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At least 1,657 records · Page 92

$\mathrm{CROPSR}$: an automated platform for complex genome-wide $\mathrm{CRISPR}$ g$\mathrm{RNA}$ design and validation

CRISPR/Cas9 technology has become an important tool to generate targeted, highly specific genome mutations. The technology has great potential for crop improvement, as crop genomes are tailored to optimize specific traits over generations of breeding. Many crops have highly complex and polyploid genomes, particularly those used for bioenergy or bioproducts. The majority of tools currently available for designing and evaluating gRNAs for CRISPR experiments were developed based on mammalian genomes that do not share the characteristics or design criteria for crop genomes. We have developed an open source tool for genome-wide design and evaluation of gRNA sequences for CRISPR experiments, CROPSR. The genome-wide approach provides a significant decrease in the time required to design a CRISPR experiment, including validation through PCR, at the expense of an overhead compute time required once per genome, at the first run. To better cater to the needs of crop geneticists, restrictions imposed by other packages on design and evaluation of gRNA sequences were lifted. A new machine learning model was developed to provide scores while avoiding situations in which the currently available tools sometimes failed to provide guides for repetitive, A/T-rich genomic regions. We show that our gRNA scoring model provides a significant increase in prediction accuracy over existing tools, even in non-crop genomes. CROPSR provides the scientific community with new methods and a new workflow for performing CRISPR/Cas9 knockout experiments. CROPSR reduces the challenges of working in crops, and helps speed gRNA sequence design, evaluation and validation. We hope that the new software will accelerate discovery and reduce the number of failed experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Free-spray characteristics and spray-wall interactions of methanol on a gasoline direct injector under flash-boiling and non-flash-boiling conditions

Methanol is considered a promising alternative fuel for internal combustion engines (ICEs) due to its high-octane number, fast laminar flame speed, and elevated latent heat of vaporization, all of which support higher compression ratios and improved thermal efficiency. However, its substantial latent heat of vaporization also poses cold-start challenges, such as misfire and fuel film deposition. This study aims to investigate methanol spray morphology and spray-wall interaction using the Spray M injector from the Engine Combustion Network within a constant-pressure flow vessel. A recently developed unified numerical framework capable of modeling both flash and non-flash boiling sprays is validated against experimental liquid volume fraction data acquired via 3-D computed tomography. Here, the results reveal that flash boiling significantly alters the spray morphology, leading to smaller droplets and spray collapse due to enhanced air-entrainment-induced turbulence. Quantitative agreement between experiments and simulations confirms this behavior. Coupled 0-D equilibrium and 3-D computational fluid dynamics analyses show that flash boiling accelerates evaporation and reduces fuel residence time, while non-flash conditions maintain a persistent liquid core more susceptible to wall wetting. Wall temperature diagnostics reveal that spray collapse alters heat transfer patterns by shifting cooling effects. Mixture fraction analysis indicates that evaporation is primarily governed by shear-layer turbulence, though deviations from adiabatic equilibrium mixing emerge under low-turbulence conditions. Finally, increasing fuel, ambient, and wall temperatures reduces wall wetting and film thickness, mitigating cold-start risks. These findings enhance the understanding of methanol sprays’ behavior and support its adoption as a viable, alternative fuel for ICEs.

Engine Combustion Network↗

Argon equation of state data to 1 TPa: Shock compression experiments and simulations

Argon is the most abundant noble gas on Earth and its noble, atomic fluid nature makes it an excellent candidate for comparison of experiment and theory at extreme conditions. For this study, we performed a combined computational and experimental study on shock compressed cryogenic liquid argon. Using Sandia's Z machine, we shock compressed liquid argon to 600 GPa and reshock states up to 950 GPa. Laser shock experiments at the Omega Laser facility extend the principal Hugoniot to 1000 GPa and provided temperature data along the principal Hugoniot. The plate impact experiments and laser shock experiments used well-characterized impedance matching standards and demonstrate consistent results between the two platforms over a common range. Density functional theory based molecular dynamics simulations provided additional data on the Hugoniot to 600 GPa. The combined experimental data and simulation results provide constraints on the development of new equation of state models at extreme conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Observation of persistent species temperature separation in inertial confinement fusion mixtures

