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At least 739 records · Page 41

Why don't we share data and code? Perceived barriers and benefits to public archiving practices

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Multispin Clifford codes for angular momentum errors in spin systems

The physical symmetries of a system play a central role in quantum error correction. Here, in this work we encode a qubit in a collection of systems with angular momentum symmetry (spins), extending the tools developed by Gross for single large spins. By considering large spins present in atomic systems and focusing on their collective symmetric subspace, we develop codes with octahedral symmetry capable of correcting errors up to second order in angular momentum operators. These errors include the most physically relevant noise sources such as microwave control errors and optical pumping. We additionally explore qubit codes that exhibit distance scaling commensurate with the surface code while permitting transversal single-qubit Clifford operations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Restricted Boltzmann machines and matrix product states of one-dimensional translationally invariant stabilizer codes

We discuss the relations between restricted Boltzmann machine (RBM) states and the matrix product states (MPS) for the ground states of 1D translational invariant stabilizer codes. A generic translational invariant and finitely connected RBM state can be expressed as an MPS, and the matrices of the resulting MPS are of rank 1. We dub such an MPS as an RBM-MPS. This provides a necessary condition for exactly realizing a quantum state as an RBM state, if the quantum state can be written as an MPS. For generic 1D stabilizer codes having a nondegenerate ground state with periodic boundary condition, we obtain an expression for the lower bound of their MPS bond dimension, and an upper bound for the rank of their MPS matrices. In terms of RBM, we provide an algorithm to derive the RBM for the cocycle Hamiltonians whose MPS matrices are proved to be of rank 1. Moreover, the RBM-MPS produced by our algorithm has the minimal bond dimension. A family of examples is provided to explain the algorithm. Furthermore, we finally conjecture that these features hold true for all the 1D stabilizer codes having a nondegenerate ground state with periodic boundary condition, as long as their MPS matrices are of rank 1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Production of energetic light fragments in extensions of the CEM and LAQGSM event generators of the Monte Carlo transport code MCNP6 [Production of energetic light fragments in CEM, LAQGSM, and MCNP6]

We extend the cascade-exciton model (CEM), and the Los Alamos version of the quark-gluon string model (LAQGSM), event generators of the Monte Carlo N-particle transport code version 6 (MCNP6), to describe production of energetic light fragments (LF) heavier than 4 He from various nuclear reactions induced by particles and nuclei at energies up to about 1 TeV/nucleon. In these models, energetic LF can be produced via Fermi breakup, preequilibrium emission, and coalescence of cascade particles. Initially, we study several variations of the Fermi breakup model and choose the best option for these models. Then, we extend the modified exciton model (MEM) used by these codes to account for a possibility of multiple emission of up to 66 types of particles and LF (up to 28 Mg) at the preequilibrium stage of reactions. Then, we expand the coalescence model to allow coalescence of LF from nucleons emitted at the intranuclear cascade stage of reactions and from lighter clusters, up to fragments with mass numbers A ≤ 7, in the case of CEM, and A ≤ 12, in the case of LAQGSM. Next, we modify MCNP6 to allow calculating and outputting spectra of LF and heavier products with arbitrary mass and charge numbers. The improved version of CEM is implemented into MCNP6. Lastly, we test the improved versions of CEM, LAQGSM, and MCNP6 on a variety of measured nuclear reactions. The modified codes give an improved description of energetic LF from particle- and nucleus-induced reactions; showing a good agreement with a variety of available experimental data. They have an improved predictive power compared to the previous versions and can be used as reliable tools in simulating applications involving such types of reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Code package for calculating modified cosmic ionization and thermal histories with dark matter and other exotic energy injections

Here we present a new public Python package, DarkHistory, for computing the effects of dark matter annihilation and decay on the temperature and ionization history of the early universe. DarkHistory simultaneously solves for the evolution of the free electron fraction and gas temperature, and for the cooling of annihilation/decay products and the secondary particles produced in the process. Consequently, we can self-consistently include the effects of both astrophysical and exotic sources of heating and ionization, and automatically take into account backreaction, where modifications to the ionization/temperature history in turn modify the energy-loss processes for injected particles. We introduce a number of worked examples, demonstrating how to use the code in a range of different configurations, in particular for arbitrary dark matter masses and annihilation/decay final states. Possible applications of DarkHistory include mapping out the effects of dark matter annihilation/decay on the global 21 cm signal and the epoch of reionization, as well as the effects of exotic energy injections other than dark matter annihilation/decay. The code is available at https://github.com/hongwanliu/DarkHistory with documentation at https://darkhistory.readthedocs.io. Data files required to run the code can be downloaded at https://doi.org/10.7910/DVN/DUOUWA.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dynamics of genetic code evolution: The emergence of universality

We study the dynamics of genetic code evolution. The model of Vetsigian et al. [Proc. Natl. Acad. Sci. USA 103, 10696 (2006)] and Vetsigian [Collective evolution of biological and physical systems, Ph.D. thesis, 2005] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on convergence and optimality score. We show that by allowing specific parameters to vary with time, the solution exhibits attractor dynamics. Finally, we study automorphisms of the genetic code arising due to this model. We use this to examine the scaling of the solutions to re-examine universality and find that there is a direct link to mutation rate.

