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At least 91 records · Page 5

Impact of gas background on XFEL single-particle imaging

Abstract Single-particle imaging (SPI) using X-ray free-electron Lasers (XFELs) offers the potential to determine protein structures at high spatial and temporal resolutions without the need for crystallization or vitrification. However, the technique faces challenges due to weak diffraction signals from single proteins and significant background scattering from gases used for sample delivery. A recent observation of a diffraction pattern from an isolated GroEL protein complex Ekeberg T et al. (Light Sci Appl 13:15, 2024.https://doi.org/10.1038/274s41377-023-01352-7) had similar numbers of signal and background photons. Ongoing efforts aim to reduce the background created by sample delivery, with one approach replacing most of the used gas with helium Yenupuri T et al. (Sci Rep 14:4401, 2024.https://doi.org/10.1038/s41598-024-54605-9). In this study, we investigate the effects of a reduced background on the resolution limits for SPI of isolated proteins under different experiment conditions. As a test case, we used GroEL, and we used experimentally derived parameters for our simulations. We observe that background significantly impacts the achievable resolution, particularly when the signal strength is comparable to the background. This is best exemplified at 6.0 keV, where a background reduction by a factor of 10 leads to a resolution improvement from 1.9 to 1.2 nm, for a dataset of$$10^4$$patterns.

Science & Technology - Other Topics

Soft-hard framework with exact four-momentum conservation for small systems

A new framework, called x-scape, for the combined study of both hard and soft transverse momentum sectors in high-energy proton-proton (𝑝−𝑝) and proton-nucleus (𝑝−𝐴) collisions is set up. A dynamical initial state is set up using the 3d-Glauber model with transverse locations of hotspots within each incoming nucleon. A hard scattering that emanates from two colliding hotspots is carried out using the Pythia generator. Initial state radiation from the incoming hard partons is carried out in a new module called I-matter, which includes the longitudinal location of initial splits. The energy-momentum of both the initial hard partons and their associated beam remnants is removed from the hot spots, depleting the energy-momentum available for the formation of the bulk medium. Outgoing showers are simulated using the matter generator, and results are presented for both cases, allowing for and not allowing for energy loss. First comparisons between this hard-soft model and single inclusive hadron and jet data from 𝑝−𝑝 and minimum bias 𝑝−Pb collisions are presented. Single hadron spectra in 𝑝−𝑝 are used to carry out a limited (in number of parameters) Bayesian calibration of the model. Fair comparisons with data are indicative of the utility of this new framework. Theoretical studies of the correlation between jet 𝑝 𝑇 and event activity at mid and forward rapidity are carried out.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Teleoperation of Construction Robots Using Human Interaction: Case Study Examples: Preprint

The integration of advanced teleoperation methods in construction robotics has the potential to enhance productivity and safety in demanding environments. Among different methods, hand gestures have emerged as an intuitive approach, enabling seamless communication between human operators and robotic systems. This study demonstrates the use of hand gestures for controlling a model robotic excavator and a virtual robotic arm in construction applications. Two case study examples are presented. In the first case study, a series of hand gestures are performed to control a model robotic excavator's bucket and arm movements. The second case study focuses on using hand gestures to control a virtual robotic arm to perform a material handling task in a simulated environment. In both cases, the performed hand gestures are all successfully captured and interpreted by the gesture-based teleoperation method to conduct the corresponding tasks, which demonstrates the application of the gesture-based control method for various types of construction robots. Also, the limitations of the gesture-based teleoperation method (e.g., recognition delay, sensitivity to motion outliers) are discussed. Future work will focus on developing a digital twin system to support gesture-based teleoperation for a wider range of construction robots.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

High-Resolution Simulations of Geological CO 2 Injection: Application to the SPE11 Benchmark

Geological carbon sequestration (GCS) will play a critical role in decarbonization and in facilitating the transition to clean energy systems. Because CO 2 is highly mobile, ensuring its safe and permanent injection into subsurface geological formations involves monitoring over larger spatial domains and longer time periods than is typical for hydrocarbon reservoirs. This can benefit from simulation tools capable of modeling key CO 2 trapping mechanisms, particularly those optimized for speed and scalability on high-performance computing systems. Using isothermal versions of the SPE11B and SPE11C benchmark cases, we conduct a mesh refinement study simulating CO 2 injection into kilometer-scale rock formations at centimeter resolution with the GEOS open-source simulation framework. We focus on how mesh refinement improves the accuracy of convective mixing in both 2D and 3D simulations. The computational costs associated with achieving a converged solution highlight the need for predictive upscaling techniques. A systematic performance scaling analysis—including both central processing unit (CPU) and graphics processing unit (GPU) architectures—complements the “Results” section.

Geosciences

Investigation of Point-Contact Strategies for CFD Simulations of Pebble-Bed Reactor Cores