The injection and mixing of contaminant mass into the fuel in inertial confinement fusion (ICF) implosions is a primary factor preventing ignition. ICF experiments have recently achieved an alpha-heating regime, in which fusion self-heating is the dominant source of yield, by reducing the susceptibility of implosions to instabilities that inject this mass. We report the results of unique separated reactants implosion experiments studying pre-mixed contaminant as well as detailed high-resolution three-dimensional simulations that are in good agreement with experiments. At conditions relevant to mixing regions in high-yield implosions, we observe persistent chunks of contaminant that do not achieve thermal equilibrium with the fuel throughout the burn phase. The assumption of thermal equilibrium is made in nearly all computational ICF modeling and methods used to infer levels of contaminant from experiments. We estimate that these methods may underestimate the amount of contaminant by a factor of two or more.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A Visual Comparison of Silent Error Propagation

High-performance computing (HPC) systems play a critical role in facilitating scientific discoveries. Their scale and complexity (e.g., the number of computational units and software stack) continue to grow as new systems are expected to process increasingly more data and reduce computing time. However, with more processing elements, the probability that these systems will experience a random bit-flip error that corrupts a program's output also increases, which is often recognized as silent data corruption. Analyzing the resiliency of HPC applications in extreme-scale computing to silent data corruption is crucial but difficult. An HPC application often contains a large number of computation units that need to be tested, and error propagation caused by error corruption is complex and difficult to interpret. Here, to accommodate this challenge, we propose an interactive visualization system that helps HPC researchers understand the resiliency of HPC applications and compare their error propagation. Our system models an application's error propagation to study a program's resiliency by constructing and visualizing its fault tolerance boundary. Coordinating with multiple interactive designs, our system enables domain experts to efficiently explore the complicated spatial and temporal correlation between error propagations. At the end, the system integrated a nonmonotonic error propagation analysis with an adjustable graph propagation visualization to help domain experts examine the details of error propagation and answer such questions as why an error is mitigated or amplified by program execution.

97 MATHEMATICS AND COMPUTING↗

L{sup ∞} error bound of conservative compact difference scheme for the generalized symmetric regularized long-wave (GSRLW) equations

In this paper, we design a compact finite difference scheme which preserves the original conservative properties to solve the generalized symmetric regularized long-wave equations. The existence of the difference solution is proved by the Brouwer fixed-point theorem. Applying the discrete energy method, the convergence and stability of the difference scheme is obtained, and its numerical convergence order is O(τ{sup 2}+h{sup 4}) in the L{sup ∞}-norm for u and ρ. For computing the nonlinear algebraic system generated by the compact scheme, a decoupled iterative algorithm is constructed and proved to be convergent. Numerical experiment results show that the theory is accurate and the method is efficient and reliable.

97 MATHEMATICS AND COMPUTING↗

On the Correspondence Between Atmosphere-Only and Coupled Simulations for Radiative Feedbacks and Forcing From CO 2

Atmosphere-only experiments are widely used to investigate climate feedbacks simulated in more computationally expensive fully coupled global climate model simulations. We confirm that this remains a valid approach by comparing the radiative feedbacks and forcing between coupled and atmosphere-only simulations for the latest models taking part in the 6th phase of the Coupled Model Intercomparison Project (CMIP6). For global-mean cloud feedbacks, we find a better than previously known correspondence between these experiments, which applies even to the response of individual cloud properties (amount, altitude, and optical depth) and holds even when considering atmosphere-only simulations of only 1 yr duration. For regional cloud feedbacks, the correspondence between the two experiments is generally present at every geographic location except for the tropical Pacific but takes longer experiments to reveal. For the lapse rate and surface albedo feedbacks, the correspondence between the two experiments is weaker due to the non-uniform warming pattern and loss of sea ice in the coupled experiment. For the across-model relationship between 4xCO 2 effective radiative forcing and feedback, we find a different behavior across experiments in CMIP6 than in CMIP5, casting doubt on the physical significance of previous results that highlighted an anti-correlation between the two quantities. Overall, these results confirm the utility of atmosphere-only experiments particularly to study cloud feedbacks, which are the dominant source of inter-model spread in climate sensitivity.

