UC Santa Cruz Previously Published Works

Total Cost of Ownership and Evaluation of Google Cloud Resources for the ATLAS Experiment at the LHC

(2025)

Abstract: The ATLAS Google Project was established as part of an ongoing evaluation of the use of commercial clouds by the ATLAS Collaboration, in anticipation of the potential future adoption of such resources by WLCG grid sites to fulfil or complement their computing pledges. Seamless integration of Google cloud resources into the worldwide ATLAS distributed computing infrastructure was achieved at large scale and for an extended period of time, and hence cloud resources are shown to be an effective mechanism to provide additional, flexible computing capacity to ATLAS. For the first time a total cost of ownership analysis has been performed, to identify the dominant cost drivers and explore effective mechanisms for cost control. Network usage significantly impacts the costs of certain ATLAS workflows, underscoring the importance of implementing such mechanisms. Resource bursting has been successfully demonstrated, whilst exposing the true cost of this type of activity. A follow-up to the project is underway to investigate methods for improving the integration of cloud resources in data-intensive distributed computing environments and reducing costs related to network connectivity, which represents the primary expense when extensively utilising cloud resources.

Quantifying local fishing mortality rates to inform monitoring design for marine reserves

(2025)

In the spatial management of marine resources, there are a variety of contexts in which it is valuable to estimate local, site-specific demographic rates, particularly harvest rates. For example, in the case of no-take marine reserves, estimating the fishing mortality rate (F) prior to reserve implementation can inform quantitative expectations for increases in the abundance of protected populations in the reserve. Additionally, estimating F after implementation could be used to detect poaching. Often the data available for these estimates are length-abundance survey data, such as from visual diver or camera surveys. One can estimate F by fitting models to population size-structure data; understanding how the accuracy of such estimates depends on sampling effort and fish life history can inform monitoring approaches. Here, we quantified the capacity of a state-space integral projection model (SS-IPM) to estimate local F, and how that depends on life history, the true value of F, and monitoring sampling design. We found that estimates of F were (a) more accurate for species with lower natural mortality rates and (b) less precise for higher values of F. Yet, with enough sampling effort, estimates of F were generally within 10% of the true value. In general, estimating local F reliably requires sampling ≥ 100 fish each year over at least 12–15 years. We used empirical data from California to illustrate these general results, which could inform adaptive management plans for other marine reserves globally.

Measurement of the top quark mass with the ATLAS detector using t t ¯ events with a high transverse momentum top quark

(2025)

The mass of the top quark is measured using top-quark-top-antiquark pair events with high transverse momentum top quarks. The dataset, collected with the ATLAS detector in proton–proton collisions at s=13 TeV delivered by the Large Hadron Collider, corresponds to an integrated luminosity of 140 fb⁻¹. The analysis targets events in the lepton-plus-jets decay channel, with an electron or muon from a semi-leptonically decaying top quark and a hadronically decaying top quark that is sufficiently energetic to be reconstructed as a single large-radius jet. The mean of the invariant mass of the reconstructed large-radius jet provides the sensitivity to the top quark mass and is simultaneously fitted with two additional observables to reduce the impact of the systematic uncertainties. The top quark mass is measured to be mt=172.95±0.53 GeV, which is the most precise ATLAS measurement from a single channel.

Cover page of Rapid synthesis of single-layer iron-doped 2H tungsten sulfide via magnetic induction heating for piezocatalytic reduction of oxygen to hydrogen peroxide

Rapid synthesis of single-layer iron-doped 2H tungsten sulfide via magnetic induction heating for piezocatalytic reduction of oxygen to hydrogen peroxide

(2025)

Transition metal dichalcogenides have been attracting extensive attention as effective piezocatalysts for a wide range of applications, in particular, environmental remediation. Herein, WS2 nanoflowers with 2H-rich ultrathin petals are prepared by rapid synthesis based on magnetic induction heating (MIH) of sodium tungstate and thiourea, and the 2H phase is further enriched by Fe doping, in contrast to conventional pyrolysis that produces largely 1 T phase. Among the series, the sample prepared at 400 A for 10 s with an iron loading of ca. 0.1 wt% (3-Fe/WS2-400) exhibits the strongest piezoelectric response and greatest catalytic activity towards the selective reduction of oxygen to hydrogen peroxide under ultrasonic irradiation, reaching an ultrahigh H2O2 generation rate of 4.68 mM g⁻¹ h⁻¹, over 47 times higher than that of bulk-like WS₂. This is due to enhanced adsorption of O2 and manipulation of the electronic band structure by Fe doping that becomes favorable for oxygen reduction to H2O2, as manifested in theoretical studies based on density functional theory calculations. This unique property can be exploited for environmental remediation, as exemplified in the effective degradation of a range of organic pollutants. Results from this study highlight the unique potential of MIH in the structural engineering of functional nanomaterials for sustainable energy technologies.

