmax25 profile achieved comparable performance to the scheme with the measured Vcmax25 profile. Both 1D-SCOPE and 3D-Helios accurately modeled GPP (SCOPE: R2 = 0.87, Bias = 0.55 µmol m⁻² s⁻¹; Helios: R2 = 0.9, Bias = 0.22 µmol m⁻² s⁻¹) under the most complex scheme, and their responses to vertical and seasonal variation in leaf traits were consistent, demonstrating the robustness of our findings. Based on our findings, we propose a scalable framework for parameterizing leaf traits to improve GPP simulations. This study contributes to improving the representation of leaf trait dynamics in canopy-level photosynthesis models, potentially enhancing our ability to predict crop productivity and understand agroecosystem carbon dynamics.

Photosynthesis↗

DOE OSTI2025

Learning the simplicity of scattering amplitudes

The simplification and reorganization of complex expressions lies at the core of scientific progress, particularly in theoretical high-energy physics. This work explores the application of machine learning to a particular facet of this challenge: the task of simplifying scattering amplitudes expressed in terms of spinor-helicity variables. We demonstrate that an encoder-decoder transformer architecture achieves impressive simplification capabilities for expressions composed of handfuls of terms. Lengthier expressions are implemented in an additional embedding network, trained using contrastive learning, which isolates subexpressions that are more likely to simplify. The resulting framework is capable of reducing expressions with hundreds of terms—a regular occurrence in quantum field theory calculations—to vastly simpler equivalent expressions. Starting from lengthy input expressions, our networks can generate the Parke-Taylor formula for five-point gluon scattering, as well as new compact expressions for five-point amplitudes involving scalars and gravitons.

Cheung, Clifford [California Institute of Technolo↗

DOE OSTI2021

Flowsheet Evaluation of Dissolving Used Nuclear Fuel in PUREX Solvent

This study explores the potential benefit to the used nuclear fuel actinide recovery flowsheet of a process simplification and establish the experimental work needed to develop the simplified flowsheet. The simplification is based on replacing acid dissolution of used nuclear fuel with dissolution in the tri-butyl phosphate solvent used in the industrially mature Plutonium Uranium Reduction Extraction flowsheet. Though characterized by considerable uncertainty, simplified flowsheets appear feasible and potentially offer significant reductions in process complexity, nitrate inventory, secondary liquid effluent generation and plant footprint. Initial development of the technology should focus on key fission product and actinide dissolution as a function of process conditions and understanding the fundamental chemistry of tri-butyl phosphate solvent chemistry. Development of ancillary technologies for minor actinide separations and fuel pretreatment for tritium management is also recommended.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Parametric Study of 239 Pu and 235 U Mass Equivalency in Spherical Geometries

In this technical document, parametric studies were performed to determine if a bounding mass equivalency can be used to simplify multi-material models in MCNP6 for criticality evaluations. The studies explored the simplification of MCNP6 models by substituting materials, particularly 239 Pu for 235 U. The initial hypothesis for the material simplification is based on the subcritical mass limits from the ANSI/ANS- 8.1 standard which states that for water reflected metal spheres the limits are 20.1 kg 235 U and 5.0 kg 239 Pu. Using those masses, it was hypothesized that a 20.1 kg sphere of 235 U and a 5.0 kg sphere of 239 Pu could be considered to have the same multiplication. Given that equivalency, 4kg 235 U could be modeled by 1kg 239 Pu (i.e., a mass ratio of 4:1). The parametric studies compare the materials 239 Pu and 235 U independently and in multi-material spherical models. Critical mass, critical thickness, critical mass ratio and critical thickness ratio values are presented as functions of inner radius. keff values are presented as a function of inner radius at different mass ratios and total masses. Results indicate that the conservative bounding mass equivalency is one. That is, if substituting 239 Pu for 235 U it should be done on a gram for gram basis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