58 GEOSCIENCES↗

ClusterCAD: a computational platform for type I modular polyketide synthase design

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unifying principles for catalytic hydrotreating processes (Final Technical Report)

This project builds on the hypothesis that the hydrotreating processes for the removal of oxygen and sulfur are fundamentally similar at the atomic-scale and existing knowledge from the treatment of petroleum derived feedstock can be leveraged for the design of novel catalysts for the upgrade of bio-oil. We tested this hypothesis by comparing computed potential energy diagrams for hydrodesulfurization (HDS) of thiophene over MoS 2 with hydrodeoxygenation (HDO) of furan over MoO 3 and concluded that certain aspects, such as catalyst promotion with transition metals, are valid strategies for both reactions. On the other hand, we also noticed significant differences in the mechanism for hydrogen (H 2 ) activation, which requires sites with metallic character. While MoS 2 is known to have metallic edge states that can catalyze H 2 dissociation, this elementary step is prohibitively slow on defect-free oxides. Only in the presence of vacancies or by creating metal/oxide interfaces can efficient H 2 activation sites during HDO be formed. The need for bifunctional catalyst when it comes to efficient and selective HDO or dehydrogenation reactions was further corroborated in joint experimental and theoretical studies of the Guerbet reaction for the coupling of biomass derived oxygenates over PdCu alloys, nitrate reduction over In-promoted Pd nanoparticles, and ethylene dehydroaromatization over Ga-exchanged ZSM-5 zeolites. All of these catalytic systems have in common that catalytic sites with distinct functional requirements are needed to create a working catalyst. Detailed computational studies were carried out for HDO of m -cresol and phenol on Ru-modified TiO 2 surfaces, which allowed us to attribute catalytic activity to the metal/oxide interface. A surprising finding was that heterolytic cleavage of the H-H bond across the Ru/TiO 2 interface was critically important, despite lower barriers for homolytic H 2 activation on Ru metal. The explanation lies in the high barriers for hydrogen spillover from Ru to TiO 2 , which becomes unnecessary in the heterolytic activation pathway. Moreover, we also reported that proton transfer steps between metal and oxide sites are mediated by weakly adsorbed surface water. During attempts to develop and validate a kinetic Monte Carlo (kMC) model for HDO reactions at the Ru/TiO 2 interface, it became clear that lateral interactions are paramount to describe realistic surface chemistry and without these interactions, the reduction and hydroxylation behavior from our simulations was inconsistent with reported experiments. To assess the importance of lateral interactions in popular computational catalyst design strategies relying on the identification of reactivity descriptors, which can be used along with Brønsted–Evans–Polanyi (BEP) and scaling relations as input to a microkinetic model (MKM) to make predictions for activity or selectivity trends, we compared predicted trends with those obtained from descriptor-based kMC models. We critically evaluated the benefits of kMC over MKM in terms of trend predictions and computational cost when using only a small set of input parameters. After confirming that in the absence of lateral interactions the kMC and MKM approaches yield identical trends and mechanistic information, we observed substantial differences between the two kinetic models when lateral interactions were introduced. The mean-field implementation applies coverage corrections directly to the descriptors, causing an artificial overprediction of the activity of strongly binding metals. In contrast, the cluster expansion in kMC implementation can differentiate among the highly active metals but it is very sensitive to the set of included interaction parameters. Considering that computational screening relies on a minimal set of descriptors, for which MKM makes reasonable trend predictions at a ca. three orders of magnitude lower computational cost than kMC, we concluded that the MKM approach does provide an overall better entry point for computational catalyst design. Overall, this project has led to 11 peer-reviewed publications, and their scientific is impact is well illustrated by their combined 702 citations.

08 HYDROGEN↗

Charged particle transport coefficient challenges in high energy density plasmas

High energy density physics (HEDP) and inertial confinement fusion (ICF) research typically relies on computational modeling using radiation-hydrodynamics codes in order to design experiments and understand their results. These tools, in turn, rely on numerous charged particle transport and relaxation coefficients to account for laser energy absorption, viscous dissipation, mass transport, thermal conduction, electrical conduction, non-local ion (including charged fusion product) transport, non-local electron transport, magnetohydrodynamics, multi-ion-species thermalization, and electron-ion equilibration. In many situations, these coefficients couple to other physics, such as imposed or self-generated magnetic fields. Furthermore, how these coefficients combine are sensitive to plasma conditions as well as how materials are distributed within a computational cell. Uncertainties in these coefficients and how they couple to other physics could explain many of the discrepancies between simulation predictions and experimental results that persist in even the most detailed calculations. This paper reviews the challenges faced by radiation-hydrodynamics in predicting the results of HEDP and ICF experiments with regard to these and other physics models typically included in simulation codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Design and implementation of a Thomson parabola for fluence dependent energy-loss measurements at the Neutralized Drift Compression eXperiment

