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At least 577 records · Page 32

Inter-cofactor protein remodeling rewires short-circuited transmembrane electron transfer

Intraprotein electron transfer (ET) requires explicit local control of the environment of cofactors to influence their intermolecular distances, relative orientations, and redox properties. Efficient, longer-range ET often utilizes molecular orbitals of aromatic residues present in the intervening space. Here, revitalization of a vestigial ET pathway in the bacterial photosynthetic reaction center is achieved by scanning with tryptophans to uncover markedly improved routes of electron conduction in a key stabilizing step spanning 15 Å between tetrapyrrole and quinone cofactors. This ET event is maximally enhanced by pairing one or more tryptophans with a threonine to influence quinone binding and/or redox potential. Synergistic effects of these substitutions increase the yield of that ET step to ~95%. Joining these substitutions with mutant residues that improve initial ET steps dramatically enhances transmembrane charge separation via this redesigned version of a pathway that is quantitatively inactive in the native protein-cofactor complex.

Biophysical chemistry↗

Flexible metal–gas batteries: a potential option for next-generation power accessories for wearable electronics

Flexible metal–gas batteries have become increasingly attractive for use in wearable electronics in the recent years due to their large theoretical energy density and superior adaptability to irregular geometric surfaces, such as the human body. With continuous improvements in design strategies and assembly technologies, the fabrication of various advanced flexible metal–gas batteries has been attempted. In spite of these efforts, the synchronous integration of high flexibility, safety, comfort, and high performance into flexible metal–gas batteries with specifically functionalized configurations still remains a formidable challenge. To resolve these dilemmas, the redesign of cathode catalysts, gel polymer electrolyte, and battery configurations/components has been investigated. In this paper, we review the recent technical advances together with the major dilemmas facing currently available flexible metal–gas batteries, highlighting how flexible cathodes and gel polymer electrolytes with various structures and components can affect the electrochemical performance and functionality of flexible metal–gas batteries. Flexible Zn–air, Li–O 2 /air, and Li–CO 2 batteries are mainly exemplified to elucidate their promising potential. Finally, based on our considerations, unresolved technical hurdles and future research perspectives involving flexible metal–gas batteries for wearable electronics are proposed.

25 ENERGY STORAGE↗

Enhancing generative molecular design via uncertainty-guided fine-tuning of variational autoencoders

In recent years, deep generative models have been successfully applied to various molecular design tasks, particularly in the life and materials sciences. One critical challenge for pre-trained generative molecular design (GMD) models is to fine-tune them to be better suited for downstream design tasks that aim at optimizing specific molecular properties. However, redesigning and training an existing effective generative model from scratch for each new design task are impractical. Furthermore, the black-box nature of typical downstream tasks that involve property prediction makes it nontrivial to optimize the generative model in a task-specific manner. In this work, we propose an uncertainty-guided fine-tuning strategy that can effectively enhance a pre-trained variational autoencoder (VAE) for GMD through performance feedback in an active learning setting. The strategy begins by quantifying the model uncertainty of the generative model using an efficient active subspace-based UQ (uncertainty quantification) scheme. Next, the decoder diversity within the characterized model uncertainty class is explored to expand the viable space of molecular generation. The low-dimensionality of the active subspace makes this exploration tractable using a black-box optimization scheme, which in turn enables us to identify and leverage a diverse set of high-performing models to generate enhanced molecules. Empirical results across six target molecular properties using multiple VAE-based generative models demonstrate that our uncertainty-guided fine-tuning strategy consistently leads to improved models that outperform the original pre-trained models.

97 MATHEMATICS AND COMPUTING↗

Development of a Versatile, Full-featured Search Functionality for Indico

Indico, CERN’s popular open-source tool for event management, is in widespread use among facilities that make up the HEP community. It is extensible through a robust plugin architecture that provides features such as search and video conferencing integration. In 2018, Indico version 2 was released with many notable improvements, but without a full-featured search functionality that could be implemented easily outside of CERN. At both Fermi and Brookhaven National Laboratories, the user community viewed the lack of this popular feature as a significant impediment to deployment of the new software. In the meantime, CERN embarked upon a major redesign of their core search service, one that would also necessitate a rewrite of the Indico search interface. Seeing this pressing need, the two US labs decided to collaborate, with assistance from the CERN development team, on a project to develop the requisite search functionality for the larger user community. The resulting design exploits the simplified schema defined in the new CERN Search micro-service, based on Invenio and Elasticsearch, while still providing a flexible path to implementation for alternative backend search services. It is intended to provide a software package that can be installed easily and used out of the box, by anyone at any site. This paper will discuss the design choices and architectural challenges, and provide an overview of the deployment and use of these new plugins.