59 BASIC BIOLOGICAL SCIENCES↗

Flag Gadgets Based on Classical Codes

Fault-tolerant syndrome extraction is a key ingredient in implementing fault-tolerant quantum computation. While conventional methods use a number of extra qubits that are linear in the weight of the syndrome, several improvements have been introduced using flag gadgets. In this work, we develop a framework to design flag gadgets using classical codes. Using this framework, we show how to perform fault-tolerant syndrome extraction for any stabilizer code with arbitrary distance using exponentially fewer qubits than conventional methods when qubit measurement and reset are relatively slow compared to a round of error correction. In particular, our method requires only ( 2 t + 1 ) t ⌈ log 2 ( w ) ⌉ flag qubits to fault-tolerantly measure a weight- w stabilizer. We further take advantage of the saving provided by our construction to fault-tolerantly measure multiple stabilizers using a single gadget and show that it maintains the same exponential advantage when it is used to fault-tolerantly extract the syndromes of quantum low-density parity-check codes. Using the developed framework, we perform computer-assisted search to find several small examples where our constructions reduce the number of qubits required. These small examples may be relevant to near-term experiments on small-scale quantum computers. Published by the American Physical Society 2024

Anker, Benjamin↗

Modeling betatron radiation using particle-in-cell codes for plasma wakefield accelerator diagnostics

The analysis of plasma wakefield acceleration experimental measurements, particularly in the characterization of photons emitted through the betatron radiation mechanism, requires the development of accurate numerical models. These computational models are crucial for supporting modern instrumentation designed to measure the single-shot, double-differential angular-energy radiation spectra resulting from interactions between beams and plasmas. Motivated by the needs of such applications, this paper presents detailed numerical models of betatron radiation generated in beam-plasma acceleration experiments. These models are based on the integration of the Liénard-Wiechert (LW) potentials, applied to computed particle trajectories. The particle trajectories are generated using three distinct methods: first, by tracking particles through idealized fields in the blowout regime of PWFA; second, by obtaining trajectories using the fast quasistatic particle-in-cell (PIC) code quickpic; and third, obtaining trajectories from the fully self-consistent PIC code osiris. To ensure the accuracy and reliability of these models, the paper includes various benchmark tests using analytical expressions, as well as employing the PIC code epoch, which takes an alternative approach by using a Monte Carlo quantum electrodynamics (QED)-based radiation model. Additionally, the paper presents simulations of the expected experimental betatron radiation spectra, taking into account parameters relevant to PWFA and plasma photocathode experiments at the SLAC FACET-II facility.

Yadav, M. [University of California, Los Angeles, ↗

The FEFF code

FEFF is a real-space multiple-scattering Green’s function code for simulating a variety of X-ray spectroscopies as well as ground-state and excited-state electronic structure. It is perhaps best known for its use in extended X-ray absorption fine-structure (EXAFS) calculations, particularly within various analysis codes such as DEMETER and LARCH. In addition to EXAFS, FEFF can also be used to calculate X-ray absorption near-edge structure (XANES), X-ray emission spectroscopy (XES), electron energy loss spectra (EELS) and many other spectroscopic quantities. Here, the basic approach used for the calculations is described, focusing on the most important approximations and aspects of the simulations. Here, the capabilities of the FEFF code, including those of the Java-based graphical user interface JFEFF, are also briefly described.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Real-time Implementation of Grid Code Compliant Grid Edge Energy Management System

Integrated distributed energy resources (DER) in a distribution system need to follow grid codes to avoid violations that result in DER/circuit segment disconnection. To comply with grid code requirements at the grid edge level, network constrained grid edge energy management system (EMS) can be deployed. The objective of grid edge EMS is to provide economic solution for active and reactive power DER setpoints at each dispatch interval and ensure voltage regulation to support secure interconnection of the grid edge segment to the distribution system with multiple inverter based DER units. In this work, real-time simulation of grid code compliant grid edge EMS is deployed in a realistic feeder circuit segment. For real-time simulation, communication between the grid edge EMS and DERs is done exploiting IEC 61850-7-420. It enables interoperability among different DERs and grid edge EMS. No prior art has deployed IEC 61850-7-420 GOOSE communication protocol for grid edge EMS. Conversion of IEC 61850 GOOSE messages to Modbus communication protocol is also performed to communicate with grid edge EMS in commodity-off the shelf embedded boards in this work. The real-time simulation in OPAL-RT real-time digital simulator shows the out-performance of grid edge EMS by reducing the voltage violation in the distribution circuit.

