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DOE OSTI2020

System code evaluation of near-term accident tolerant claddings during pressurized water reactor station blackout accidents

Following the Fukushima Daiichi nuclear accident in 2011, researches on Accident-tolerant fuels (ATFs) are currently of high interest in not only the nuclear industry but also governmental and international organizations. In this work, a quantitative evaluation of the performance of monolithic FeCrAl cladding and Cr-coated Zircaloy cladding has been performed for Pressurized Water Reactor (PWR) Station Blackout (SBO) accidents. A generic PWR model has been built in system thermal-hydraulics code TRACE based on the Surry Nuclear Power Station with counter-current natural circulation modelling capability for hotleg and steam generator U-tube components during the accidents. The base model results are then compared to MELCOR and RELAP simulations to verify the system component implementation in TRACE. Two PWR SBO scenarios were investigated, including: short-term SBO and long-term SBO with early reactor coolant pump (RCP) seal failure. These scenarios are defined to be very similar to the accidents studied in the State-of-the-Art Reactor Consequence Analysis (SOARCA) project. TRACE code is modified to reflect the oxidation kinetics of FeCrAl and Cr-coating. Larson-Miller creep rupture model is also implemented in TARCE using its built-in control systems to simulate the creep rupture of hotlegs. Additionally, the comparison between the TRACE models with and without the counter-current flow modeling resulted in significant difference when comparing ATF cladding to Zircaloy for short term SBO, while it marginal impacted the performance during long term SBO with RCP seal failure. For short term SBO, both ATF cladding underwent hot leg creep rupture ~20 min after Zircaloy cladding. While Zircaloy and Cr-coated cladding had generated significant amount of hydrogen gas (>10 kg) before the creep rupture event, FeCrAl cladding had only generated <0.5 kg of hydrogen gas. For long term SBO with RCP seal failure, significant hydrogen generation and fuel melting was predicted before hot leg creep rupture for the ATF cladding while providing only 10–20 min additional coping time compared to Zircaloy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Selection of Sampling and Surrogate Modeling Methods for State-Point Evaluations of an AGN-201M Reactor

Nuclear reactor digital twins (DTs) have been proposed for use as a safeguards technology to efficiently monitor new and novel reactors as they come online. A safeguards DT needs to be capable of detecting misuse and diversion as they occur, requiring physics models to be accurate and efficient. Mathematical surrogate models are capable of achieving the necessary efficiency and can largely maintain the accuracy of higher-order models given a quality training sample. The Multiphysics Object-Oriented Simulation Environment (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models. Utilizing an operational AGN-201M reactor’s specifications, two surrogate types were trained on samples of variable size, and using Cartesian products, Latin hypercube sampling, and quadrature sampling, each was compared and evaluated on accuracy when compared to a full-order Monte Carlo model. Both surrogate types were able to capture reactivity changes within 0.05 $ of the Monte Carlo model while reducing the computation costs by eight orders of magnitude.

MOOSE↗

DOE OSTI2023

Comparison of Tritium Dose Calculations from MACCS, UFOTRI, and ETMOD

Tritium exhibits unique environmental behavior because of its potential interactions with water and organic substances. Modeling the environmental consequences of tritium releases can be relatively complex and thus an evaluation of MACCS is needed to understand what updates, if any, are needed in MACCS to account for the behavior of tritium. We examine documented tritium releases and previous benchmarking assessments to perform a model intercomparison between MACCS and state-of-practice tritium-specific codes UFOTRI and ETMOD to quantify the difference between MACCS and state of practice models for assessing tritium consequences. Additionally, information to assist an analyst in judging whether a postulated tritium release is likely to lead to significant doses is provided.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2026

Depletion benchmark for a high-assay low-enriched uranium fuel experiment in the advanced test reactor

Reactor physics depletion benchmarks for high-assay low-enriched uranium (HALEU) fuel are limited in number. In particular, there is limited data for HALEU benchmarks for U-10Mo (uranium-10% molybdenum) plate fuel that is being developed for use in the United States’ high performance research reactors including the Advanced Test Reactor (ATR), Advanced Test Reactor Critical Facility (ATR-C), High Flux Isotope Reactor (HFIR), Massachusetts Institute of Technology Reactor (MITR), University of Missouri Research Reactor (MURR), National Bureau of Standards Reactor (NBSR). These six reactors currently operate with highly enriched uranium dispersed fuel in an aluminum matrix. In support of conversion to a HALEU fuel, qualification of U-10Mo formed into a monolithic foil is being performed. Fuel qualification involves irradiating fuel specimens in the ATR. The irradiation tests provide an opportunity to benchmark depletion capabilities of reactor physics codes in support of the ATR operation, as well as develop benchmarks that can be used by other institutions to benchmark other reactor physics codes. This paper documents the development of a benchmark model of the irradiation of the ATR Full-size plate In center flux trap Position 7 (AFIP-7) experiment using the depletion codes MC21 and Advanced Dimensional Depletion for Engineering of Reactors (ADDER).