Constanta, Penelope↗

Multithreading ATLAS offline software: A retrospective

For Run 3, ATLAS redesigned its offline software, Athena, so that the main workflows run completely multithreaded. The resulting substantial reduction in the overall memory requirements allows for better use of machines with many cores. This note will discuss the performance achieved by the multithreaded reconstruction, the process of migrating the large ATLAS code base, and tools and techniques that were useful in debugging threading-related problems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Integration of RNTuple in ATLAS Athena

After using ROOT’s TTree I/O subsystem for over two decades and storing more than an exabyte of compressed High Energy Physics (HEP) data, advances in technology have motivated a complete redesign, RNTuple, which breaks backward-compatibility to take better advantage of these storage options. The RNTuple I/O subsystem has been designed to address performance bottlenecks and other shortcomings of TTree. Specifically, RNTuple comes with an updated, more compact binary data format that can be stored both in ROOT files and natively in object stores. It is designed for modern storage hardware (e.g. high-throughput low-latency NVMe SSDs), and provides robust and easy to use interfaces. The binary format of RNTuple is scheduled to become production grade in 2024, and recently has become mature enough to start exploring the integration into software used by HEP experiments. In this contribution, we discuss the developments to support the features as required by the ATLAS analysis Event Data Model (EDM) in RNTuple, which will enable its integration into the Athena software framework. With these developments in place, we evaluate the performance of the current most recent versions of RNTuple-based ATLAS data sets and compare this to that of TTree.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

ROOT’s RNTuple I/O Subsystem: The Path to Production

The RNTuple I/O subsystem is ROOT’s future event data file format and access API. It is driven by the expected data volume increase at upcoming HEP experiments, e.g. at the HL-LHC, and recent opportunities in the storage hardware and software landscape such as NVMe drives and distributed object stores. RNTuple is a redesign of the TTree binary format and API and has shown to deliver substantially faster data throughput and better data compression both compared to TTree and to industry standard formats. In order to let HENP computing workflows benefit from RNTuple’s superior performance, however, the I/O stack needs to connect efficiently to the rest of the ecosystem, from grid storage to (distributed) analysis frameworks to (multithreaded) experiment frameworks for reconstruction and ntuple derivation. With the RNTuple binary format soon arriving at its first production release, we present RNTuple’s feature set, integration efforts, and its performance impact on the time-to-solution. We show the latest performance figures of RDataFrame analysis code of realistic complexity, comparing RNTuple and TTree as data sources. We discuss RNTuple’s approach to functionality critical to the HENP I/O (such as multithreaded writes, fast data merging, schema evolution) and we provide an outlook on the road to its use in production.

Blomer, Jakob↗

Small high cooling power space cooler

The small High Efficiency pulse tube Cooler (HEC) cooler, that has been produced and flown on a number of space infrared instruments, was originally designed to provide cooling of 10 W @ 95 K. It achieved its goal with >50% margin when limited by the 180 W output ac power of its flight electronics. It has also been produced in 2 stage configurations, typically for simultaneously cooling of focal planes to temperatures as low as 35 K and optics at higher temperatures. The need for even higher cooling power in such a low mass cryocooler is motivated by the advent of large focal plane arrays. With the current availability at NGAS of much larger power cryocooler flight electronics, reliable long term operation in space with much larger cooling powers is now possible with the flight proven 4 kg HEC mechanical cooler. Even though the single stage cooler design can be re-qualified for those larger input powers without design change, we redesigned both the linear and coaxial version passive pulse tube cold heads to re-optimize them for high power cooling at temperatures above 130 K while rejecting heat to 300 K. Small changes to the regenerator packing, the re-optimization of the tuned inertance and no change to the compressor resulted in the increased performance at 150 K. The cooler operating at 290 W input power achieves 35 W@ 150 K corresponding to a specific cooling power at 150 K of 8.25 W/W and a very high specific power of 72.5 W/Kg. At these powers the cooler still maintains large stroke, thermal and current margins. In this paper we will present the measured data and the changes to this flight proven cooler that were made to achieve this increased performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Upgrade of the electron beam ion trap in Shanghai

