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At least 433 records · Page 24

Reconstruction of Charged Particle Tracks in Realistic Detector Geometry Using a Vectorized and Parallelized Kalman Filter Algorithm

One of the most computationally challenging problems expected for the High-Luminosity Large Hadron Collider (HL-LHC) is finding and fitting particle tracks during event reconstruction. Algorithms used at the LHC today rely on Kalman filtering, which builds physical trajectories incrementally while incorporating material e ects and error estimation. Recognizing the need for faster computational throughput, we have adapted Kalman-filterbased methods for highly parallel, many-core SIMD and SIMT architectures that are now prevalent in high-performance hardware. Previously we observed significant parallel speedups, with physics performance comparable to CMS standard tracking, on Intel Xeon, Intel Xeon Phi, and (to a limited extent) NVIDIA GPUs. While early tests were based on artificial events occurring inside an idealized barrel detector, we showed subsequently that our mkFit software builds tracks successfully from complex simulated events (including detector pileup) occurring inside a geometrically accurate representation of the CMS-2017 tracker. Here, we report on advances in both the computational and physics performance of mkFit, as well as progress toward integration with CMS production software. Recently we have improved the overall eciency of the algorithm by preserving short track candidates at a relatively early stage rather than attempting to extend them over many layers. Moreover, mkFit formerly produced an excess of duplicate tracks; these are now explicitly removed in an additional processing step. We demonstrate that with these enhancements, mkFit becomes a suitable choice for the first iteration of CMS tracking, and eventually for later iterations as well. We plan to test this capability in the CMS High Level Trigger during Run 3 of the LHC, with an ultimate goal of using it in both the CMS HLT and oine reconstruction for the HL-LHC CMS tracker.

Cerati, Giuseppe↗

Biosensors for detecting and/or neutralizing bioavailable uranium and related U-sensitive genetic molecular components, gene cassettes, vectors, genetic circuits, compositions, methods and systems

UO 2 F 2 biosensors, and related U-sensing and/or F-sensing genetic molecular components, genetic circuits, compositions, methods and systems are described, which in several embodiments can be used to detect and/or neutralize uranium and in particular bioavailable UO 2 F 2 .

Park, Dan Mcfarland↗

Viral‐mediated delivery of morphogenic regulators enables leaf transformation in Sorghum bicolor (L.)

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom (Bbm), Wuschel2 (Wus2), Wuschel-like homeobox protein 2a (Wox2a) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

59 BASIC BIOLOGICAL SCIENCES↗

Data for "Viral-mediated Delivery of Morphogenic Regulators Enables Leaf Transformation in Sorghum bicolor (L.)"

Recent advancements in monocot transformation, using leaf tissue as explant material, have expanded the number of grass species capable of transgenesis. However, the complexity of vectors and reliance on inducible excision of essential morphogenic regulators have so far limited widespread application. Plant RNA viruses, such as Foxtail Mosaic Virus (FoMV), present a unique opportunity to express morphogenic regulator genes, such as Babyboom ( Bbm ), Wuschel2 ( Wus2 ), Wuschel-like homeobox protein 2a ( Wox2a ) and the GROWTH-REGULATING FACTOR 4 (GRF4) GRF-INTERACTING FACTOR 1 (GIF1) fusion protein transiently in leaf explant tissues. Furthermore, altruistic delivery of conventional and viral vectors could provide opportunities to simplify vectors used for leaf transformation—facilitating vector optimization and reducing reliance on morphogenic regulator gene integration. In this study, both viral and conventional T-DNA vectors were tested for their ability to promote the formation of embryonic calli, a critical step in leaf transformation protocols, using Sorghum bicolor leaf explants. Although conventional leaf transformation vectors yielded viable embryonic calli (43.2 ± 2.9%: GRF4-GIF1, 50.2 ± 3%: Bbm/Wus2), altruistic conventional vectors employing the GRF4-GIF1 morphogenic regulator resulted in improved efficiencies (61.3 ± 4.7%). Altruistic delivery was further enhanced with the use of viral vectors employing both GRF4-GIF1 and Bbm/Wus2 regulators, resulting in 75.1 ± 2.3% and 79.2 ± 2.5% embryonic calli formation, respectively. Embryonic calli generated from both conventional and viral vectors produced shoots expressing fluorescent reporters, which were confirmed using molecular analysis. This work provides an important proof-of-concept for the use of both altruistic vectors and viral-expressed morphogenic regulators for improving plant transformation.