Nielsen, Joseph W. [Idaho National Laboratory (INL↗

DOE OSTI2021

Data-Driven Exploration of Climate Attractor Manifolds For Long-Term Predictability

Focal Area: This white paper responds to Focal Area 3. We seek to gain insight into decadal-scale climate predictability by applying novel manifold-finding probabilistic AI techniques to the complex data produced by Earth System models (ESMs) such as E3SM. The associated portfolio of research activities leverages DOE’s asset mix of HPC platforms, climate expertise, climate simulation codes, and AI expertise. Science Challenge: Climate and climate models are dynamical systems exhibiting properties that are interpretable through chaos theory. The theory contains an important concept that is relevant to multi-decade-scale climate prediction: a chaotic attractor. While the space containing all the possible states of the Earth’s atmosphere and ocean, the possible weather, is large, the realized states tend to stay near the smaller-dimensioned attractor. This behavior is responsible for the “order behind the irregularity” [1] of climate phenomena. Climate change can be thought of as a change in the properties of the attractor, and predicting the climate over years to decades is equivalent to predicting how those properties will change. To date, the attractor has been a useful conceptual tool, but has not been amenable to direct characterization. A new development is the advent of efficient high-dimensional manifold-finding probabilistic AI techniques, which permit a data-driven characterization of the ESM attractor and its probability distribution over weather states. Such a characterization would result in a natural dimensional reduction — a “non-linear Principal Components Analysis (PCA) adapted to climate simulation data” — leading to important advances in scenario-based long-term climate prediction, long-term prediction of water cycle extremes, ESM verification, inter-model comparison, and process model development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Wall heating by subcritical energetic electrons generated by the runaway electron avalanche source *

Abstract Subcritical energetic electrons (SEEs) produced by the runaway electron (RE) avalanche source at energies below the runaway threshold are found to be the primary contributor to surface heating of plasma-facing components (PFCs) during final loss events. This finding is supported by theoretical analysis, computational modeling with the Kinetic Orbit Runaway electrons Code (KORC), and qualitative agreement with DIII-D experimental observations. The avalanche source generates significantly more secondary electrons below the runaway threshold, which thermalize rapidly when well-confined. However, during a final loss event, the RE beam impacts the first wall, and SEEs are deconfined before they can thermalize. Additionally, because the energy deposition length decreases faster than energy, the deposited energy density, and thus the maximum PFC surface temperature change, is larger for SEEs than REs. KORC simulations employ an analytic first wall to model particle deconfinement onto a non-axisymmetric wall composed of individual tiles. PFC surface heating is calculated using a 1D model extended to include an energy-dependent deposition length scale. Simulations of DIII-D qualitatively agree with infrared (IR) imaging only when SEEs from the avalanche source are included. These results demonstrate that SEEs are the dominant contributor to PFC surface heating and indicate that the avalanche source plays a critical role in the PFC damage caused during final loss events. The prominence of SEEs also has important implications for interpreting IR imaging, one of the primary diagnostics for RE-wall interaction diagnosis, despite REs dominating the energy and current density. This result improves predictions of wall damage due to post-disruption REs to estimate material lifetime and design RE mitigation systems for ITER and future reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

