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At least 685 records · Page 38

Different roles of circular RNAs with protein coding potentials

Circular RNAs are a class of recently identified long non-coding RNAs. Various experiments reveled that they are covalently closed molecules and are resistant to attack by exonucleases. These RNA molecules are linked to various diseases. Interestingly, though they belong to the class of non-coding RNAs, some of them are experimentally verified to code for protein products. Till date there are no reports regarding the structural aspects of the protein products from these circular RNA molecules. In this work, an attempt has been made to analyze the structural details of the proteins obtained from the circular RNA molecules. Only those circular RNAs were selected for which there was direct experimental evidences of generation of protein products. The work for the first time elucidates the molecular details of the protein products obtained from circular RNA molecules.

60 APPLIED LIFE SCIENCES↗

Regulation mechanism of long non-coding RNA in plant response to stress

Highlights: • LncRNAs can regulate gene expression at transcription and post-transcription, epigenetic level, and many biological processes. • In this review, we discuss the regulation mechanism of long non-coding RNA in plant response to stress. • This review will provide strong evidence for lncRNAs to explore new ideas and new targets for prevention and control. Long non-coding RNA (lncRNA) is a non-coding RNA greater than 200 nucleotides in length. LncRNAs can regulate gene expression at transcription and post-transcription, epigenetic level, and plays an important role in a wide range of biological processes such as genomic imprinting, chromatin remodeling, transcriptional activation, transcriptional interference and cell cycle. It becomes the current hot topics in the study of molecular biology and genetics. Emerging evidence proposed that lncRNAs play important roles in response to both abiotic and biotic stress. In this review, we discuss the role of lncRNAs in drought resistance, salt resistance, disease resistance, and immunity of plants, providing strong evidence for exploring the important role of lncRNAs in plant resistance, in order to explore new ideas and new targets for prevention and control.

60 APPLIED LIFE SCIENCES↗

Benchmarking of massively parallel phase-field codes for directional solidification

We present a detailed benchmark comparing two state-of-the-art phase-field implementations for simulating alloy solidification under experimentally relevant conditions. The study investigates the directional solidification of Al-3wt%Cu under high-velocity solidification conditions and SCN-0.46wt% camphor under microgravity conditions from National Aeronautics and Space Administration (NASA) DECLIC-DSI-R experiments. Both codes, one employing finite-difference discretization with uniform mesh and GPU-acceleration (GPU-PF) and the other one employing finite-element discretization with adaptive-mesh and CPU-parallelization (PRISMS-PF), solve the same quantitative phase-field formulation that incorporates an anti-trapping current for the solidification of dilute alloys. We evaluate the predictions of each code for dendritic morphology, primary spacing, and tip dynamics in both 2D and 3D, as well as their numerical convergence and computational performance. While existing benchmark problems have primarily focused on simplified or small-scale simulations, they do not reflect the computational and modeling challenges posed by employing experimentally relevant time and length scales. Our results provide a practical framework for assessing phase-field code performance as well as validating and facilitating their application in integrated computational materials engineering (ICME) workflows that require integration with realistic experimental data.

36 MATERIALS SCIENCE↗

A finite-temperature Hartree–Fock code for shell-model Hamiltonians

The codes HFgradZ.py and HFgradT.py find axially symmetric minima of a Hartree–Fock energy functional for a Hamiltonian supplied in a shell model basis. The functional to be minimized is the Hartree–Fock energy for zero-temperature properties or the Hartree–Fock grand potential for finite-temperature properties (thermal energy, entropy). The minimization may be subjected to additional constraints besides axial symmetry and nucleon numbers. A single-particle operator can be used to constrain the minimization by adding it to the single-particle Hamiltonian with a Lagrange multiplier. One can also constrain its expectation value in the zero-temperature code. Also the orbital filling can be constrained in the zero-temperature code, fixing the number of nucleons having given $K^π$ quantum numbers. So, this is particularly useful to resolve near-degeneracies among distinct minima.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn–Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. In this paper, we present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Finally, using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.