Energy management system↗

Visualization and Analysis Requirements for In Situ Processing for a Large-Scale Fusion Simulation Code

In situ techniques have become a very active research area since they have been shown to be an effective way to combat the issues associated with the ever growing gap between computation and I/O bandwidth. In order to take full advantage of in situ techniques with a large-scale simulation code, it is critical to understand the breadth and depth of its analysis requirements. In this paper, we present the results of a survey done with members of the XGC1 fusion simulation code team in order to gather their requirements for analysis and visualization. We look at these requirements from the perspective of in situ processing and present a list of XGC1 analysis tasks performed by its physicists, engineers, and visualization specialists. This analysis of the specific needs and use cases of a single code is important in understanding the nature of the needs that simulations have in terms of data movement and usage for visualization and analysis, now and in the future.

Kress, James M.↗

Automatic Code Generation for High-Performance Graph Algorithms

Graph problems are common across fields of scientific computing and social sciences. However, despite their importance, implementing graph algorithms effectively on modern computing systems is a challenging task that requires significant programming effort and generally results in customized implementations. Current computing and memory hierarchies are not architected for irregular computations resulting in challenges for graph algorithms to achieve high performance on those architectures. In this paper, we present GraphX, a novel compiler framework and DSL designed to simplify the development of efficient graph algorithms and achieve high performance on modern computing systems. GraphX consists of a DSL for efficient implementation of graph algorithms, various optimizations, such as support for sparse linear algebra and workspace transformations, optimized graph primitives, including semiring and masking, and a high-performance code generation engine. Using GraphX, users can implement graph algorithms using a semantically-rich language with graph-oriented operators. GraphX uses these semantics to automatically generate efficient code for target architectures, increasing performance and portability across architectures. The composable nature of GraphX makes it possible to extend the set of optimizations and architectures without modifying the source code. We demonstrate GraphX outperforms state-of-the-art graph libraries, such as LAGraph, up to $3.7 speedup in semiring operations, $2.19 speedup in an important sparse computational kernel, and $9.05 speedup in graph processing algorithms.

compiler, graph algorithms, semiring, masking, wor↗

Proposed Material Properties, Allowable Stresses, and Design Curves of Diffusion Bonded Alloy 800H for the ASME Code Section III Division 5

Abstract Increased interest in compact heat exchangers (CHXs) to serve as intermediate heat exchangers of very high temperature reactors resulted in significant research and development on their design, analysis, and construction. Printed circuit heat exchangers are a type of CHXs with high thermal efficiency and compactness achieved through diffusion bonding a stack of etched plates with millimeter scaled channels. The diffusion bonding process changes the microstructural and mechanical properties of the wrought metal plates. The current nonnuclear design code ASME section VIII, division 1 captures the material property change through a “joint efficiency factor.” However, the current nuclear design code ASME section III, division 5 does not address or support the diffusion bonded material properties. Hence, there is a need to develop allowable stresses, isochronous curves, and fatigue life curves for various diffusion bonded alloys. In this study, Alloy 800H material was selected to establish the diffusion bonded material properties under tension, creep, fatigue, and creep-fatigue loads at elevated temperatures in the range 550–760 °C. A set of tests on diffusion bonded Alloy 800H (DB 800H) were performed and the acquired data are used in developing allowable stresses Sy, Su, Sr, Sm, St, Smt, So, isochronous curves and fatigue life curves according to the ASME section III, division 5 requirements. This paper also presents detailed procedures used in developing the ASME code section III division 5 design provisions for diffusion bonded Alloy 800H.

Engineering↗

Application of C ( t )-Integral Solutions in Extending ASME BPVC Section XI Division 2 Code Case N-934 for Transient Creep Crack Growth

Creep crack growth is a phenomenon which arises in damaged metallic structures under combined primary and secondary loads in the creep regime. The High Temperature Flaw Evaluation Code Committee of the American Society of Mechanical Engineers Boiler and Pressure Vessel Code (BPVC) is evaluating methods in extending Code Case N-934 to capture transient creep crack growth. Here, this paper provides context and basic examples on the selected approach to transient creep crack growth methods based on the C(t)-integral. The basis for selected C(t)-integral solution as analytical method is established, including an overview of its derivation. Practical assessments of a crack growing under creep conditions in a realistic component are conducted to illustrate the analytical approach. Additional considerations in the application of the analytical methods and limitations are discussed.

