CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates

The ArgoNeuT Detector in the NuMI Low-Energy beam line at Fermilab

The ArgoNeuT liquid argon time projection chamber has collected thousands of neutrino and antineutrino events during an extended run period in the NuMI beam-line at Fermilab. This paper focuses on the main aspects of the detector layout and related technical features, including the cryogenic equipment, time projection chamber, read-out electronics, and off-line data treatment. The detector commissioning phase, physics run, and first neutrino event displays are also reported. The characterization of the main working parameters of the detector during data-taking, the ionization electron drift velocity and lifetime in liquid argon, as obtained from through-going muon data complete the present report.Comment: 43 pages, 27 figures, 5 tables - update referenc

Perspectives of Imaging of Single Protein Molecules with the Present Design of the European XFEL. - Part I - X-ray Source, Beamlime Optics and Instrument Simulations

The Single Particles, Clusters and Biomolecules (SPB) instrument at the European XFEL is located behind the SASE1 undulator, and aims to support imaging and structure determination of biological specimen between about 0.1 micrometer and 1 micrometer size. The instrument is designed to work at photon energies from 3 keV up to 16 keV. This wide operation range is a cause for challenges to the focusing optics. In particular, a long propagation distance of about 900 m between x-ray source and sample leads to a large lateral photon beam size at the optics. The beam divergence is the most important parameter for the optical system, and is largest for the lowest photon energies and for the shortest pulse duration (corresponding to the lowest charge). Due to the large divergence of nominal X-ray pulses with duration shorter than 10 fs, one suffers diffraction from mirror aperture, leading to a 100-fold decrease in fluence at photon energies around 4 keV, which are ideal for imaging of single biomolecules. The nominal SASE1 output power is about 50 GW. This is very far from the level required for single biomolecule imaging, even assuming perfect beamline and focusing efficiency. Here we demonstrate that the parameters of the accelerator complex and of the SASE1 undulator offer an opportunity to optimize the SPB beamline for single biomolecule imaging with minimal additional costs and time. Start to end simulations from the electron injector at the beginning of the accelerator complex up to the generation of diffraction data indicate that one can achieve diffraction without diffraction with about 0.5 photons per Shannon pixel at near-atomic resolution with 1e13 photons in a 4 fs pulse at 4 keV photon energy and in a 100 nm focus, corresponding to a fluence of 1e23 ph/cm^2. This result is exemplified using the RNA Pol II molecule as a case study

QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept examples to target both the genomics research community and quantum application developers in a self-contained manner. The details of the implementation are discussed for the various layers of the quantum full-stack accelerator design. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/prince-ph0en1x/QuASeR.Comment: 24 page

Hardware Acceleration of Neural Graphics

Rendering and inverse-rendering algorithms that drive conventional computer graphics have recently been superseded by neural representations (NR). NRs have recently been used to learn the geometric and the material properties of the scenes and use the information to synthesize photorealistic imagery, thereby promising a replacement for traditional rendering algorithms with scalable quality and predictable performance. In this work we ask the question: Does neural graphics (NG) need hardware support? We studied representative NG applications showing that, if we want to render 4k res. at 60FPS there is a gap of 1.5X-55X in the desired performance on current GPUs. For AR/VR applications, there is an even larger gap of 2-4 OOM between the desired performance and the required system power. We identify that the input encoding and the MLP kernels are the performance bottlenecks, consuming 72%,60% and 59% of application time for multi res. hashgrid, multi res. densegrid and low res. densegrid encodings, respectively. We propose a NG processing cluster, a scalable and flexible hardware architecture that directly accelerates the input encoding and MLP kernels through dedicated engines and supports a wide range of NG applications. We also accelerate the rest of the kernels by fusing them together in Vulkan, which leads to 9.94X kernel-level performance improvement compared to un-fused implementation of the pre-processing and the post-processing kernels. Our results show that, NGPC gives up to 58X end-to-end application-level performance improvement, for multi res. hashgrid encoding on average across the four NG applications, the performance benefits are 12X,20X,33X and 39X for the scaling factor of 8,16,32 and 64, respectively. Our results show that with multi res. hashgrid encoding, NGPC enables the rendering of 4k res. at 30FPS for NeRF and 8k res. at 120FPS for all our other NG applications

Summary: Working Group on QCD and Strong Interactions

In this summary of the considerations of the QCD working group at Snowmass 2001, the roles of quantum chromodynamics in the Standard Model and in the search for new physics are reviewed, with empahsis on frontier areas in the field. We discuss the importance of, and prospects for, precision QCD in perturbative and lattice calculations. We describe new ideas in the analysis of parton distribution functions and jet structure, and review progress in small-$x$ and in polarization.Comment: Snowmass 2001. Revtex4, 34 pages, 4 figures, revised to include additional references on jets and lattice QC

Development and Applications of a Real-time Magnetic Electron Energy Spectrometer for Use with Medical Linear Accelerators

Purpose – This work presents a design for a real-time electron energy spectrometer, and provides data analysis methods and characterization of the real-time system. This system is intended for use with medical linear accelerators (linacs). The goal is 1 Hz acquisition of the energy range 4-25 MeV, reconstructed in 0.1 MeV increments. Methods – Our spectrometer uses a nominal 0.54 T permanent magnet block as the dispersive element and scintillating fibers coupled to a CCD camera as the position sensitive detector. A broad electron beam produced by a linac is collimated by a 6.35 mm dimeter aperture at the entrance to the spectrometer. The collimated beam is dispersed by the magnetic field onto a row of 60 vertical 1 mm x 1 mm square scintillating fibers mounted to a lateral face of the magnet. Detector response functions (DRFs) were created using a simplified physics model of the spectrometer to determine electron trajectories within the magnet block from the entrance aperture to the detector plane. The DRFs were used in an iterative method to transform the fiber signal intensity versus position into an energy spectrum. We made measurements on an Elekta Infinity linac; each available energy (7, 9, 10, 11, 13, 16, 20 MeV) was investigated. Measurements were used to assess setup reproducibility, pinhole mismatch, dose rate effects, temporal stability, and linac detuning. Results – Our reconstruction method was able to reconstruct energy spectra from idealized simulations to within 0.14 MeV ± 0.28 MeV of the ideal FWHM value, and 0.06 MeV ± 0.12 MeV of the ideal most probable energy, Ep0. The measured spectral stability was consistent with the expected linac operating stability. The system achieved a refresh rate of 0.8 Hz during real-time operation. Conclusions – We developed a real-time electron energy spectrometer that measures electron energies from 4 to 25 MeV with a continuous readout rate of 0.8 Hz. The device can be used for assessing linac performance as a routine clinical tool, assist in diagnostic maintenance and repair, or potentially provide a more efficient method for beam tuning and matching