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At least 1,279 records · Page 71

Band Gap Modulation by Two-Dimensional h-BN Nanostructure

Two-dimensional hexagonal boron nitride (h-BN) as a graphene-like material was investigated due to its impending applications in electronics. The h-BN band gap E{sub g} as an important factor and its variation between bilayer ZrSe{sub 2} sheets were explored under an external electric field. The initially indirect band gap is found to convert to direct band gap by means of density functional theory. Additionally, the band gap is modulated by van der Waals corrections from 0.21220 to 0.01770 eV. Based on the results, the proposed heterostructure is converted to the direct band gap, and band gap smoothly decreased from 0.25440 to 0.0436 eV following the application of external electric field from 0.2 to 0.6 eV. Moreover, ZrSe{sub 2}|h-BN|ZrSe{sub 2} is investigated under the applied biaxial compressive strain from 1 to 4%. The findings demonstrated that the gap was decreased by any compressive strain amplification, while the semiconducting behavior in the heterostructure attained to the semi-metallic performance under the increasing strain.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Modeling Resonances of Dielectric Spheres in the Terahertz Range

We have studied the resonance properties of dielectric spheres with subwavelength dimensions in the optical and terahertz frequency range. Distribution of the electric field vector in a sphere irradiated by a plane polarized wave has been numerically simulated using the finite element method. The obtained results clearly demonstrate that it is in principle possible to use resonances of various orders in dielectric spheres for the amplification of current in a conducting antenna with dimensions several times smaller than the radiation wavelength. In the case of resonances within short spectral intervals, it is possible to provide a current density gain up to 25–30 dB as compared to that in the absence of a dielectric sphere surrounding the antenna.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Diverse tumour susceptibility in Collaborative Cross mice: identification of a new mouse model for human gastric tumourigenesis

Objective: The Collaborative Cross (CC) is a mouse population model with diverse and reproducible genetic backgrounds used to identify novel disease models and genes that contribute to human disease. Since spontaneous tumour susceptibility in CC mice remains unexplored, we assessed tumour incidence and spectrum. Design: We monitored 293 mice from 18 CC strains for tumour development. Genetic association analysis and RNA sequencing were used to identify susceptibility loci and candidate genes. We analysed genomes of patients with gastric cancer to evaluate the relevance of genes identified in the CC mouse model and measured the expression levels of ISG15 by immunohistochemical staining using a gastric adenocarcinoma tissue microarray. Association of gene expression with overall survival (OS) was assessed by Kaplan-Meier analysis. Results: CC mice displayed a wide range in the incidence and types of spontaneous tumours. More than 40% of CC036 mice developed gastric tumours within 1 year. Genetic association analysis identified Nfκb1 as a candidate susceptibility gene, while RNA sequencing analysis of non-tumour gastric tissues from CC036 mice showed significantly higher expression of inflammatory response genes. In human gastric cancers, the majority of human orthologues of the 166 mouse genes were preferentially altered by amplification or deletion and were significantly associated with OS. Higher expression of the CC036 inflammatory response gene signature is associated with poor OS. Finally, ISG15 protein is elevated in gastric adenocarcinomas and correlated with shortened patient OS. Conclusions: CC strains exhibit tremendous variation in tumour susceptibility, and we present CC036 as a spontaneous laboratory mouse model for studying human gastric tumourigenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Production, quality assurance and quality control of the SiPM Tiles for the DarkSide-20k Time Projection Chamber

The DarkSide-20k dark matter direct detection experiment will employ a 21 m 2 silicon photomultiplier (SiPM) array, instrumenting a dual-phase 50 tonnes liquid argon Time Projection Chamber (TPC). SiPMs are arranged into modular photosensors called Tiles, each integrating 24 SiPMs onto a printed circuit board (PCB) that provides signal amplification, power distribution, and a single-ended output for simplified readout. Tiles are further grouped into Photo-Detector Units (PDUs). This paper details the production of the Tiles and the Quality Assurance and Quality Control (QA-QC) protocol established to ensure their performance and uniformity. The production and QA-QC of the Tiles are carried out at Nuova Officina Assergi (NOA), an ISO-6 clean room facility at LNGS. This process includes wafer-level cryogenic characterisation, precision die attaching, wire bonding, and extensive electrical and optical validation of each Tile. The overall production yield exceeds 83.5%, matching the requirements of the DarkSide-20k production plan. These results validate the robustness of the Tile design and its suitability for operation in a cryogenic environment.