KokkACC: Enhancing Kokkos with OpenACC

Template metaprogramming is gaining popularity as a high-level solution for achieving performance portability on heterogeneous computing resources. Kokkos is a representative approach that offers programmers high-level abstractions for generic programming while most of the device-specific code generation and optimizations are delegated to the compiler through template specializations. For this, Kokkos provides a set of device-specific code specializations in multiple back ends, such as CUDA and HIP. Unlike CUDA or HIP, OpenACC is a high-level and directive-based programming model. This descriptive model allows developers to insert hints (pragmas) into their code that help the compiler to parallelize the code. The compiler is responsible for the transformation of the code, which is completely transparent to the programmer. This paper presents an OpenACC back end for Kokkos: KokkACC. As an alternative to Kokkos’s existing device-specific back ends, KokkACC is a multi-architecture back end providing a high-productivity programming environment enabled by OpenACC’s high-level and descriptive programming model. Moreover, we have observed competitive performance; in some cases, KokkACC is faster (up to 9×) than NVIDIA’s CUDA back end and much faster than OpenMP’s GPU offloading back end. This work also includes implementation details and a detailed performance study conducted with a set of mini-benchmarks (AXPY and DOT product) and three mini-apps (LULESH, miniFE and SNAP, a LAMMPS proxy mini-app).

Valero Lara, Pedro↗

DOE OSTI2021

Fast ion transport by sawtooth instability in the presence of ICRF-NBI synergy in JET plasmas

JET experiments have shown that the three-ion scenarios using waves in the ion cyclotron range of frequencies (ICRF) is an efficient way to build fast ion population through beam ion acceleration by radio frequency (RF) waves. Here, such a heating scheme is applied to plasmas with at least two thermal ion species. Analysis of mixed discharges with complex heating schemes requires a workflow that allows to model thermal and fast ion transport consistently. This paper is dedicated to modelling of a mixed plasma discharge with significant fraction of fast ions and contributes to development of fast ion transport models. For interpretive analysis with the TRANSP code a JET hydrogen-deuterium (HD) plasma discharge with neutral beam injection (NBI) and ICRF heating has been chosen. The task is complicated by NBI-ICRF synergy and plasma magnetohydrodynamic activity, like sawtooth crashes. D beam ions accelerated by RF waves form a high energy tail in fast ion distribution. Significant difference between the neutron rate computed by TRANSP and measured one is observed if the same diffusivity for electrons and ions is assumed. Sensitivity studies show that uncertainties in input plasma parameters and thermal ion transport models are crucial for modelling mixed plasma discharges and increased D transport is required to reach the plasma composition consistent with diagnostic measurements at the plasma edge. Fast ion redistribution by a sawtooth instability is characterised by non-resonant transport due to reconnection of magnetic field lines and resonant transport caused by resonance interaction between the instability and fast ions. With ORBIT simulations it has been shown that resonant interaction strongly affects fast ions of high energies, like beam ions accelerated by RF waves and fusion products. For the considered case, fast ion profiles simulated by ORBIT remain peaked after the sawtooth crashes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Two-dimensional coherent spectrum of high-spin models via a quantum computing approach

Here in this work we present and benchmark a quantum computing approach to calculate the two-dimensional coherent spectrum (2DCS) of high-spin models. Our approach is based on simulating their real-time dynamics in the presence of several magnetic field pulses, which are spaced in time. We utilize the adaptive variational quantum dynamics simulation algorithm for the study due to its compact circuits, which enables simulations over sufficiently long times to achieve the required resolution in frequency space. Specifically, we consider an antiferromagnetic quantum spin model that incorporates Dzyaloshinskii-Moriya interactions and single-ion anisotropy. The obtained 2DCS spectra exhibit distinct peaks at multiples of the magnon frequency, arising from transitions between different eigenstates of the unperturbed Hamiltonian. By comparing the one-dimensional coherent spectrum with 2DCS, we demonstrate that 2DCS provides a higher resolution of the energy spectrum. We further investigate how the quantum resources scale with the magnitude of the spin using two different binary encodings of the high-spin operators: the standard binary encoding and the Gray code. At low magnetic fields both encodings require comparable quantum resources, but at larger field strengths the Gray code is advantageous. Numerical simulations for spin models with increasing number of sites indicate a polynomial system-size scaling for quantum resources. Lastly, we compare the numerical 2DCS with experimental results on a rare-earth orthoferrite system. The observed strength of the magnonic high-harmonic generation signals in the 2DCS of the quantum high-spin model aligns well with the experimental data, showing significant improvement over the corresponding mean-field results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Development of an Improved RELAP5-3D Model for the High Temperature Test Facility