DECOVALEX-2023: Task F2 Salt Final Report

The subject of Task F of DECOVALEX-2023 concerns performance assessment modelling of radioactive waste disposal in deep mined repositories. The primary objectives of Task F are to build confidence in the models, methods, and software used for performance assessment (PA) of deep geologic nuclear waste repositories, and/or to bring to the fore additional research and development needed to improve PA methodologies. In Task F2- (salt), these objectives have been accomplished through staged development and comparison of the models and methods used by participating teams in their PA frameworks. Coupled-process submodels and deterministic simulations of the entire PA model for a reference scenario for waste disposal in domal salt have been conducted. The task specification has been updated continuously since the initiation of the project to reflect the staged development of the conceptual repository model and performance metrics. Thermal, hydrological, mechanical, and chemical properties of individual components of the engineered and natural system were chosen for relevance by participating teams. The salt reference case system was characterized using data and measurements collected at relevant underground research laboratories (URLs), field sites, and simulation results from teams with specialized modelling capability. Participating teams made a wide range of model assumptions from compartmentalized networks to full 3D models of the salt formation. No single contributed model includes full-fidelity representation of all the features, events, and processes (FEPs) detailed in the task specification, but almost all features and processes are represented in at least one model. Despite differences in the modelling strategies developed by participating teams, all models indicate that salt compaction and radionuclide diffusion are key processes in the repository, and for the FEPs and model scenario considered, little of the disposed radionuclides will migrate beyond the repository seal over the 100,000 year simulations. In general, the model output quantities have the largest differences over the short term and near the waste. The models tend to be more similar further from waste and at later time. Disparities between the models are believed to be due to differing simplifications from the task specification, some of which are chosen simplifications to reduce complexity, and some are restrictions imposed by the modelling tools. A second round of this task has been accepted for DECOVALEX-2027 in conjunction with Task F1 on crystalline PA modelling. The future round includes waste package heating, improved modelling of salt creep closure, additional comparisons of coupled-process sub-models, and the impact of repository engineering design on radionuclide migration in the repository. Participants will also propose and finalize a set of uncertain inputs for the reference case simulations, propagate these uncertainties in a set of realizations, and conduct sensitivity analyses on the simulation results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Small-scale Assessment of Simplified Ceramic Waste Form Processing

The feasibility of directly processing glass-bonded sodalite ceramic waste form materials by heating a mixture of Zeolite 4A, chloride salt, and sodium borosilicate binder glass was demonstrated by generating laboratory-scale materials. This direct processing method eliminates pre-setting the moisture content of the Zeolite 4A, eliminates the step of occluding salt in the prepared Zeolite 4A prior to processing, and can be conducted using larger particle sizes of crushed Zeolite 4A and crushed borosilicate glass than those called for in the current method. These simplifications are expected to facilitate material transfer and handling in a hot cell or controlled atmosphere environment and be more readily implemented at large scale than the current method. Most materials made to assess these simplifications were directly processed at 925 °C for two hours in an argon atmosphere glovebox, but one material was processed at 925 °C for four hours and one material was processed at 880 °C for two hours. Sodalite was generated and became microencapsulated by the binder glass in all materials. The microstructures were uniform throughout each product, were similar in all products, and were similar to the microstructures of materials made previously using the pressureless consolidation or hot isostatic pressing methods. Various formulations showed the efficiency of sodalite generation was not sensitive to the salt-to-Zeolite 4A ratio or salt-to-glass mass ratio, although a greater relative mass of glass is required to encapsulate sodalite generated from large particles of aggregated Zeolite 4A. The upper limit of salt loadings that can be effectively processed remains to be determined. The effectiveness of direct processing provided new insights into the conversion mechanism. The salt was likely dissolved into the glass that transported NaCl into the Zeolite 4A aggregates and sodalite was generated in situ as NaCl migrated from the outside of the aggregate inward. Other salt cations (e.g., potassium, strontium, cesium, and probably lithium) remain dissolved in the glass encapsulating the zeolite/sodalite domains. When the glass solidifies during cooling, small halite inclusion phases form in glass within sodalite domains and large mixed salt inclusions form in glass surrounding the sodalite due to the low solubility of chloride in the (solid) glass. Other salt cations were oxidized during processing and formed inclusions in the bulk glass (e.g., neodymium). Initial degradation tests show the dissolution behavior of directly processed CWF (SCWF) materials is similar to CWF materials made using different methods.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Recent Progress in Modulated Photothermal Radiometry

In this review, the emerging work using a technique known as modulated photothermal radiometry (MPTR) is evaluated. As MPTR has matured, the previous discussions on theory and modeling have become increasingly limited in their applicability to the current state of the art. After a brief history of the technique, the currently used thermodynamic theory is explained, highlighting the commonly applied simplifications. The validity of the simplifications is explored via modeling. Various experimental designs are compared, and the differences are explored. New applications, as well as emerging analysis techniques, are presented to emphasize the trajectory of MPTR.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1973

Computerized logic design of digital circuits

This manual presents a computer program that performs all the work required for the logic design of digital counters or sequential circuits and the simplification of Boolean logic expressions. The program provides both the experienced and inexperienced logic designer with a comprehensive logic design capability. The manual contains Boolean simplification and sequential design theory, detailed instructions for use of the program, a large number of illustrative design examples, and complete program documentation.