Acerbi, F. [Fondazione Bruno Kessler]↗

Mapping of the transient electric field causing spark suppression in Micromegas of the ATLAS New Small Wheels

Resistive strips Micromegas are employed in the ATLAS New Small Wheel project. They have already been installed and operate in the experimental cavern of the ATLAS experiment at CERN. This work attempts to describe the mechanism of the surface electric charge spread on a resistive strip of the Micromegas detector and the created transient electric field leading to the suppression of the spark rate in the amplification region. The electric field spatial mapping is calculated versus time by using the accurate 3-layer geometry as a function of the resistive layer thickness around its value used in Micromegas detectors. We also used the approximated method based on 2-layer geometry to investigate its discrepancy from the accurate one.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optical stochastic cooling at Fermilab’s IOTA ring

Stochastic cooling (SC) constitutes one of the greatest conceptual and technological achievements in particle beam cooling. Numerous SC systems have been built in the microwave regime and used to extend the science reach of accelerator facilities worldwide. The ability to sense and correct the particle ensemble using high-bandwidth feedback systems is at the core of the concept. Here, we describe the first realization of SC at optical frequencies and bandwidths. The demonstration was recently carried out at Fermilab’s integrable optics test accelerator (IOTA) storage ring using the transit-time method of optical stochastic cooling (OSC) and achieved an integrated system bandwidth of approximately 20 THz, which is more than 2000 times that of conventional SC systems. This demonstration establishes the foundation for more advanced OSC experiments with high-gain amplification, currently underway at Fermilab, and the eventual application of OSC to colliders and other accelerator facilities.

Jarvis, Jonathan D. [Fermilab]↗

Millions of targets under attack: a macroscopic characterization of the DoS ecosystem

Denial-of-Service attacks have rapidly increased in terms of frequency and intensity, steadily becoming one of the biggest threats to Internet stability and reliability. However, a rigorous comprehensive characterization of this phenomenon, and of countermeasures to mitigate the associated risks, faces many infrastructure and analytic challenges. We make progress toward this goal, by introducing and applying a new framework to enable a macroscopic characterization of attacks, attack targets, and DDoS Protection Services (DPSs). Our analysis leverages data from four independent global Internet measurement infrastructures over the last two years: backscatter traffic to a large network telescope; logs from amplification honeypots; a DNS measurement platform covering 60% of the current namespace; and a DNS-based data set focusing on DPS adoption. Our results reveal the massive scale of the DoS problem, including an eye-opening statistic that one-third of all / 24 networks recently estimated to be active on the Internet have suffered at least one DoS attack over the last two years. We also discovered that often targets are simultaneously hit by different types of attacks. In our data, Web servers were the most prominent attack target; an average of 3% of the Web sites in .com, .net, and .org were involved with attacks, daily. Finally, we shed light on factors influencing migration to a DPS.

Jonker, Mattijs↗

DEDUPKV: A Space-Efficient and High-Performance Key-Value Store via Fine-Grained Deduplication

Log-Structured Merge Tree (LSM-tree) based key-value stores excel in write-intensive environments but suffer from data duplication, consuming up to 49% of storage space in LSM-tree-based key-value store deployments. Traditional solutions like compression and coarse-grained file system-level deduplication introduce overhead or have limited effectiveness. In this study, we propose DedupKV, a fine-grained deduplication framework tailored for LSM-tree, maximizing data reduction efficiency while minimizing write stalls and read overheads. DedupKV features three key innovations: (1) FLUSH-integrated inline deduplication, which removes duplicates during memory-to-storage writes; (2) WAL file-based offline deduplication, repurposing write-ahead logs to avoid double writes; and (3) elastic execution, dynamically balancing inline and offline deduplication based on memory pressure and workload intensity. Additionally, dynamic granularity management reduces deduplication metadata overhead. We implemented these four ideas in RocksDB for the first time and conducted experiments in a Linux environment. Our evaluation shows that WAL file-based offline deduplication and DedupKV outperform BlobDB by 33% and 23%, respectively, in write-heavy workloads, while reducing write amplification by 1.2 ×, 2 ×, and 1.6 × for real KV datasets.

Jamil, Safdar [Sogang University]↗

SlimIO: Lightweight I/O Path Design for Write Isolation in FDP-backed In-Memory Databases

In-Memory Databases (IMDBs) are widely used with HPC applications to manage transient data, often using snapshot-based persistence for backups. Redis, a representative IMDB, employs both snapshot and Write-Ahead Log (WAL) mechanisms, storing data on persistent devices via the traditional kernel I/O path. This method incurs syscall overhead, I/O contention between processes, and SSD garbage collection (GC) delays. To address these issues, we propose SlimIO, which adopts I/O passthru to minimize syscall overhead and inter-process I/O interference. Additionally, it leverages Flexible Data Placement (FDP) SSDs as backup storage to avoid performance degradation from SSD GC. Experimental results show that SlimIO reduces snapshot time by up to 25%, increases query throughput by up to 30% during non-snapshot periods, and lowers 99.9%-ile latency by up to 50%. Furthermore, it achieves a write amplification factor (WAF) of 1.00, indicating no redundant internal writes, thus extending SSD lifespan.