High-temperature gas-cooled reactors (HTGRs) are rapidly approaching deployment. Confidence in transient analysis of these systems for design, optimization, and licensing calculations requires modeling and simulation tools that have been validated against data relevant to HTGR conditions. The High Temperature Test Facility (HTTF) is an integral effects thermal hydraulics test facility for prismatic HTGRs. In spring and summer of 2019, HTTF was used for a series of experiments that now serve as the basis for the OECD/NEA Thermal Hydraulic Code Validation Benchmark for High Temperature Gas-Cooled Reactors using HTTF Data (HTGR T/H Benchmark). This benchmark contains problems for systems code, computational fluid dynamics (CFD), and coupled systems code/CFD modeling representing lower plenum mixing and both the depressurized and pressurized conduction cooldown (DCC and PCC respectively) transients. Benchmark problems include exercises for code-to-code and code-to-data comparisons as well as an exercise for error scaling between HTTF and the Modular High Temperature Gas-Cooled Reactor, which serves as the basis for the HTTF design. Previous analysis as part of the HTGR T/H benchmark used a RELAP5-3D model developed at Idaho National Laboratory (INL) and demonstrated an ability to reproduce trends in the measured data but difficulties reproducing experimental values within their uncertainty. These difficulties were largely attributed to assumptions made during the development of the initial RELAP5-3D model, which predated the HTTF experiments. A significant cause of difficulty reproducing the measured temperatures may be the radial nodalization of the previous RELAP5-3D model. The new model provides a finer nodalization to assess the impact of radial nodalization and allows for asymmetric heating within the core, which was a feature of multiple HTTF experiments. In this paper, we present the new RELAP5-3D model of HTTF. In addition to describing the new model, this paper compares the new and old models and provides results for a full-power steady state, a DCC, and a PCC in HTTF. These analyses are based on the code-to-code comparison exercises for the DCC and PCC problems of the HTGR T/H benchmark. We present the results of these exercises from the new model and compare them to the results of the old model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Advancement of hybrid fluid-kinetic modeling for HEDP and ICF science

We report on the development progress of a hybrid fluid-kinetic code for simulating fluids and plasmas in a wide range of environments, such as laser–matter interactions, inertial confinement fusion, magnetic confinement fusion, and pulsed power. The suite of numerical tools under development utilizes heterogeneous computer architectures and leverages the benefits of particle–based simulation techniques. By working to combine the kinetic particle-in-cell (PIC) model with a particle-based fluid simulation technique, such as smoothed particle hydrodynamics, we are developing a flexible framework capable of accurately modeling complex flows within and between kinetic and fluid regimes. The TriForce code is under development as a C++ framework for parallel, 3D, particle-based, hybrid ﬂuid-kinetic plasma simulations. The ﬂuid half of TriForce will be based upon the meshless smoothed-particle-hydrodynamics (SPH) approach, well-suited for shear, mixing, and turbulence, whereas the kinetic half resembles a traditional particle-in-cell (PIC) code; other particle-based approaches to fluid modeling that do use a mesh are also possible to use and are under investigation. Maxwell’s electromagnetic field equations are solved either via explicit or implicit algorithms or approximated via resistive magnetohydrodynamics (MHD) using an Ohm’s law and resulting induction equation (extended MHD is under development). A primary goal of enabling direct comparisons, from the same code, between results from the variants of MHD and implicit electromagnetic solutions is to improve our fundamental understanding of systems with magnetic ﬁelds. The code is under development to recover results from both radiation-MHD and fully kinetic codes in those limits, and is continuing to be developed from other follow-on grants to operate in between where both descriptions may co-exist and interact. For certain applications, it is desired for a simulation to contain ﬂuid ions and electrons as well as kinetic ions and electrons. Typically, it is too computationally intensive to model a full-scale ICF or HEDP experiment fully kinetically since many cycles are expended with very small time steps on modeling the ﬂuid part of a material that is well treated by the ﬂuid approximation. In this case, many traditional PIC particles can be replaced with a single ﬂuid particle representing the thermal part of the distribution function, and there are fewer needed kinetic particles, which describe the non-thermal part and can be sub-cycled relative to the ﬂuid particle advance. Furthermore, a pure ﬂuid code may, depending on the problem, simply lack many physically important details that are beyond the scope of its reduced approximations and assumptions. In this report, we summarize the objectives achieved in the development of the collisional and kinetic half of the code, and the physics problems to which the code has been applied in the areas of advanced and innovative fusion concepts, pulsed power, and magneto-inertial fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Denudation, solute export, landscape evolution modeling, and geographic information system data for the East River watershed, Colorado, USA (2020-2024)