Observation of VVZ production at s = 13 TeV with the ATLAS detector

(2025)

A search for the production of three massive vector bosons, VVZ(V=W,Z), in proton–proton collisions at s=13 TeV is performed using data with an integrated luminosity of 140 fb−1 recorded by the ATLAS detector at the Large Hadron Collider. Events produced in the leptonic final states WWZ→ℓνℓνℓℓ (ℓ=e,μ), WZZ→ℓνℓℓℓℓ, ZZZ→ℓℓℓℓℓℓ, and the semileptonic final states WWZ→qqℓνℓℓ and WZZ→ℓνqqℓℓ, are analysed. The measured cross section for the pp→VVZ process is 660−90+93(stat.)−81+88(syst.) fb, and the observed (expected) significance is 6.4 (4.7) standard deviations, representing the observation of VVZ production. In addition, the measured cross section for the pp→WWZ process is 442±94(stat.)−52+60(syst.) fb, and the observed (expected) significance is 4.4 (3.6) standard deviations, representing evidence of WWZ production. The measured cross sections are consistent with the Standard Model predictions. Constraints on physics beyond the Standard Model are also derived in the effective field theory framework by setting limits on Wilson coefficients for dimension-8 operators describing anomalous quartic gauge boson couplings.

Cover page of Islet‐2 Is Required for the Survival of Islet‐Expressing Retinal Ganglion Cells but Not for Their Pathfinding to the Contralateral Dorsal Lateral Geniculate Nucleus

Islet‐2 Is Required for the Survival of Islet‐Expressing Retinal Ganglion Cells but Not for Their Pathfinding to the Contralateral Dorsal Lateral Geniculate Nucleus

(2025)

Retinal ganglion cells (RGCs) exhibit remarkable diversity owing to their expression of developmentally expressed transcription factors. Many transcription factors are expressed in unique RGC populations, but their roles within these populations remain undiscovered. The transcription factor Islet-2 (Isl2) is expressed in approximately 30%-40% of contralateral projecting RGCs. Previous work by others found increased ipsilateral innervation of the dorsal lateral geniculate nucleus (dLGN) in Isl2 mutant mice, implicating Isl2 in promoting a contralateral RGC axon trajectory. Since Isl2 mutant mice suffer early neonatal lethality, the role of Isl2 in RGC specification has not been fully explored. To test the role of Isl2 in RGC development, two lines of retina-specific Isl2 mutant mice were generated. Contrary to the findings in Isl2 null mice, Isl2 retinal deletion does not lead to early postnatal lethality or increased ipsilateral projections to the dLGN. Instead, there is a significant reduction in the size of the dLGN and a mild reduction in the size of the ipsilateral projection to the dLGN. Retinal Isl2 mutants also exhibit diminished expression of genes characteristic of Isl2-expressing RGCs, along with increased retinal cell death during development. These findings suggest that Isl2 is required for the development and survival of Isl2-expressing RGC subtypes.

Development of a breathing lung phantom for proton CT imaging.

(2025)

Objective

To report on the design of a deformable lung phantom capable of imitating breathing motion with realistic tissue surrogate properties for proton imaging applications.

Approach

The phantom was manufactured via 3D printing and silicone moulding, with a customised structural design for motor-controlled breathing motion. The overall size of the phantom was rescaled to fit in the experimental proton CT (pCT) scanner prototype, featuring a 284 mm maximum size for the imaging field-of-view. Several flexible resins were evaluated in perspective of flexibility by varying ultraviolet exposure times, as increased exposure results in resin hardening at each layer. We optimised the structure to achieve ideal lung compression properties, while preserving its integrity to hold the weight of a solid tumour. Phantom material properties were characterised by segmentation of each component in X-ray CT and pCT images, to determine the CT number expressed in Hounsfield units and the relative stopping power (RSP) with respect to water.

Main results

We achieved non-homogenous compression in the lung using a grid structure with gradient thickness. The rigid ribcage was 3D printed using granite based material. The tumour motion implemented in the phantom design, as measured using template-matching in fluoroscopic X-ray imaging, revealed hysteretic motion with 10 mm peak-to-peak in the superior-inferior direction.

Significance

The developed deformable lung phantom imitated lung motion characteristics, featuring CT number and RSP values in the range comparable to human tissues. The developed breathing phantom is put forward for experimental motion studies in pCT imaging.

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

(2025)

RNA viruses like SARS-CoV-2 have high mutation rates, which contribute to their rapid evolution. Mutation rates depend on mutation type and can vary between sites in a virus's genome. Understanding this variation can shed light on the mutational processes at play, and is crucial for quantitative modeling of viral evolution. Using millions of SARS-CoV-2 full-genome sequences, we estimate rates of synonymous mutations for each mutation type and examine how much these rates vary between sites. We find a surprisingly high level of variability. A substantial fraction of this variability can be explained by local sequence context, genomic region, and RNA secondary structure. We estimate fitness effects of each mutation based on the number of times it actually occurs versus the number of times it is expected to occur based on a model of the above features. We identify small regions of the genome where synonymous or noncoding mutations occur much less often than expected, indicative of strong purifying selection on the RNA sequence independent of protein sequence. Overall, this work expands our basic understanding of SARS-CoV-2's evolution by characterizing the virus's mutation process at the level of individual sites and uncovering several striking mutational patterns that arise from unknown mechanisms.

A Living Experiment in Concept Formation: Hacking on the Creation of a Language for Autistic Experience

Dinishak, Janette

(2025)

Erratum: Measurement of t-channel production of single top quarks and antiquarks in pp collisions at 13 TeV using the full ATLAS Run 2 data sample

(2025)