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DOE OSTI2025

Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae

CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in Saccharomyces cerevisiae . Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.

Aptazyme↗

DOE OSTI2015

Covariances in the Generalized Nuclear Data (GND) Structure

The Generalized Nuclear Data structure (GND) is being designed as a new standard for storing evaluated nuclear data. It is intended as an eventual replacement for the ENDF-6 format, and as such must be capable of handling at a minimum all the types of data supported by ENDF-6, including central values and covariances. Containers for storing covariances in GND are being developed, with the goal of representing covariance data in a simple and concise manner, that is easy to read, understand and use. This paper presents an overview of the status of covariances in GND, and on the tools for generating and using covariance data that are being implemented in LLNL's nuclear data toolkit ‘Fudge’.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

Particle tracking acceleration via signed distance fields in direct-accelerated geometry Monte Carlo

Computer-aided design (CAD)-based Monte Carlo radiation transport is of value to the nuclear engineering community for its ability to conduct transport on high-fidelity models of nuclear systems, but it is more computationally expensive than native geometry representations. This work describes the adaptation of a rendering data structure, the signed distance field, as a geometric query tool for accelerating CAD-based transport in the direct-accelerated geometry Monte Carlo toolkit. Demonstrations of its effectiveness are shown for several problems. The beginnings of a predictive model for the data structure's utilization based on various problem parameters is also introduced.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

A fast method for optical simulation of flood maps of light-sharing detector modules

Optical simulation of the detector module level is highly desired for Position Emission Tomography (PET) system design. Commonly used simulation toolkits such as GATE are not efficient in the optical simulation of detector modules with complicated light-sharing configurations, where a vast amount of photons need to be tracked. Here, we present a fast approach based on a simplified specular reflectance model and a structured light-tracking algorithm to speed up the photon tracking in detector modules constructed with polished finish and specular reflector materials. We also simulated conventional block detector designs with different slotted light guide patterns using the new approach and compared the outcomes with those from GATE simulations. And while the two approaches generated comparable flood maps, the new approach was more than 200–600 times faster. The new approach has also been validated by constructing a prototype detector and comparing the simulated flood map with the experimental flood map. The experimental flood map has nearly uniformly distributed spots similar to those in the simulated flood map. In conclusion, the new approach provides a fast and reliable simulation tool for assisting in the development of light-sharing-based detector modules with a polished surface finish and using specular reflector materials.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2016

Determining initial enrichment, burnup, and cooling time of pressurized-water reactor spent fuel assemblies by analyzing passive gamma spectra measured at the Clab interim-fuel storage facility in Sweden

The purpose of the Next Generation Safeguards Initiative (NGSI)–Spent Fuel (SF) project is to strengthen the technical toolkit of safeguards inspectors and/or other interested parties. The NGSI–SF team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay measurements of spent fuel assemblies: (1) verify the initial enrichment, burnup, and cooling time of facility declaration; (2) detect the diversion or replacement of pins; (3) estimate the plutonium mass [which is also a function of the variables in (1)]; (4) estimate the decay heat; and (5) determine the reactivity of spent fuel assemblies. Since August 2013, a set of measurement campaigns has been conducted at the Central Interim Storage Facility for Spent Nuclear Fuel (Clab), in collaboration with Swedish Nuclear Fuel and Waste Management Company (SKB). One purpose of the measurement campaigns was to acquire passive gamma spectra with high-purity germanium and lanthanum bromide scintillation detectors from Pressurized Water Reactor and Boiling Water Reactor spent fuel assemblies. The absolute 137 Cs count rate and the 154 Eu/ 137 Cs, 134 Cs/ 137 Cs, 106 Ru/ 137 Cs, and 144 Ce/ 137 Cs isotopic ratios were extracted; these values were used to construct corresponding model functions (which describe each measured quantity’s behavior over various combinations of burnup, cooling time, and initial enrichment) and then were used to determine those same quantities in each measured spent fuel assembly. Furthermore, the results obtained in comparison with the operator declared values, as well as the methodology developed, are discussed in detail in the paper.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Linear models to perform treaty verification tasks for enhanced information security