gene editing↗

Summer Internship Report: ARA2 Benchmarking

Over the past decade, the RISC-V Instruction Set Architecture (ISA) has emerged as a significant player in both academic and industrial processor design due to its open-source nature, modular extension system, and versatility across domains ranging from microcontrollers to high-performance computing (HPC). One of its most important recent advancements is the RISC-V Vector Extension (RVV), which enables explicit data-level parallelism through vector registers and vectorized instructions. Unlike traditional SIMD (Single Instruction, Multiple Data) architectures that fix vector lengths at design time, RVV uses the concept of VLEN (vector register length) as a hardware-independent parameter and allows software to adapt dynamically to the available vector width. This flexible approach ensures portability across implementations while enabling scalable performance. The ARA2 core is a parameterizable RISC-V vector processor developed at the Integrated Systems Lab at ETH Zürich and the University of Bologna. Designed as a tightly-coupled accelerator to a scalar RISC-V core, ARA2 implements the RVV 1.0 specification and offers tunable architectural parameters such as the number of vector lanes, VLEN, and cache sizes.

97 MATHEMATICS AND COMPUTING↗

Isometries and the double copy

In the standard derivation of the Kerr-Schild double copy, the geodicity of the Kerr-Schild vector and the stationarity of the spacetime are presented as assumptions that are necessary for the single copy to satisfy Maxwell’s equations. However, it is well known that the vacuum Einstein equations imply that the Kerr-Schild vector is geodesic and shear-free, and that the spacetime possesses a distinguished vector field that is simultaneously a Killing vector of the full spacetime and the flat background, but need not be timelike with respect to the background metric. We show that the gauge field obtained by contracting this distinguished Killing vector with the Kerr-Schild graviton solves the vacuum Maxwell equations, and that this definition of the Kerr-Schild double copy implies the Weyl double copy when the spacetime is Petrov type D. When the Killing vector is taken to be timelike with respect to the background metric, we recover the familiar Kerr-Schild double copy, but the prescription is well defined for any vacuum Kerr-Schild spacetime and we present new examples where the Killing vector is null or spacelike. While most examples of physical interest are type D, vacuum Kerr-Schild spacetimes are generically of Petrov type II. We present a straightforward example of such a spacetime and study its double copy structure. Our results apply to real Lorentzian spacetimes as well as complex spacetimes and real spacetimes with Kleinian signature, and provide a simple correspondence between real and self-dual vacuum Kerr-Schild spacetimes. This correspondence allows us to study the double copy structure of a self-dual analog of the Kerr spacetime. We provide evidence that this spacetime may be diffeomorphic to the self-dual Taub-NUT solution.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mallat Scattering Transformation based surrogate for Magnetohydrodynamics