This data package contains geographic information system (GIS) layers and tabular datasets associated with the study of lithologic controls on denudation, solute export, carbon-scaling relationships, and transient landscape evolution in the East River watershed near Crested Butte, Colorado, USA. The package includes GIS layers used to produce the Figure 2 map, including drainage, hillshade, lithology, sample locations, and basin polygons, together with comma-separated value (CSV) tables and matching CSV data dictionaries. One group of tables reports sample-level and catchment-level information for river-sediment samples analyzed for in situ-produced cosmogenic beryllium-10 (10Be), including sample names, outlet elevations, geographic coordinates, upstream drainage area, rock-type classes, production-rate scaling scheme, analyzed nuclide, catchment-averaged denudation rates, and associated lower and upper analytical uncertainties. Sample and catchment attributes provide the basis for comparing denudation rates across intrusive, shale, sedimentary, and mixed-lithology settings. A second group of tables reports supporting information for landscape-evolution modeling and the mapped geologic framework of the study area. Included files list parameter values and definitions for the two-phase landscape-evolution simulations, summarize full-domain model erosion fluxes and topographic metrics for different simulation configurations, provide a fixed-area carbon-model scaling table, and summarize mapped geologic units within the East River study domain, including geologic code, formation name, lithologic description, mapped area, and lithologic class grouping. Model outputs and geologic summaries support interpretation of transient landscape behavior and its relation to the mapped distribution of shale, intrusive, sedimentary, and surficial units. A third group of tables reports hydrologic and hydrochemical information used to quantify dissolved export from the watershed. Included files provide site-level values for drainage area, mean annual solute export, standard error of annual export, area-normalized solute yield, and equivalent weathering rate for five East River monitoring sites, along with metadata describing the number, sampling cadence, and date range of discharge records and partial and full total dissolved solids observations used in the solute-yield analyses. The package also contains a supplementary daily ion-load time series with daily mean discharge, discharge observation counts, dissolved concentrations, and daily loads for calcium, magnesium, sodium, potassium, chloride, sulfate, nitrate, fluoride, dissolved silica, charge-balance bicarbonate, and total dissolved solids. The package contains GIS files, comma-separated value files (.csv), CSV data dictionaries, a file-level metadata table, a package-tree text file, and a readme text file.

10Be↗

DOE OSTI2024

Quantitative radiography for determining density fluctuations in HED experiments

We have developed a method to extract density fluctuation measurements from x-ray radiographs of high-energy density (HED) instability growth and turbulence experiments. We use this information to calculate density fluctuation statistics for constraining the performance of turbulent mix models in HED systems. The density calculation combines image filtering, removal of systemic effects such as backlighter variation, calculation of transmission across multiple materials, and use of tracer materials to generate an approximate single-material density field. From the density map, we calculate both average density and a variance-like moment b (density-specific-volume covariance), which we compare to our models. We infer both quantities from a single image, which is significantly more information than the historic single scalar mix width measurements. We also develop a method of analyzing simulation outputs that incorporate both the density fluctuation metric from a turbulence model and the bulk material maps from the hydrodynamic code. This analysis helps address the question of how to initialize the simulations for best comparison to data from systems with large separations of scale in the mixing perturbation initial condition. We find that our data analysis method yields 1D average density and b curves with similar morphology and amplitudes as those from preliminary simulation comparisons.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

QCOR; A Language Extension Specification for the Heterogeneous Quantum-Classical Model of Computation

Quantum computing (QC) is an emerging computational paradigm that leverages the laws of quantum mechanics to perform elementary logic operations. Existing programming models for QC were designed with fault-tolerant hardware in mind, envisioning stand-alone applications. However, the susceptibility of near-term quantum computers to noise limits their stand-alone utility. To better leverage limited computational strengths of noisy quantum devices, hybrid algorithms have been suggested whereby quantum computers are used in tandem with their classical counterparts in a heterogeneous fashion. This modus operandi calls out for a programming model and a high-level programming language that natively and seamlessly supports heterogeneous quantum-classical hardware architectures in a single-source-code paradigm. Motivated by the lack of such a model, we introduce a language extension specification, called QCOR, which enables single-source quantum-classical programming. Programs written using the QCOR library–based language extensions can be compiled to produce functional hybrid binary executables. After defining QCOR’s programming model, memory model, and execution model, we discuss how QCOR enables variational, iterative, and feed-forward QC. Additionally, QCOR approaches quantum-classical computation in a hardware-agnostic heterogeneous fashion and strives to build on best practices of high-performance computing. The high level of abstraction in the language extension is intended to accelerate the adoption of QC by researchers familiar with classical high-performance computing.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Hourly Electricity Demand Profiles for Each County in the Contiguous United States