Linear mathematical models were applied to binary-discrimination tasks relevant to arms control verification measurements in which a host party wishes to convince a monitoring party that an item is or is not treaty accountable. These models process data in list-mode format and can compensate for the presence of variability in the source, such as uncertain object orientation and location. The Hotelling observer applies an optimal set of weights to binned detector data, yielding a test statistic that is thresholded to make a decision. The channelized Hotelling observer applies a channelizing matrix to the vectorized data, resulting in a lower dimensional vector available to the monitor to make decisions. We demonstrate how incorporating additional terms in this channelizing-matrix optimization offers benefits for treaty verification. We present two methods to increase shared information and trust between the host and monitor. The first method penalizes individual channel performance in order to maximize the information available to the monitor while maintaining optimal performance. Second, we present a method that penalizes predefined sensitive information while maintaining the capability to discriminate between binary choices. Data used in this study was generated using Monte Carlo simulations for fission neutrons, accomplished with the GEANT4 toolkit. Custom models for plutonium inspection objects were measured in simulation by a radiation imaging system. Model performance was evaluated and presented using the area under the receiver operating characteristic curve.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Validation of Geant4 fragmentation for Heavy Ion Therapy

12 C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12 C ion beam, ~70% of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. Here, this work investigates the accuracy of three different nuclear fragmentation models available in the Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12 C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ~5 and ~35% with experimental measurements, the QMD using the “Frag” option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Simulation of the spatial shift in detector response for polarized protons within a calorimeter

Measurement of the helicity dependent elastic electron-proton scattering cross section provides a key means of investigating parity violation within the proton. However, such measurements exhibit potential instrumental effects associated with the detection of polarized recoiled protons. In particular, spin-orbit interactions within a massive detector induce a systematic spatial shift in the detector signal. In this study, we determine the size of this shift using the Geant4 simulation toolkit. For a typical hadron calorimeter, we found a polarization dependent shift on the order of 0.01-0.1 mm, multiple orders of magnitude smaller than the typical spatial resolution seen in hadronic calorimeters. Additionally, we provide the custom modifications required of the Geant4 source code to implement the quasi-elastic scattering of polarized protons incident on nuclei in the detector. The modifications are readily extendable to generic matter sources, and can be used for the study of additional spin dependent observables in Geant4.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

An unstructured mesh based neutronics optimization workflow

We have developed a fully automated workflow to optimize the neutronics performance of the Second Target Station (STS) at the Oak Ridge National Laboratory’s Spallation Neutron Source. The optimization workflow starts with the parametrized solid CAD engineering models and converts them into the unstructured mesh (UM) models for the neutronics calculations with MCNP6.2. Calculations are executed and their results are loaded into the Dakota optimization toolkit. Dakota analyzes the results and proposes new geometry parameters for the next design iteration. The cycle repeats until the optimal parameters are found. The automated CAD to MCNP conversion, the use of high-fidelity UM models, and the use of modern optimizer are the key elements that advance the entire optimization workflow in comparison with the original workflow. The original workflow was based on a simplified constructive solid geometry (CSG) modeling with MCNPX, mcnp_pstudy tool, and an in-house optimizer. Herein to demonstrate the new workflow, we present a case of neutronics optimization of the moderator–reflector assembly (MRA). Apart from the MRA, the workflow can optimize other major STS components, such as the spallation target, neutron beamlines, radiation shielding, and various accelerator components. Importantly, the new workflow opens the door to the advanced multi-physics multi-parameter optimization and has the potential for use in other nuclear physics and accelerator applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Optimization of the Second Target Station cold source moderators using an automated workflow