The interaction of ion beams with matter includes the investigation of the basic principles of ion stopping in heated materials. An unsolved question is the effect of different, especially higher, ion beam fluences on ion stopping in solid targets. This is relevant in applications such as in fusion sciences. To address this question, a Thomson parabola was built for the Neutralized Drift Compression eXperiment (NDCX-II) for ion energy-loss measurements at different ion beam fluences. The linear induction accelerator NDCX-II delivers 2 ns short, intense ion pulses, up to several tens of nC/pulse, or 1010-1011 ions, with a peak kinetic energy of ~1.1 MeV and a minimal spot size of 2 mm FWHM. For this particular accelerator, the energy determination with conventional beam diagnostics, for example, time of flight measurements, is imprecise due to the non-trivial longitudinal phase space of the beam. In contrast, a Thomson parabola is well suited to reliably determine the beam energy distribution. The Thomson parabola differentiates charged particles by energy and charge-to-mass ratio, through deflection of charged particles by electric and magnetic fields. During first proof-of-principle experiments, we achieved to reproduce the average initial helium beam energy as predicted by computer simulations with a deviation of only 1.4%25. Successful energy-loss measurements with 1 μm thick silicon nitride foils show the suitability of the accelerator for such experiments. The initial ion energy was determined during a primary measurement without a target, while a second measurement, incorporating the target, was used to determine the transmitted energy. The energy-loss was then determined as the difference between the two energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Framework for International Collaboration on ITER Using Large-Scale Data Transfer to Enable Near-Real-Time Analysis

The global nature of the ITER project along with its projected ~ petabyte per day data generation presents a unique challenge, but also an opportunity for the fusion community to rethink, optimize, and enhance our scientific discovery process. Recognizing this, collaborative research with computational scientists was undertaken over the past several years to create a framework for large-scale data movement across wide-area networks (WANs), to enable global near-real time analysis of fusion data. This would broaden the available computational resources for analysis/simulation, and increase the number of researchers actively participating in experiments. An official demonstration of this framework for fast, large data transfer and real-time analysis was carried out between the KSTAR tokamak in Daejeon, Korea and PPPL in Princeton, USA. Streaming large data transfer, with near real-time movie creation and analysis of the KSTAR Electron Cyclotron Emission imaging (ECEI) data, was performed using the I/O framework ADIOS, and comparisons made at PPPL with simulation results from the XGC1 code. These demonstrations were made possible utilizing an optimized network configuration at PPPL, which achieved over 8.8 Gbps (88% utilization) in throughput tests from NFRI to PPPL. This demonstration showed the feasibility for large-scale data analysis of KSTAR data, and provides a nascent framework to enable use of globally distributed computational and personnel resources in pursuit of scientific knowledge from the ITER experiment.

43 PARTICLE ACCELERATORS↗

Network Anomaly Detection Using Federated Learning

The internet is turning out to be an integral part of every-one's lives as more and more devices are being connected to serve societal needs. Our work is motivated by two ma-jor observations. Firstly, one drawback of connecting to the network is the threat of network attacks that can compromise users' private information, leading to data loss and adversely affecting productivity. There are several traditional security mechanisms to defend against these attacks, such as firewalls, virtual private networks (VPNs), demilitarized zones (DMZs), and vulnerability scanners. One way to prevent these attacks is early detection and prevention. However, these kinds of architecture do not scale very well because of their centralized nature. Secondly, we observe from heuristics and data set distributions that the majority of the requests made to a server are innocuous. Therefore, almost all server request data sets are highly imbalanced, weighted highly towards the harmless requests.

Marfo, William↗

Latest results of the Muon g-2 experiment at Fermilab

The muon magnetic anomaly, aμ = g - 2/ 2, is a low-energy observable which can be both measured and computed to high precision, making it a sensitive test of the Standard Model and a probe for new physics. The Muon g − 2 experiment at Fermilab aims to measure aμ with a final accuracy of 140 parts per billion (ppb). The experiment is based on the measurement of the muon spin anomalous precession frequency, ωa, in a magnetic field. The first result of the experiment, based on the 2018 data-taking campaign, was published in 2021 and it confirmed the previous result obtained at Brookhaven National Laboratory with a similar sensitivity of 460 ppb. In this proceeding, the result based on the 2019 and 2020 datasets is presented and the improvement in the accuracy with respect to the 2018 dataset are discussed.