This dataset provides estimated hourly electricity demand for each county in the contiguous United States from 2016-2023. The demand profiles represent the sum of two components: (1) Weighted averages of reported hourly demand profiles for North American Electric Reliability Corporation balancing authority (BA) regions and subregions, scaled to match annual estimates of county-level retail sales and direct use of electricity and weighted by the estimated percentage of county load served by each BA region or subregion. (2) Weighted averages of modeled hourly, county- and sector-level distributed photovoltaic (DPV) capacity factor profiles, scaled to match annual estimates of on-site consumption of DPV-generated electricity for each county and weighted by the percentage of consumption attributable to each sector Annual county-level retail sales are estimated by aggregating utility-reported sales to the state level and allocating the results to counties according to each county's share of state population. Annual county-level direct use is calculated by aggregating power plant-reported direct use values. Annual county-level on-site consumption of DPV-generated electricity is estimated by aggregating utility-reported net metering data to determine the amount of DPV-generated electricity sold back to the grid for each state, subtracting those values from modeled state-level DPV generation estimates, and allocating the results to counties according to each county's share of statewide modeled DPV generation. The open-source Python code used to develop this dataset is available at "Historical Load Data Repository" link below.

14 SOLAR ENERGY↗

DOE OSTI2022

Holographic measurement and bulk teleportation

Holography has taught us that spacetime is emergent and its properties depend on the entanglement structure of the dual theory. In this paper, we describe how changes in the entanglement due to a local projective measurement (LPM) on a subregion A of the boundary theory modify the bulk dual spacetime. We find that LPMs destroy portions of the bulk geometry, yielding post-measurement bulk spacetimes dual to the complementary unmeasured region A c that are cut off by end-of-the-world branes. Using a bulk calculation in AdS 3 and tensor network models of holography (in particular, the HaPPY code and random tensor networks), we show that the portions of the bulk geometry that are preserved after the measurement depend on the size of A and the state we project onto. The post-measurement bulk dual to A c includes regions that were originally part of the entanglement wedge of A prior to measurement. This suggests that LPMs performed on a boundary subregion A teleport part of the bulk information originally encoded in A into the complementary region A c . In semiclassical holography an arbitrary amount of bulk information can be teleported in this way, while in tensor network models the teleported information is upper-bounded by the amount of entanglement shared between A and A c due to finite-N effects. When A is the union of two disjoint subregions, the measurement triggers an entangled/disentangled phase transition between the remaining two unmeasured subregions, corresponding to a connected/disconnected phase transition in the bulk description. Our results shed new light on the effects of measurement on the entanglement structure of holographic theories and give insight on how bulk information can be manipulated from the boundary theory. They could also represent a first step towards a holographic description of measurement-induced phase transitions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Simulation as a sustainable trading zone: Aiming at intergenerational justice

The paper, drawing on the example of simulation codes used in nuclear physics and high-energy physics, seeks to call attention to the ethical implications of discontinuing support for simulation codes and the loss of knowledge embodied in them. Predicated on the concept of trading zones and actor network models, the paper addresses the problem of extinction of simulation codes and attempts to understand their evolution and development within those frameworks. We show that simulation codes of closed type develop to the level of creoles, becoming local languages and standards of scientific centers and disappearing as their few main developers leave, whereas codes of open types become universal languages, imposing problemsolving patterns on the entire community and crowding out other codes. The paper suggests that because of simulations’ reliance on tacit knowledge, practices entrenched in codes cannot be exhaustively explicated or transmitted through writing alone; on the contrary, the life cycle of a simulation code is determined by the life cycle of its trading zone. We examine the extent to which both of these phenomena pose a risk to the preservation of knowledge. Bearing upon intergenerational ethics, we draw analogies between the pure intergenerational problem (PIP) and the problem of preserving the knowledge implemented in simulation codes and transmitting it to future generations. We argue that for the complete transfer of knowledge, it is necessary to develop and maintain inhabitability and sustainability of simulation trading zones in a controllable way, at least until the demand for these codes is warranted to cease in the future.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