The Second Target Station (STS) at the US Department of Energy’s Oak Ridge National Laboratory is designed to become the world’s highest peak-brightness spallation source of cold neutrons. Successful completion of the STS, which is currently in the preliminary design phase, will provide transformative new capabilities to examine novel materials for future technologies. At STS, neutrons will be generated by spallation reactions in a solid tungsten target. They will be moderated and thermalized in two cold (20 K) para-hydrogen moderators. Careful optimization of these moderators is essential to the project’s success. To find optimal moderator designs, an advanced optimization workflow integrates high-fidelity neutronics calculations using the Monte Carlo N-Particle (MCNP) transport code MCNP6.2 with state-of-the-art optimization algorithms in the Dakota optimization toolkit. For each design iteration, a parametrized solid CAD geometry is generated in Creo and automatically converted into an unstructured mesh geometry by Attila 4MC for the neutronics calculation with MCNP. Iterations repeat until optimal designs are found. Herein this paper presents the results of a sensitivity and optimization study for the cylindrical and tube moderators. Both moderators can be optimized for maximum peak brightness, maximum time-integrated brightness, or any combination between these extremes. Maximum peak brightness is achieved by using smaller optimal dimensions of the moderators, whereas maximum time-integrated brightness is achieved by using larger dimensions. A Pareto front details the designs that optimally balance both brightness metrics. The Pareto front can be found in only 40–110 iterations with 4–5 design parameters when using the efficient global and Pareto-set optimization algorithms in Dakota. Additionally, important engineering constraints can be taken into account, such as the coupling between the cylindrical moderator radius and aluminum vessel wall thicknesses required to ensure structural integrity of the vessels. This interaction has a significant impact on the resulting optimal designs. Our new, highly efficient, fully automated optimization workflow will be used to optimize additional STS components in the future and can be adopted for design and optimization studies at other experimental neutron and accelerator facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Simulating gas-filled neutron detector responses with DRiFT

– Gas-filled neutron detectors have numerous applications across the nuclear engineering and nuclear physics fields. The ability to accurately model and simulate these detectors is important for those applications but is currently limited by the lack of readily-useable detector response software. Recently, the capabilities of DRiFT, a Detector Response Function Toolkit, were expanded to model gas-filled, He-3 and BF3, neutron detectors so that, combined with the radiation transport capabilities of the MCNP code, a high-fidelity treatment of gas-filled neutron detectors can be obtained. Further, this model has been validated by an experiment carried out with the Epithermal Neutron Multiplicity Counter and its capabilities have been demonstrated in two additional experiments. This work shows that utilizing DRiFT to post-process MCNP outputs produces more accurate results than using the MCNP code alone, reducing the difference between experimental and simulated results for measurements taken near the end of a He-3 tube, where the MCNP code struggles to model inactive regions of the detector, from a maximum of 35% with the MCNP code alone to 15% with the MCNP code plus DRiFT. DRiFT's diagnostic capabilities are also demonstrated with measurements for scenarios when pulse pileup or room return effects are significant and must be considered. Altogether, these measurements underpin the ability of DRiFT to accurately model and predict the behavior of gas-filled neutron detectors, making it a valuable tool for the design and testing of systems and experiments that utilize these detectors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2027

Conceptual design of highly-constrained splitters for the FFA@CEBAF energy upgrade study

The Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab is investigating a significant energy upgrade utilizing Fixed-Field Alternating-gradient (FFA) recirculating arcs. This upgrade requires the design of complex horizontal beam splitters to manage up to six concurrent beam passes. This paper presents the conceptual design of these splitters, which are subject to severe physical constraints imposed by the existing accelerator tunnel and multifaceted beam dynamics requirements for matching into the permanent-magnet FFA arcs. The design methodology, centered on multi-pass simulations in the Bmad toolkit, is detailed from the initial geometric layout through the advanced optics matching. Key results include a robust geometric arrangement that fits within the spatial boundaries and the development of multiple, flexible optics matching solutions. Furthermore, the design integrates a viable scheme for extracting high-energy beams for the experimental halls, a critical operational requirement. This work establishes a comprehensive and viable conceptual design, forming a baseline for future engineering and performance optimization studies.