Sussow, S.↗

NASA NTRS1976

A method for developing K/S boundary conditions

A method for developing the missing general K/S (Kustaanheimo/Stiefel) boundary conditions is presented, with use of the formalism of optimal control theory. As illustrative examples, the method is applied to the transfer between two position and velocity vectors and to the K/S Lambert problem to derive the missing terminal conditions. The necessary equations for a solution are then developed to the K/S Lambert problem with both the fictitious time, s, and the generalized eccentric anomaly, E, as the independent variables. The latter formulation, requiring the solution of only one nonlinear, well-behaved equation in one unknown, E, results in considerable simplification of the problem. This simplification is possible because the energy equation, in the E-formulation, is separable.

Jezewski, D. J.↗

NASA NTRS1978

Evaluation of the three-dimensional parabolic flow computer program SHIP

The three-dimensional parabolic flow program SHIP designed for predicting supersonic combustor flow fields is evaluated to determine its capabilities. The mathematical foundation and numerical procedure are reviewed; simplifications are pointed out and commented upon. The program is then evaluated numerically by applying it to several subsonic and supersonic, turbulent, reacting and nonreacting flow problems. Computational results are compared with available experimental or other analytical data. Good agreements are obtained when the simplifications on which the program is based are justified. Limitations of the program and the needs for improvement and extension are pointed out. The present three dimensional parabolic flow program appears to be potentially useful for the development of supersonic combustors.

Pan, Y. S.↗

NASA NTRS1980

Pressure and temperature fields associated with aero-optics tests

The experimental investigation carried out in a 6 x 6 ft wind tunnel on four model configurations in the aero-optics series of tests are described. The data obtained on the random pressures (static and total pressures) and total temperatures are presented. In addition, the data for static pressure fluctuations on the Coelostat turret model are presented. The measurements indicate that the random pressures and temperature are negligible compared to their own mean (or steady state) values for the four models considered, thus allowing considerable simplification in the calculations to obtain the statistical properties of the density field. In the case of the Coelostat model tests these simplifications cannot be assumed a priori and require further investigation.

Raman, K. R.↗

NASA NTRS1981

End region and current consolidation effects upon the performance of an MHD channel for the ETF conceptual design

The effects of MHD channel end regions on the overall power generation were considered. The peak plant thermodynamic efficiency was found to be slightly lower than for the active region (41%). The channel operating point for the peak efficiency was shifted to the supersonic mode (Mach No., M sub c approx. 1.1) rather than the previous subsonic operation (M sub c approx. 0.9). The sensitivity of the channel performance to the B-field, diffuser recovery coefficient, channel load parameter, Mach number, and combustor pressure is also discussed. In addition, methods for operating the channel in a constant-current mode are investigated. This mode is highly desirable from the standpoint of simplifying the current and voltage consolidation for the inverter system. This simplification could result in significant savings in the cost of the equipment. The initial results indicate that this simplification is possible, even under a strict Hall field constraint, with resonable plant thermodynamic efficiency (40.5%).

Wang, S. Y.↗

NASA NTRS1983

User alternatives in post-processing for raster-to-vector conversion

A number of Landsat-based coniferous forest stratum maps have been created of the Eldorado National Forest in California. These maps were produced in raster image format which is not directly usable by the U.S. Forest Service's vector-based Wildland Resource Information System (WRIS). As a solution, raster-to-vector conversion software has been developed for processing classified images into polygonal data structures. Before conversion, however, the digital classification images must be simplified to remove high spatial variance ('noise', 'speckle') and meet a USFS ten acre minimum requirement. A post-processing (simplification) strategy different from those commonly used in raster image processing may be desired for preparing maps for conversion to vector format, because simplification routines typically permit diagonal connections in the process of reclassifying pixels and forming new polygons. Diagonal connections are often undesirable when converting to vector format because they permit polygons to effectively cross over each other and occupy a common location. Three alternative methodologies are discussed for simplifying raster data for conversion to vector format.

Logan, T. L.↗

NASA NTRS1984

Modeling the middle atmosphere circulation

Some of the motivations for constructing models of the middle atmosphere circulation are given. These are as follows: (1) to provide a better understanding of middle atmosphere dynamics; (2) to study the coupling of middle atmosphere dynamics with radiation and chemistry; (3) to study the sensitivity of tropospheric climate modeling and/or weather forecasting to changes in the middle atmosphere; (4) to better understand the limitations of more simplified models; (5) to supply a proxy for atmospheric data for diagnostic analysis; and finally, (6) for forecast-analysis of data. Different types of models are discussed in relation to their anticipated use. Various model simplifications, such as using the quasi-geostrophic set of equations and simplified radiative transfer, are discussed as are some of the consequences of these simplifications. Some of the accomplishments of middle atmosphere circulation modeling are presented as are some of the difficulties in existing models. Finally, some of the problems in constructing and verifying middle atmosphere circulation models are discussed.

Geller, M. A.↗