36 MATERIALS SCIENCE↗

SU-E-T-590: Optimizing Magnetic Field Strengths with Matlab for An Ion-Optic System in Particle Therapy Consisting of Two Quadrupole Magnets for Subsequent Simulations with the Monte-Carlo Code FLUKA

Purpose: Aim of this study was to optimize the magnetic field strengths of two quadrupole magnets in a particle therapy facility in order to obtain a beam quality suitable for spot beam scanning. Methods: The particle transport through an ion-optic system of a particle therapy facility consisting of the beam tube, two quadrupole magnets and a beam monitor system was calculated with the help of Matlab by using matrices that solve the equation of motion of a charged particle in a magnetic field and field-free region, respectively. The magnetic field strengths were optimized in order to obtain a circular and thin beam spot at the iso-center of the therapy facility. These optimized field strengths were subsequently transferred to the Monte-Carlo code FLUKA and the transport of 80 MeV/u C12-ions through this ion-optic system was calculated by using a user-routine to implement magnetic fields. The fluence along the beam-axis and at the iso-center was evaluated. Results: The magnetic field strengths could be optimized by using Matlab and transferred to the Monte-Carlo code FLUKA. The implementation via a user-routine was successful. Analyzing the fluence-pattern along the beam-axis the characteristic focusing and de-focusing effects of the quadrupole magnets could be reproduced. Furthermore the beam spot at the iso-center was circular and significantly thinner compared to an unfocused beam. Conclusion: In this study a Matlab tool was developed to optimize magnetic field strengths for an ion-optic system consisting of two quadrupole magnets as part of a particle therapy facility. These magnetic field strengths could subsequently be transferred to and implemented in the Monte-Carlo code FLUKA to simulate the particle transport through this optimized ion-optic system.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Turbulent-convective block for the ASTRA transport code

A physical model for the enhanced transport code is presented, which explicitly takes into account the contribution of turbulent convection to the processes of particle and heat transport in the hot core of the tokamak plasma. The model is based on the specially developed CONTRA-A turbulent block, while an adapted version of the existing ASTRA transport code is used as a transport envelope. The CONTRA-A turbulent block, based on the adiabatically reduced quasi-2D magnetohydrodynamic equations, calculates the generation and self-consistent evolution of low-frequency turbulence, including the spatiotemporal structure of turbulent fluctuations of the plasma velocity, density, and temperatures of electrons and ions. Using the obtained data on fluctuations, the CONTRA-A block calculates the turbulent-convective particle and heat fluxes and transfers them to the modified ASTRA code, which computes the evolution of quasi-equilibrium plasma parameters. To illustrate the capabilities of the enhanced transport model, the results of simulations of turbulent plasma evolution in two discharge scenarios with nonstationary auxiliary plasma heating in the T-10 and T-15MD tokamaks are presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A new relativistic viscous hydrodynamics code and its application to the Kelvin–Helmholtz instability in high-energy heavy-ion collisions

Here, we construct a new relativistic viscous hydrodynamics code optimized in the Milne coordinates. We also split the conservation equations into an ideal part and a viscous part, using the Strang spitting method. In the code a Riemann solver based on the two-shock approximation is utilized for the ideal part and the Piecewise Exact Solution (PES) method is applied for the viscous part. Furthemore, we check the validity of our numerical calculations by comparing analytical solutions, the viscous Bjorken’s flow and the Israel–Stewart theory in Gubser flow regime. Using the code, we discuss possible development of the Kelvin–Helmholtz instability in high-energy heavy-ion collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Soft syndrome iterative decoding of quantum LDPC codes and hardware architectures

In practical quantum error correction implementations, the measurement of syndrome information is an unreliable step—typically modeled as a binary measurement outcome flipped with some probability. However, the measured syndrome is in fact a discretized value of the continuous voltage or current values obtained in the physical implementation of the syndrome extraction. In this paper, we use this “soft” or analog information to benefit iterative decoders for decoding quantum low-density parity-check (QLDPC) codes. Syndrome-based iterative belief propagation decoders are modified to utilize the soft syndrome to correct both data and syndrome errors simultaneously. We demonstrate the advantages of the proposed scheme not only in terms of comparison of thresholds and logical error rates for quasi-cyclic lifted-product QLDPC code families but also with faster convergence of iterative decoders. Additionally, we derive hardware (FPGA) architectures of these soft syndrome decoders and obtain similar performance in terms of error correction to the ideal models even with reduced precision in the soft information. The total latency of the hardware architectures is about 600 ns (for the QLDPC codes considered) in a 20 nm CMOS process FPGA device, and the area overhead is almost constant—less than 50% compared to min-sum decoders with noisy syndromes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