Bodenstein, R.M. [Thomas Jefferson National Accele↗

DOE OSTI2015

A computationally efficient moment-preserving Monte Carlo electron transport method with implementation in Geant4

This paper presents the theoretical development and numerical demonstration of a moment-preserving Monte Carlo electron transport method. Foremost, a full implementation of the moment-preserving (MP) method within the Geant4 particle simulation toolkit is demonstrated. Beyond implementation details, it is shown that the MP method is a viable alternative to the condensed history (CH) method for inclusion in current and future generation transport codes through demonstration of the key features of the method including: systematically controllable accuracy, computational efficiency, mathematical robustness, and versatility. A wide variety of results common to electron transport are presented illustrating the key features of the MP method. In particular, it is possible to achieve accuracy that is statistically indistinguishable from analog Monte Carlo, while remaining up to three orders of magnitude more efficient than analog Monte Carlo simulations. Lastly, it is shown that the MP method can be generalized to any applicable analog scattering DCS model by extending previous work on the MP method beyond analytical DCSs to the partial-wave (PW) elastic tabulated DCS data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Allowing for crystalline structure effects in Geant4

In recent years, the Geant4 toolkit for the Monte Carlo simulation of radiation with matter has seen large growth in its divers user community. A fundamental aspect of a successful physics experiment is the availability of a reliable and precise simulation code. Geant4 currently does not allow for the simulation of particle interactions with anything other than amorphous matter. To overcome this limitation, the GECO (GEant4 Crystal Objects) project developed a general framework for managing solid-state structures in the Geant4 kernel and validate it against experimental data. As a result, accounting for detailed geometrical structures allows, for example, simulation of diffraction from crystal planes or the channeling of charged particle.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Direct numerical simulation of reactor two-phase flows enabled by high-performance computing

Nuclear reactor two-phase flows remain a great engineering challenge, where the high-resolution two-phase flow database which can inform practical model development is still sparse due to the extreme reactor operation conditions and measurement difficulties. Owing to the rapid growth of computing power, the direct numerical simulation (DNS) is enjoying a renewed interest in investigating the related flow problems. A combination between DNS and an interface tracking method can provide a unique opportunity to study two-phase flows based on first principles calculations. More importantly, state-of-the-art high-performance computing (HPC) facilities are helping unlock this great potential. This paper reviews the recent research progress of two-phase flow DNS related to reactor applications. The progress in large-scale bubbly flow DNS has been focused not only on the sheer size of those simulations in terms of resolved Reynolds number, but also on the associated advanced modeling and analysis techniques. Specifically, the current areas of active research include modeling of sub-cooled boiling, bubble coalescence, as well as the advanced post-processing toolkit for bubbly flow simulations in reactor geometries. A novel bubble tracking method has been developed to track the evolution of bubbles in two-phase bubbly flow. Also, spectral analysis of DNS database in different geometries has been performed to investigate the modulation of the energy spectrum slope due to bubble-induced turbulence. In addition, the single-and two-phase analysis results are presented for turbulent flows within the pressurized water reactor (PWR) core geometries. The related simulations are possible to carry out only with the world leading HPC platforms. Furthermore, these simulations are allowing more complex turbulence model development and validation for use in 3D multiphase computational fluid dynamics (M-CFD) codes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Application of regression, variance, and density based global sensitivity methods to integrated VERA-CS and BISON simulations [Application of regression, variance, and density based global sensitivity methods to integrated VERA-CS and BISON simulations]

Uncertainty quantification (UQ) and sensitivity analyses (SA) are performed for coupled simulations between VERA-CS, a coupled pin resolved neutron transport and subchannel thermal hydraulics code, and the fuel performance code BISON. The interface between VERA-CS and BISON is performed in a multiphysics environment known as the LOCA Toolkit for U.S. light water reactors (LOTUS) currently under development at Idaho National Laboratory (INL). A focus is placed on using a variety of SA measures, including two regression based (Pearson and Spearman), one variance based (Sobol indices), and three moment independent measures (Delta moment independent measures with L 1 , L 2 , and L ∞ norms). The problem under inspection is a single assembly depletion case for three fuel cycles. The figures of merit are the minimum departure from nucleate boiling ratio (MDNBR), maximum fuel centerline temperature (MFCT), and gap conductance at peak power (GCPP). SA results show MDNBR to be linear with consistent rankings throughout the fuel cycles. MFCT is linear, but with a change in rankings at the switch from open gap to closed gap models. GCPP is nonlinear at intermediate states that coincide with the onset of contact between fuel and cladding. Furthermore, these nonlinear states allow for the showcasing of higher order SA measures over first order methods.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