36 MATERIALS SCIENCE↗

Dynamic load balancing with enhanced shared-memory parallelism for particle-in-cell codes

Furthering our understanding of many of today’s interesting problems in plasma physics – including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects – requires large-scale kinetic simulations using particle-in-cell (PIC) codes. However, these simulations are extremely demanding, requiring that contemporary PIC codes be designed to efficiently use a new fleet of exascale computing architectures. To this end, the key issue of parallel load balance across computational nodes must be addressed. We discuss the implementation of dynamic load balancing by dividing the simulation space into many small, self-contained regions or ‘‘tiles,’’ along with shared-memory (e.g., OpenMP) parallelism both over many tiles and within single tiles. The load balancing algorithm can be used with three different topologies, including two space-filling curves. Here, we tested this implementation in the code Osiris and show low overhead and improved scalability with OpenMP thread number on simulations with both uniform load and severe load imbalance. Compared to other load-balancing techniques, our algorithm gives order-of-magnitude improvement in parallel scalability for simulations with severe load imbalance issues.

97 MATHEMATICS AND COMPUTING↗

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated partition, whilst in others they are integral to all compute nodes - often with multiple GPUs per node - and provide the majority of a machine's compute performance. In light of this trend, it is becoming essential that codes deployed on HPC are updated to execute on accelerator hardware. Here, in this paper, we introduce a GPU implementation of the 3D blood flow simulation code HemeLB that has been developed using CUDA C++. We demonstrate how taking advantage of NVIDIA GPU hardware can achieve significant performance improvements compared to the equivalent CPU only code on which it has been built whilst retaining the excellent strong scaling characteristics that have been repeatedly demonstrated by the CPU version. With HPC positioned on the brink of the exascale era, we use HemeLB as a motivation to provide a discussion on some of the challenges that many users will face when deploying their own applications on upcoming exascale machines.

59 BASIC BIOLOGICAL SCIENCES↗

hPIC2: A hardware-accelerated, hybrid particle-in-cell code for dynamic plasma-material interactions

The exascale era of high performance computing promises to bring the field of computational plasma physics ever closer to the goal of accurate multiscale modeling. Such computers will rely on hardware acceleration to offload work to dedicated components, notably general-purpose graphics processing units (GPUs). However, devices from different manufacturers require software to be written with different parallel programming models, greatly increasing the code maintenance burden of applications designed to perform on more than one such device. hPIC2 is a hybrid plasma simulation code developed with the Kokkos performance portability framework to target the architectures that will drive exascale computing for the foreseeable future. As a hybrid simulation code, hPIC2 investigates the simultaneous use of various plasma models on the same domain, at the same time. hPIC2 also optionally couples to RustBCA, which accurately models ion-material interactions using the binary collision approximation (BCA) method. In conclusion, hPIC2 therefore achieves scalable performance on a variety of computing architectures when simulating complex and diverse plasmas, particularly near plasma-material interfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

EUTERPE: A global gyrokinetic code for stellarator geometry

The current state of the EUTERPE code is described with emphasis on the implemented models and their numerical implementation. The code solves the multi-species electromagnetic gyrokinetic equations in the full volume of a three-dimensional domain. Noise reduction of the particle-in-cell method is achieved by using a δf-method and Fourier filters. The field equations are discretized with B-splines and the resulting system of equations is solved iteratively. For linear simulations a phase-factor transformation is applied in order to strongly reduce the necessary grid resolution. Apart from the full gyrokinetic model, other numerically less expensive hybrid models are also implemented. They are mainly tailored for comparison with fluid theory and for studying the interaction of the bulk plasma with fast particles. The code is parallelized for CPUs by particle and domain decomposition. Good scalability up to several thousand nodes is demonstrated.

97 MATHEMATICS AND COMPUTING↗

SIMULATeQCD: A simple multi-GPU lattice code for QCD calculations

The rise of exascale supercomputers has fueled competition among GPU vendors, driving lattice QCD developers to write code that supports multiple APIs. Moreover, new developments in algorithms and physics research require frequent updates to existing software. These challenges have to be balanced against constantly changing personnel. At the same time, there is a wide range of applications for HISQ fermions in QCD studies. This situation encourages the development of software featuring a HISQ action that is flexible, high-performing, open source, easy to use, and easy to adapt. In this technical paper, we explain the design strategy, provide implementation details, list available algorithms and modules, and show key performance indicators for SIMULATeQCD, a simple multi-GPU lattice code for large-scale QCD calculations, mainly developed and used by the HotQCD collaboration. The code is publicly available on GitHub.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

TRANSP integrated modeling code for interpretive and predictive analysis of tokamak plasmas