Lee, Sangyun [Sogang University]↗

Novel Liquid Argon Time-Projection Chamber Readouts

Liquid argon time-projection chambers (LArTPCs) have become a prominent tool for experiments in particle physics. Recent years have yielded significant advances in the techniques used to capture the signals generated by these cryogenic detectors. This article summarizes these novel developments for detection of ionization electrons and scintillation photons in LArTPCs. New methods to capture ionization signals address the challenges of scaling traditional techniques to the large scales necessary for future experiments. Pixelated readouts improve signal fidelity and expand the applicability of LArTPCs to higher-rate environments. Methods that leverage amplification in argon enable measurements in the keV regime and below. Techniques to enhance collection of argon scintillation photons improve calorimetry and expand the physics program for very large detectors. Future efforts aim to demonstrate systems for the combined detection of both electrons and photons.

43 PARTICLE ACCELERATORS↗

Probing Electrode-Electrolyte Interfaces Using Nano-Gap Surface-Enhanced Raman Spectroscopy and Imaging

Performance of portable electronic devices and electric vehicles is currently limited by the energy density, lifetime and safety of lithium rechargeable batteries. Overcoming those limitations requires in-depth understanding of the electrode-electrolyte interfaces. Surface-enhanced Raman spectroscopy (SERS) can provide a critical component to this effort as an in situ technique with ultrahigh surface sensitivity that provides quantitative molecular specificity. SERS relies on local electromagnetic field amplification generated by surface plasmon resonance (SPR) at the surface of metal nanoparticles (NPs) with sub-wavelength dimensions. The most significant Raman enhancements have been observed when the local SPRs of multiple NPs interact. This occurs when the NPs are in close proximity (less than 10 nm), which could be achieved in ordered NP monolayers if they could be assembled reproducibly. Methods to assemble gold NPs into large area (cm2) monolayers will be presented. The interparticle gap can be tuned between 1 and 4 nm by using surface ligands of different sizes. The Au NP monolayers exhibit high SERS sensitivity (enhancement factor greater than 107). This allows for the measurement of electrolyte components across a broad range of concentrations. Components include lithium hexafluorophosphate (LiPF6), fluoroethylene carbonate (FEC), ethylene carbonate (EC) and diethyl carbonate (DEC). The investigation of solutions of LiPF6 in EC + DEC binary solvents using SERS allows for the determination of the solvent coordination numbers, which range from 2 to 5. This result is in sharp contrast to the bulk values calculated from infrared spectroscopy, which range from 3 to 7. Numerical simulations show that the electromagnetic field is concentrated in the nanogap, indicating the information of the aprotic electrolyte solution structures is obtained from the immediately adjacent area of the solid substrate. Our findings facilitate a better understanding of the structure of solvated ions in close proximity to the electrode surface.

Yang, Guang↗

lasy v0.1

Lasy is a Python library that facilitates numerical simulations of the interaction of complex laser pulses with plasmas. More specifically, lasy offers many ways to define complex laser pulses (e.g. from commonly-known analytical formulas, from experimental measurements, etc.) and then computes and saves the corresponding laser field in a standardized file. This file can then be read by external plasma simulation codes, that will then simulate the interaction between the complex laser pulse and a plasma. Lasy is useful for instance for numerical simulations of plasma-based particle accelerators, plasma-based laser amplification, etc. Lasy avoids having to duplicate the code that defines complex laser pulses in each plasma simulation codes, and instead provides a trusted, centralized implementation.

Lehe, Remi↗

raogroupuiuc/yl_variantcalling

NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Deewan, Anshu↗

FOILPOLARS (Grassmannian Foil Shape Sweeps for Polar Generation) [SWR-26-095]

FOILPOLARS (Grassmannian Foil Shape Sweeps for Polar Generation): Multifidelity aerodynamic polar data generation for hydrofoil/tidal-turbine airfoil sections. Foilpolars ties together three pieces: *AeroSandbox supplies the baseline airfoil coordinates (UIUC database). *G2Aero parameterizes those shapes on a Grassmannian manifold (Karcher mean + PGA basis) and samples new perturbed shapes around that basis. *XFoil (panel method) and NeuralFoil (neural-network surrogate, shipped with AeroSandbox) each solve the resulting shapes for lift, drag, moment, and pressure at the swept angles of attack, Reynolds numbers, and n_crit values. Design optimization of foil shapes in a computationally efficient way requires polars data across many candidate shapes, not just a handful of baseline foils. However, high-fidelity CFD at that scale is too costly, and naive shape perturbation strays from realistic geometries. FOILPOLARS addresses this by loading baseline airfoils (via AeroSandbox) and mapping them onto a Grassmannian manifold (via G2Aero), computing a Karcher mean and principal geodesic analysis (PGA) basis. New shapes are sampled by perturbing PGA coefficients, keeping them close to the manifold of realistic foils. Each sampled shape is evaluated across a configurable sweep of angle of attack, Reynolds number, and critical amplification factor using two solvers: XFoil (panel method) and NeuralFoil (neural-network surrogate), producing a paired dataset of lift, drag, moment, pressure, convergence, and confidence, indexed alongside each shape's PGA coefficients and shared Grassmannian basis in a single xarray dataset. From this, FOILPOLARS produces convergence summaries and comparison plots per shape, Reynolds number, and n_crit. A command-line interface exposes each pipeline stage independently, supporting data-driven design, optimization, and machine-learning workflows for foils.