RISMC industry application #1 (ECCS/LOCA). Core characterization automation: Lattice codes interface for PHISICS/RELAP5-3D

The United States Nuclear Regulatory Commission (U.S. NRC) is currently proposing rule-making “10 CFR 50.46c” to revise the loss-of-coolant-accident (LOCA) and emergency core cooling system (ECCS) acceptance criteria to include the effects of higher burn-up on cladding performance. The key implications of this proposition are that the cladding performance cannot be evaluated anymore as separated from other disciplines, but needs to be evaluated in a coupled manner with other physics. The Risk-Informed Safety Margin Characterization (RISMC) Pathway initiated several programs at Idaho National Laboratory (INL) to support the industry in the transition to the new rule. One of these programs is the Industry Application #1 (IA1). IA1’s goal is to develop an Integrated Evaluation Model (IEM) called LOCA Toolkit for the US (LOTUS). This tool connects five major disciplines involved in LOCA analysis, among them is (automated) core design (CD-A). Here, this paper focuses solely on the design of LOTUS' CD-A module as well as a demonstration application of the CD-A module to a generic Pressurized Water Reactor (PWR). The demonstration of the other LOTUS disciplines together with a demonstration example of the final risk-informed safety margin analysis is published in a separate paper. LOTUS is meant to provide the methodology framework into which the user can plug his established tools and codes. With the CD-A, the plant owner/operator will characterize his core design with the tools he has. He will then integrate his tools/methods into the LOTUS framework for the downstream safety analysis. For the current CD-A demonstration, the tools used are the already coupled codes PHISICS and RELAP5-3D, while cross section generation is done using the Studsvik lattice code HELIOS-2.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

59 Co(p,X) spallation reaction cross sections for 250 MeV to 2 GeV protons

Cobalt is an advantageous target for probing the physics of nuclear spallation, because it is a naturally mono-isotopic element ( 59 Co), and its per-nucleon binding energy (BE/A = 8.768 MeV) is near the maximum value for all nuclei. We measured nuclear spallation cross sections for the 59 Co(p,X) reaction at five kinetic energies ranging from 250 MeV to 2 GeV. Cross sections for the production of 58 Co, 57 Co, 57 Mn, 56 Co, 56 Mn, 56 Cr, 55 Fe, 53 Fe, 54 Mn, 52 Mn, 51 Cr, 49 Cr, 48 V, 47 Sc, 46 Sc, 44 Sc, and 44 Scm are reported. Where comparable data exist in the EXFOR reaction database, we find that our measured cross sections generally agree. In many cases, we provide data for reactions or energies not currently reported in EXFOR. Our cross sections also provide evidence for the presence of α-clusters within the 59 Co nucleus, a surprising result given the asymmetry in Z (27) and N (32) for this nucleus. Finally, we use our measurements to evaluate the accuracy of spallation cross section simulations from GEANT4-based radiation transport toolkit, performed with the INCLXX-, Bertini-, and Binary-ion-cascade (BIC) based physics lists. This benchmarking activity revealed that the simulations overestimated the cross sections by a factor of ∼2–4 on average, and that the INCL-XX physics list provides the most reliable results. This evaluation informs the selection of the GEANT4 physics lists used for the analysis of data from NASA’s Psyche mission, which will measure γ rays and neutrons resulting from spallation reactions occurring on the surface of an asteroid whose surface is thought to be rich in iron-nickel metal.

43 PARTICLE ACCELERATORS↗