This paper provides a comprehensive review of the TRANSP code, a sophisticated tool for interpretive and predictive analysis of tokamak plasmas, detailing its major capabilities and features. It describes the equations for particle, power, and momentum balance analysis, as well as the poloidal field diffusion equations. The paper outlines the spatial and time grids used in TRANSP and details the equilibrium assumptions and solvers. Various models for heating and current drive and radiation, including updates to the NUBEAM model, are discussed. The handling of large-scale events such as sawtooth crashes and pellet injections is examined, along with the predictive capabilities for advancing plasma profiles. The integration of TRANSP with the ITER Integrated Modeling and Analysis Suite (IMAS) is highlighted, demonstrating enhanced data access and analysis capabilities. Additionally, the paper discusses best practices and continuous integration techniques to enhance TRANSP's robustness. The suite of TRANSP tools, designed for efficient data analysis and simulation, further supports the optimization of tokamak operations and coupling with other tokamak codes. Continuous development and support ensure that TRANSP remains a major code for the analysis of experimental data for controlled thermonuclear fusion, maintaining its critical role in supporting the optimization of tokamak operations and advancing fusion research.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A code-independent generalized actuator line model for wind farm aerodynamics over simple and complex terrain

Actuator line model representations of wind turbines reduce the simulation cost of wind farm aerodynamics relative to blade geometry resolving simulations. However, most implementations are code specific and may not have proper load balancing when run in parallel. Here, a generalized actuator line model (GALM) is developed to overcome this implementation drawback of existing approaches. The GALM can be coupled to any existing microscale solver with minimal or no modifications. The coupling of our GALM model with the open-source microscale code CgWind is used to demonstrate both its ease of use and fidelity. The results obtained from the coupled-model simulations are validated for both isolated turbine in wind tunnel experiments and measurements in offshore wind farm. Finally, an operational wind farm over complex terrain is demonstrated. The simulations show that wake meandering and power production are strongly influenced by terrain impacts. Access information for obtaining the code is provided.

17 WIND ENERGY↗

The GBS code for tokamak scrape-off layer simulations

We describe a new version of GBS, a 3D global, flux-driven plasma turbulence code to simulate the turbulent dynamics in the tokamak scrape-off layer (SOL), superseding the code presented by Ricci et al. (2012) [14]. The present work is driven by the objective of studying SOL turbulent dynamics in medium size tokamaks and beyond with a high-fidelity physics model. We emphasize an intertwining framework of improved physics models and the computational improvements that allow them. The model extensions include neutral atom physics, finite ion temperature, the addition of a closed field line region, and a non-Boussinesq treatment of the polarization drift. GBS has been completely refactored with the introduction of a 3-D Cartesian communicator and a scalable parallel multigrid solver. We report dramatically enhanced parallel scalability, with the possibility of treating electromagnetic fluctuations very efficiently. The method of manufactured solutions as a verification process has been carried out for this new code version, demonstrating the correct implementation of the physical model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An electrostatic Particle-In-Cell code on multi-block structured meshes

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.

36 MATERIALS SCIENCE↗

RISMC industry application #1 (ECCS/LOCA). Core characterization automation: Lattice codes interface for PHISICS/RELAP5-3D

The United States Nuclear Regulatory Commission (U.S. NRC) is currently proposing rule-making “10 CFR 50.46c” to revise the loss-of-coolant-accident (LOCA) and emergency core cooling system (ECCS) acceptance criteria to include the effects of higher burn-up on cladding performance. The key implications of this proposition are that the cladding performance cannot be evaluated anymore as separated from other disciplines, but needs to be evaluated in a coupled manner with other physics. The Risk-Informed Safety Margin Characterization (RISMC) Pathway initiated several programs at Idaho National Laboratory (INL) to support the industry in the transition to the new rule. One of these programs is the Industry Application #1 (IA1). IA1’s goal is to develop an Integrated Evaluation Model (IEM) called LOCA Toolkit for the US (LOTUS). This tool connects five major disciplines involved in LOCA analysis, among them is (automated) core design (CD-A). Here, this paper focuses solely on the design of LOTUS' CD-A module as well as a demonstration application of the CD-A module to a generic Pressurized Water Reactor (PWR). The demonstration of the other LOTUS disciplines together with a demonstration example of the final risk-informed safety margin analysis is published in a separate paper. LOTUS is meant to provide the methodology framework into which the user can plug his established tools and codes. With the CD-A, the plant owner/operator will characterize his core design with the tools he has. He will then integrate his tools/methods into the LOTUS framework for the downstream safety analysis. For the current CD-A demonstration, the tools used are the already coupled codes PHISICS and RELAP5-3D, while cross section generation is done using the Studsvik lattice code HELIOS-2.