Over the last few years the Shanghai electron beam ion trap (EBIT) has been successfully redesigned and rebuilt. The original machine, developed under collaboration with the Shanghai Institute of Applied Physics, first produced an electron beam in 2005. It could be tuned with electron energies between 1 and 130 keV and beam current up to 160 mA. After several years of operation, it was found that several modifications for improvements were necessary to reach the goals of better electron optics, higher photon detection, and ion injection efficiencies, and more economical running costs. The upgraded Shanghai-EBIT is made almost entirely from Ti instead of stainless steel and achieves a vacuum of less than 10{sup −10} Torr, which helps to minimize the loss of highly changed ions through charge exchange. Meanwhile, a more compact structure and efficient cryogenic system, and excellent optical alignment have been of satisfactory. The magnetic field in the central trap region can reach up till 4.8 T with a uniformity of 2.77 × 10{sup −4}. So far the upgraded Shanghai-EBIT has been operated up to an electron energy of 151 keV and a beam current of up to 218 mA, although promotion to even higher energy is still in progress. Radiation from ions as highly charged as Xe{sup 53+,} {sup 54+} has been produced and the characterization of current density is estimated from the measured electron beam width.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Large improvement of phosphorus incorporation efficiency in n-type chemical vapor deposition of diamond

Microwave plasma enhanced chemical vapor deposition is a promising way to generate n-type, e.g., phosphorus-doped, diamond layers for the fabrication of electronic components, which can operate at extreme conditions. However, a deeper understanding of the doping process is lacking and low phosphorus incorporation efficiencies are generally observed. In this work, it is shown that systematically changing the internal design of a non-commercial chemical vapor deposition chamber, used to grow diamond layers, leads to a large increase of the phosphorus doping efficiency in diamond, produced in this device, without compromising its electronic properties. Compared to the initial reactor design, the doping efficiency is about 100 times higher, reaching 10%, and for a very broad doping range, the doping efficiency remains highly constant. It is hypothesized that redesigning the deposition chamber generates a higher flow of active phosphorus species towards the substrate, thereby increasing phosphorus incorporation in diamond and reducing deposition of phosphorus species at reactor walls, which additionally reduces undesirable memory effects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Construction and measurements of an improved vacuum-swing-adsorption radon-mitigation system

In order to reduce backgrounds from radon-daughter plate-out onto detector surfaces, an ultra-low-radon cleanroom is being commissioned at the South Dakota School of Mines and Technology. An improved vacuum-swing-adsorption radon mitigation system and cleanroom build upon a previous design implemented at Syracuse University that achieved radon levels of ∼0.2 Bq m{sup −3}. This improved system will employ a better pump and larger carbon beds feeding a redesigned cleanroom with an internal HVAC unit and aged water for humidification. With the rebuilt (original) radon mitigation system, the new low-radon cleanroom has already achieved a > 300× reduction from an input activity of 58.6 ± 0.7 Bq m{sup −3} to a cleanroom activity of 0.13 ± 0.06 Bq m{sup −3}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Obligation of occupational safety and health (OSH) legislation by designers and manufacturers: Perception of enforcement officers

Designers and manufacturers of plants are responsible to design or redesign the process, product and workplace with consideration of eliminating hazards or controlling risks as early as possible at design stage.The purpose of this paper is to determine the perception of enforcement officers towards compliance and implementation of OSH legislation by the designers and manufacturers of plant.The research partners was a goverment department that enforce the related OSH laws to designers and manufacturers of the plant. A total of 59 technical staffs were surveyed together with examination of the sekunder data from the department to evaluate overall OSH legal obligation by the industries. This study demonstrate how OSH regulators play the roles to influence the industries to perform better in OSH.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Upgrade of the beam extraction system of the GTS-LHC electron cyclotron resonance ion source at CERN

Linac3 is the first accelerator in the heavy ion injector chain of the Large Hadron Collider (LHC), providing multiply charged heavy ion beams for the CERN experimental program. The ion beams are produced with GTS-LHC, a 14.5 GHz electron cyclotron resonance ion source, operated in afterglow mode. Improvement of the GTS-LHC beam formation and beam transport along Linac3 is part of the upgrade program of the injector chain in preparation for the future high luminosity LHC. A mismatch between the ion beam properties in the ion source extraction region and the acceptance of the following Low Energy Beam Transport (LEBT) section has been identified as one of the factors limiting the Linac3 performance. The installation of a new focusing element, an einzel lens, into the GTS-LHC extraction region is foreseen as a part of the Linac3 upgrade, as well as a redesign of the first section of the LEBT. Details of the upgrade and results of a beam dynamics study of the extraction region and LEBT modifications will be presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Low-noise kinetic inductance traveling-wave amplifier using three-wave mixing