Sorbara, Matteo [INFN, Rome2; Rome U., Tor Vergata↗

IER-518: Data Analysis for High Multiplication Subcritical Experiments [Slides]

This presentation begins with a discussion of goals & motivation. This lecture then covers: experimental configurations, computational models, experimental measurements and simulations. Finally, this presentation concludes with data analysis & results plus a conclusion.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Numerical simulations of the Los Alamos gapstick experiment

The gapstick is a high explosive (HE) sensitivity test recently developed at Los Alamos. The experiment design was motivated by the traditional gap test and consists of a series of HE and inert pellets in a rate stick configuration. The inert pellets are made increasingly longer so that eventually the attenuated shock is unable to initiate the next HE pellet. While the gapstick is a mechanically simple experiment it poses several challenges for numerical simulation. In particular, accurately modeling the HE initiation and detonation phenomena requires a reactive burn model with sufficient mesh resolution to capture the reaction scales. In this work, the Scaled Uniform Reactive Front (SURF) and Arrhenius Wescott-Stewart-Davis (AWSD) burn models are used for simulations of a PBX 9501 (95 wt% HMX, 5% binder) gapstick. Furthermore, the material model for the inert pellet material, Polyvinylidene Fluoride (PVDF), has a direct influence on the shock propagation and a new equation of state (EOS) calibration for PVDF is developed using available Hugoniot data. Despite some challenges, the simulations are able to reasonably predict shock transit velocities and detonation failure in the gapstick.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A roadmap toward scaling, reasoning and self-evolving foundation models for nuclear and particle physics

Foundation models have revolutionized artificial intelligence, with Large Language Models demonstrating unprecedented capabilities in multimodal understanding, reasoning and tool use. Nuclear and particle physics stands at a critical juncture where similar transformative potential awaits realization. The field generates exabytes of experimental data, exascale simulations, and decades of theoretical insights — yet these remain largely disconnected from modern Artifical Intelligence (AI) capabilities, with most physics AI applications confined to narrow, task-specific models that suffer from domain shifting when applied to real experimental data. We present a roadmap for FM4NPP (Foundation Model for Nuclear and Particle Physics), systematically scaling from current proof-of-concept models to trillion-parameter architectures capable of autonomous discovery. Our approach advances three critical frontiers: unified data infrastructure integrating detector data, scientific knowledge and computational tools across global facilities; multi-facility foundation models enabling cross-experiment knowledge transfer and accelerated discovery; and agentic AI capabilities for reasoning and autonomous tool use. The resulting self-evolving FM4NPP will transform physics research by converting time-intensive data analysis, theory derivation and computational bottlenecks into rapid AI–human collaborative discovery. This paradigm shift promises to fundamentally accelerate scientific progress in nuclear and particle physics, enabling researchers to focus on high-level insights while AI handles routine analysis and explores vast parameter spaces beyond human capacity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Comparative Analysis of Imaging and Measurements of Micrometer-Scale Fracture Aperture Fields Within a Heterogeneous Rock Using PET and X-ray CT

Knowledge of the spatial distribution of fracture apertures is essential for reliable characterization of flow and transport processes in fractured systems and for better understanding of physicochemical matrix–fracture interactions. Here, we propose and test two image-based methods, thereby extending the current experimental capabilities to characterize aperture size distribution in structurally heterogeneous geologic porous media noninvasively. The first approach utilizes an inversion method based on the dataset acquired from positron emission tomography (PET) and the second approach considers an extension of the classic missing attenuation technique that relies on clinical X-ray computed tomography (X-ray CT). Independent sets of imaging experiments are conducted on a fractured basalt core with heterogeneous matrix properties and aperture distributions to compare the two methodologies. A repeat of each experiment is conducted to verify the proposed workflows. The performance of these two imaging techniques is systematically evaluated through the analysis of signal-to-noise ratio, minimum fracture size detectability, and measurement errors. While both approaches provide a reliable estimation of fracture aperture distributions, PET yields a signal-to-noise ratio that is substantially higher than the corresponding X-ray CT measurements. Furthermore, uncertainties of the aperture values for PET are considerably lower ($\bar {\sigma}_{\text {d}} = 15\%$) compared to those obtained from X-ray CT ($\bar {\sigma}_{\text {d}} = 29\%$), allowing for the detection of minimum aperture sizes of 20 $\mu$m with 70% confidence level. Finally, these approaches provide key experimental tools for better understanding dynamic hydromechanical fracture properties in geologic systems.

58 GEOSCIENCES↗