Sandhu, Rimple [National Laboratory of the Rockies↗

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters - Fluke- Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3’UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores - mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Lastly, our results exemplify how genetics, epigenetics and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.

59 BASIC BIOLOGICAL SCIENCES↗

BCL10 Mutations Define Distinct Dependencies Guiding Precision Therapy for DLBCL

Activated B cell–like diffuse large B-cell lymphomas (ABC-DLBCL) have unfavorable outcomes and chronic activation of CARD11–BCL10–MALT1 (CBM) signal amplification complexes that form due to polymerization of BCL10 subunits, which is affected by recurrent somatic mutations in ABC-DLBCLs. Herein, we show that BCL10 mutants fall into at least two functionally distinct classes: missense mutations of the BCL10 CARD domain and truncation of its C-terminal tail. Truncating mutations abrogated a motif through which MALT1 inhibits BCL10 polymerization, trapping MALT1 in its activated filament-bound state. CARD missense mutations enhanced BCL10 filament formation, forming glutamine network structures that stabilize BCL10 filaments. Mutant forms of BCL10 were less dependent on upstream CARD11 activation and thus manifested resistance to BTK inhibitors, whereas BCL10 truncating but not CARD mutants were hypersensitive to MALT1 inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL, and further precision can be achieved by selecting therapy based on specific biochemical effects of distinct mutation classes.

60 APPLIED LIFE SCIENCES↗

New York City Impacts on a Regional Heat Wave

Abstract Extreme heat events are projected to increase in magnitude and frequency throughout this century due to increasing global temperatures, making it critically important to acquire improved understanding of their genesis and interactions with large cities. This study presents an application of the factor separation method to assess combined impacts of a synoptic scale heat wave, urban land cover, and urban energy and momentum fluxes on temperatures and winds over New York City via use of high resolution simulations (1 km grid spacing) with an urbanized WRF model. Results showed that, while the heat wave had the largest contribution to temperatures (> 8°C), urban surface factors matched it in highly urbanized areas. Surface factors matched this in highly urbanized areas during night and early morning hours, with contributions up to 5°C, when calm land breeze conditions result in a strong urban heat island. Positive interactions between all factors during morning and nighttime indicate urban heat island amplification of up to 4°C during the heat wave. Midtown Manhattan vertical cross-sections, where urban canopies are most dense, showed a change in the sign (from positive to negative) of the contribution of the urban fluxes between night and day below 500 m, possibly due to radiation blocking and increased thermal storage by buildings as well as frictional effects opposing the incoming warm air.

54 ENVIRONMENTAL SCIENCES↗

Atmosphere–Ocean Coupled Energy Budgets of Tropical Convective Discharge–Recharge Cycles

An energy budget combining atmospheric moist static energy (MSE) and upper ocean heat content (OHC) is used to examine the processes impacting day-to-day convective variability in the tropical Indian and western Pacific Oceans. Feedbacks arising from atmospheric and oceanic transport processes, surface fluxes, and radiation drive the cyclical amplification and decay of convection around suppressed and enhanced convective equilibrium states, referred to as shallow and deep convective discharge–recharge (D–R) cycles, respectively. The shallow convective D–R cycle is characterized by alternating enhancements of shallow cumulus and stratocumulus, often in the presence of extensive cirrus clouds. The deep convective D–R cycle is characterized by sequential increases in shallow cumulus, congestus, narrow deep precipitation, wide deep precipitation, a mix of detached anvil and altostratus and altocumulus, and once again shallow cumulus cloud types. Transitions from the shallow to deep D–R cycle are favored by a positive “column process” feedback, while discharge of convective instability and OHC by mesoscale convective systems (MCSs) contributes to transitions from the deep to shallow D–R cycle. Variability in the processes impacting MSE is comparable in magnitude to, but considerably more balanced than, variability in the processes impacting OHC. Variations in the quantity of atmosphere–ocean coupled static energy (MSE + OHC) result primarily from atmospheric and oceanic transport processes, but are mainly realized as changes in OHC. MCSs are unique in their ability to rapidly discharge both lower-tropospheric convective instability and OHC.

54 ENVIRONMENTAL SCIENCES↗