97 MATHEMATICS AND COMPUTING↗

Experimental validation of simplified radionuclide transport bubble scrubbing code in sodium coolant pool

Solid radionuclides released following fuel pin failure may become entrained in gaseous fission products and be rapidly transported through the coolant pool to the cover gas region. Sensitivity studies on radionuclide transport have identified this potential pathway as one of both high concern and high uncertainty. The simplified radionuclide transport scrubbing code utilizes classical aerosol scrubbing mechanisms to model this phenomenon and predict aerosol masses reaching the cover gas region. This paper serves to validate this code in a sodium environment while conducting a parametric study to analyze the effects of aerosol size, bubble size, pool temperature, pool depth, aerosol density, and aerosol concentration. Through a series of experimental tests, it was determined that aerosol sizes ranging from 0.001 to 1.0 µm are of primary concern as aerosols in this range have a ratio of aerosol mass entering the sodium pool from the fuel pin to aerosol mass exiting the sodium pool to the cover gas region of less than 10. Further, the experimental results were found to match the trends found in the scrubbing model closely, but significantly more scrubbing was seen experimentally. Decreasing bubble size and increasing pool depth and aerosol density were all found to increase scrubbing both experimentally and theoretically. Pool temperature was found to have a negligible effect on scrubbing amounts; however, this was largely due to a subsequent increase in bubble size corresponding to increasing temperatures which offset the increase in scrubbing due to increased temperature. Varying aerosol concentration was found to have no effect on scrubbing ratios. A final series of tests was conducted for a more prototypic fuel pin failure with a heterogenous bubble swarm. From these tests, it was found that the experimental scrubbing quantities were larger than for the single bubble case. Overall, it was found that the simplified bubble transport scrubbing code accurately models the trends of the bubble scrubbing but provides a conservative estimate of scrubbing quantities. Model limitations fail to model the complex phenomena present for fission product scrubbing via bubble transport, but match trends seen experimentally.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Modelling the nonlinear plasma response to externally applied three-dimensional fields with the Stepped Pressure Equilibrium Code

Small-amplitude, symmetry-breaking magnetic field perturbations, including resonant magnetic perturbations (RMPs) and error fields, can profoundly impact plasma properties in both tokamaks and stellarators. In this work, we perform the first comparison between the Stepped Pressure Equilibrium Code (SPEC) (a comparatively fast and efficient equilibrium code based on energy-minimisation principles) and M3D-C 1 (a high-fidelity albeit computationally expensive initial-value extended-magnetohydro-dynamic (MHD) code) to assess the conditions under which SPEC can be used to model the nonlinear, non-ideal plasma response to an externally applied (m = 2,n = 1) RMP field in an experimentally relevant geometry. We find that SPEC is able to capture the plasma response in the weakly nonlinear regime – meaning perturbation amplitudes below the threshold for break up of the separatrix and onset of secondary magnetic island formation – when around half of the total toroidal flux is enclosed in the volume containing the q = 2 resonant surface. Further, the observed dependence of SPEC solutions on input parameters, including toroidal flux and the number of volumes into which the plasma is partitioned, indicates that additional exploration of the underlying Multi-Region Relaxed MHD physics model is needed to constrain the choice of parameters. Nonetheless, this work suggests promising applications of SPEC to optimisation and fusion plasma design.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The DESC stellarator code suite Part 3: Quasi-symmetry optimization

The DESC stellarator optimization code takes advantage of advanced numerical methods to search the full parameter space much faster than conventional tools. Only a single equilibrium solution is needed at each optimization step thanks to automatic differentiation, which efficiently provides exact derivative information. A Gauss–Newton trust-region optimization method uses second-order derivative information to take large steps in parameter space and converges rapidly. With just-in-time compilation and GPU portability, high-dimensional stellarator optimization runs take orders of magnitude less computation time with DESC compared to other approaches. This paper presents the theory of the DESC fixed-boundary local optimization algorithm along with demonstrations of how to easily implement it in the code. Example quasi-symmetry optimizations are shown and compared to results from conventional tools. Three different forms of quasi-symmetry objectives are available in DESC, and their relative advantages are discussed in detail. In the examples presented, the triple product formulation yields the best optimization results in terms of minimized computation time and particle transport. This paper concludes with an explanation of how the modular code suite can be extended to accommodate other types of optimization problems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