Abstract A Machine and Deep Learning (MLDL) methodology is developed and applied to give a high fidelity, fast surrogate for 2D resistive MagnetoHydroDynamic (MHD) simulations of Magnetic Liner Inertial Fusion (MagLIF) implosions. The resistive MHD code is used to generate an ensemble of implosions with different liner aspect ratios, initial gas preheat temperatures (that is, different adiabats), and different liner perturbations. The liner density and magnetic field as functions of x , y , and z were generated. The Mallat Scattering Transformation (MST) is taken of the logarithm of both fields and a Principal Components Analysis (PCA) is done on the logarithm of the MST of both fields. The fields are projected onto the PCA vectors and a small number of these PCA vector components are kept. Singular Value Decompositions of the cross correlation of the input parameters to the output logarithm of the MST of the fields, and of the cross correlation of the SVD vector components to the PCA vector components are done. This allows the identification of the PCA vectors vis-a-vis the input parameters. Finally, a Multi Layer Perceptron (MLP) neural network with ReLU activation and a simple three layer encoder/decoder architecture is trained on this dataset to predict the PCA vector components of the fields as a function of time. Details of the implosion, stagnation, and the disassembly are well captured. Examination of the PCA vectors and a permutation importance analysis of the MLP show definitive evidence of an inverse turbulent cascade into a dipole emergent behavior. The orientation of the dipole is set by the initial liner perturbation. The analysis is repeated with a version of the MST which includes phase, called Wavelet Phase Harmonics (WPH). While WPH do not give the physical insight of the MST, they can and are inverted to give field configurations as a function of time, including field-to-field correlations.

97 MATHEMATICS AND COMPUTING↗

Supporting data for climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics

This data supports the conclusions found in climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics. Included here are (i) the binarized geolocation vectors used for exhaustive vector comparisons, (ii) the resulting climatic networks, (iii) the results of applying Markov clustering to the climatic networks, and (iv) the results of applying Correlation-of-Correlations (cor-cor) to the climatic networks. The set of binarized geolocation vectors that are used as inputs for the Combinatorial Metrics library (CoMet) are of the form comet-UUUUUxVVVVV-XXXX-YYYY.shuffled.tped where UUUUU is the number of vectors, VVVVV is the length of each vector, XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a geolocation vector of binary elements A (i.e., 0) and T (i.e., 1). The set of climatic networks that are used for downstream network analysis are of the form network-U-way-XXXX-YYYY.parsed.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to an edge linking two geolocations (defined by latitude and longitude) with its corresponding edge weight (i.e., DUO score). The set of cluster results are of the form clusters-U-way-XXXX-YYYY-thresh-VVVV-inflation-WWW.clustered.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, YYYY is the ending year, VVVV is the similarity threshold, and WWW is the Markov clustering inflation rate. Each line corresponds to a single cluster and is composed of a number of corresponding geolocations (defined by latitude and longitude). The set of cor-cor results are of the form corcor-U-way-XXXX-YYYY.cumulative.txt where U is the order of the comparison (2-way or 3-way), XXXX is the starting year, and YYYY is the ending year. Each line corresponds to a single geolocation with it's corresponding cor-cor value.

54 ENVIRONMENTAL SCIENCES↗

Drug Resistance in Filarial Parasites Does Not Affect Mosquito Vectorial Capacity

Parasite drug resistance presents a major obstacle to controlling and eliminating vector-borne diseases affecting humans and animals. While vector-borne disease dynamics are affected by factors related to parasite, vertebrate host and vector, research on drug resistance in filarial parasites has primarily focused on the parasite and vertebrate host, rather than the mosquito. However, we expect that the physiological costs associated with drug resistance would reduce the fitness of drug-resistant vs. drug-susceptible parasites in the mosquito wherein parasites are not exposed to drugs. Here we test this hypothesis using four isolates of the dog heartworm (Dirofilaria immitis)—two drug susceptible and two drug resistant—and two vectors—the yellow fever mosquito (Aedes aegypti) and the Asian tiger mosquito (Ae. albopictus)—as our model system. Our data indicated that while vector species had a significant effect on vectorial capacity, there was no significant difference in the vectorial capacity of mosquitoes infected with drug-resistant vs. drug-susceptible parasites. Consequently, contrary to expectations, our data indicate that drug resistance in D. immitis does not appear to reduce the transmission efficiency of these parasites, and thus the spread of drug-resistant parasites in the vertebrate population is unlikely to be mitigated by reduced fitness in the mosquito vector.

59 BASIC BIOLOGICAL SCIENCES↗