We have fabricated a wide-bandwidth, high dynamic range, low-noise cryogenic amplifier based on a superconducting kinetic inductance traveling-wave device. The device was made from NbTiN and consisted of a long, coplanar waveguide on a silicon chip. By adding a DC current and an RF pump tone, we are able to generate parametric amplification using three-wave mixing (3WM). The devices exhibit gain of more than 15 dB across an instantaneous bandwidth from 4 to 8 GHz. The total usable gain bandwidth, including both sides of the signal-idler gain region, is more than 6 GHz. The noise referred to the input of the devices approaches the quantum limit, with less than 1 photon excess noise. We compare these results directly to the four-wave mixing amplification mode, i.e., without DC-biasing. We find that the 3WM mode allows operation with the pump at lower RF power and at frequencies far from the signal. We have used this knowledge to redesign the amplifiers to utilize primarily 3WM amplification, thereby allowing for direct integration into large scale qubit and detector applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Edge multi-energy soft x-ray diagnostic in Experimental Advanced Superconducting Tokamak

A multi-energy soft x-ray (ME-SXR) diagnostic has been built for electron temperature profile in the edge plasma region in Experimental Advanced Superconducting Tokamak (EAST) after two rounds of campaigns. Originally, five preamplifiers were mounted inside the EAST vacuum vessel chamber attached to five vertically stacked compact diode arrays. A custom mechanical structure was designed to protect the detectors and electronics under constraints of the tangential field of view for plasma edge and the allocation of space. In the next experiment, the mechanical structure was redesigned with a barrel structure to absolutely isolate it from the vacuum vessel. Multiple shielding structures were mounted at the pinhole head to protect the metal foils from lithium coating. The pre-amplifiers were moved to the outside of the vacuum chamber to avoid introducing interference. Twisted copper cooling tube was embedded into the back-shell near the diode to limit the temperature of the preamplifiers and diode arrays during vacuum vessel baking when the temperature reached 150 °C. Electron temperature profiles were reconstructed from ME-SXR measurements using neural networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bandwidth enhancement of electromagnetic coupled nonuniform H-shaped microstrip patch antenna for higher band of Wi-MAX applications

The bandwidth enhancement of a stacked non-uniform electromagnetically coupled H-shaped Microstrip Antenna (SNHMA) with tapered edges is analyzed and simulated using the IE3D simulator. The proposed antenna prototype is drafted on FR-4 material and stacked further with an air discontinuity of 0.3 mm to the next layer. The various parameters optimized to achieve the best performance from the modified SNHMA primarily include a)length b)width of the patch c)air gap thickness. The redesigned antenna serves at two distinct frequencies with an elevated bandwidth of 30.85 % at the central frequency 5.762 GHz, approximately four times the bandwidth of the standard patch having the same dimensions. The simulated radiation patterns (E-plane and H-plane) are exhibited within the range of frequencies where the broadband response is observed. The specifications of the proposed structure make it promising for the higher band of Wi-MAX applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Comparative analysis of numerical models of pipe handling equipment used in offshore drilling applications

Design of offshore drilling equipment is a task that involves not only analysis of strict machine specifications and safety requirements but also consideration of changeable weather conditions and harsh environment. These challenges call for a multidisciplinary approach and make the design process complex. Various modeling software products are currently available to aid design engineers in their effort to test and redesign equipment before it is manufactured. However, given the number of available modeling tools and methods, the choice of the proper modeling methodology becomes not obvious and – in some cases – troublesome. Therefore, we present a comparative analysis of two popular approaches used in modeling and simulation of mechanical systems: multibody and analytical modeling. A gripper arm of the offshore vertical pipe handling machine is selected as a case study for which both models are created. In contrast to some other works, the current paper shows verification of both systems by benchmarking their simulation results against each other. Such criteria as modeling effort and results accuracy are evaluated to assess which modeling strategy is the most suitable given its eventual application.

97 MATHEMATICS AND COMPUTING↗