This study numerically investigated the effects of various contact strategies on the thermal hydraulic behavior within a structured bed of 100 explicitly modeled pebbles. Four contact strategies and two thermal hydraulic conditions were considered. The strategies to avoid contact singularities include decreasing the pebble diameter, increasing the pebble diameter, bridging the pebble surfaces near the contact region, and capping the pebble surfaces near the contact region. One strategy, Strategy 3a, which involves bridging with a cylinder equal to 10% of the pebble diameter, was selected as the baseline strategy because it addressed the contact singularity while minimizing the geometric changes that affect the bed porosity. The two thermal hydraulic conditions were full-power operation (Case 1) and pressurized loss of forced cooling or PLOFC (Case 2). Simulations of the conjugate heat transfer within the structured bed were performed using the Reynolds-averaged Navier–Stokes approach with the realizable k-ϵ turbulence model and two-layer all y + wall treatment. The thermal-fluid quantities of interest were compared between the contact strategies for each case. In Case 1, the hydraulic behavior was sensitive to the contact strategy, with large differences in the pressure drop (30%) and volume-average velocity (4%). The thermal behavior was not sensitive, with less than a 0.5% difference across the strategies. To better understand the separate effects of each heat transfer mode, Case 2 was divided into the following subcases: conduction (Case 2a); conduction/radiation (Case 2b); and conduction/radiation/convection (Case 2c). Case 2a represents an early phase of the PLOFC transient. Case 2b represents an intermediate phase of the PLOFC transient, with the pebble temperatures sufficiently high for the radiative heat transfer to be non-negligible. Case 2c represents a late phase of the PLOFC transient after the establishment of the natural circulation of the heat transfer fluid. For Case 2, large differences in the contact strategy were observed only in Case 2a with only conduction. The difference in the maximum pebble temperature was 23% in Case 2a, 2% in Case 2b, and 0.3% in Case 2c.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Kinetic Modeling of Secondary Organic Aerosol in a Weather-Chemistry Model: Parameterizations, Processes, and Predictions for GOAmazon

Secondary organic aerosol (SOA) forms and evolves in the atmosphere through many pathways and processes, over diverse spatial and time scales. Hence, there is a need to represent these widely-varying kinetic processes in large-scale atmospheric models to allow for accurate predictions of the abundance, properties, and impacts of SOA. In this work, we integrated a kinetic, process-level model (simpleSOM-MOSAIC) into a weather-chemistry model (WRF-Chem) to simulate the oxidation chemistry and microphysics of atmospheric SOA. simpleSOM-MOSAIC simulates multigenerational gas-phase chemistry, autoxidation reactions, heterogeneous oxidation, oligomerization, and phase-state-influenced gas/particle partitioning of SOA. As a case study, the integrated WRF-Chem-simpleSOM-MOSAIC (WC-SSM) model was used to simulate the photochemical evolution downwind of a large city (Manaus, Brazil) in the Amazon and, in turn, study the anthropogenic and biogenic interactions in an otherwise pristine environment. Consistent with previous work, we found that OA was enhanced by up to a factor of four in the urban plume due to elevated hydroxyl radical (OH) concentrations, relative to the background, and that this OA was dominated by SOA from biogenic precursors (80%). Further, in addition to accurately simulating the OA enhancement in the urban plume, the model reproduced the magnitude of the OA oxygen-to-carbon (O:C) ratio and broadly tracked the evolution of the aerosol size distribution. Our work highlights the importance of including an integrated, kinetic representation of SOA processes in an atmospheric model

54 ENVIRONMENTAL SCIENCES

Molecular Modes Elucidate the Nuclear Magnetic Resonance Relaxation of Viscous Fluids

The Bloembergen, Purcell, and Pound (BPP) theory of nuclear magnetic resonance (NMR) relaxation in fluids dating back to 1948 continues to be the linchpin in interpreting NMR relaxation data in applications ranging from characterizing fluids in porous media to medical imaging (MRI). The BPP theory is founded on assuming molecules are hard spheres with 1 H– 1 H dipole pairs reorienting randomly; assumptions that are severe in light of modern understanding of liquids. Nevertheless, it is intriguing to this day that the BPP theory was consistent with the original experimental data for glycerol, a hydrogen-bonding molecular fluid for which the hard-sphere-rigid-dipole assumption is inapplicable. To better understand this incongruity, atomistic molecular simulations are used to compute 1 H NMR T 1 relaxation dispersion (i.e., frequency dependence) in two contrasting cases: glycerol, and a (non hydrogen-bonding) viscosity standard. At high viscosities, simulations predict distinct functional forms of T 1 for glycerol compared to the viscosity standard, in agreement with modern measurements, yet both in contrast to BPP theory. The cause of these departures from BPP theory is elucidated, without assuming any relaxation models and without any free parameters, by decomposing the simulated T 1 response into dynamic molecular modes for both intramolecular and intermolecular interactions. The decomposition into dynamic molecular modes provides an alternative framework to understand the physics of NMR relaxation for viscous fluids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

A Perspective on Quantum Computing Applications in Quantum Chemistry Using 25-100 Logical Qubits

The intersection of quantum computing and quantum chemistry represents a promising frontier for achieving quantum utility in domains of both scientific and societal relevance. Owing to the exponential growth of classical resource requirements for simulating quantum systems, quantum chemistry has long been recognized as a natural candidate for quantum computation. This perspective focuses on identifying scientifically meaningful use cases where early fault-tolerant quantum computers, which are considered to be equipped with approximately 25-100 logical qubits, could deliver tangible impact. While recent advances in classical computing have pushed the boundaries of tractable simulations to unprecedented scales, this logical-qubit regime represents the first window where quantum devices can pursue qualitatively distinct strategies, such as polynomial-scaling phase estimation, direct simulation of quantum dynamics, and active-space embedding, that remain challenging for classical solvers, such as multireference charge-transfer and conical-intersection states central to photochemistry and materials design. We highlight near-term opportunities in algorithm and software design, discuss representative chemical problems suited for quantum acceleration, and propose strategic roadmaps and collaborative pathways for advancing practical quantum utility in quantum chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Laser wavelength dependence of particle acceleration mechanisms in high intensity laser–solid density plasma interactions

We investigate the generation of relativistic electrons and the subsequent ion acceleration due to target-normal sheath acceleration when ultra-intense (⁠ I > 10 18 W/cm 2 ⁠) short pulse (⁠ τ L < 10ps⁠) lasers are incident onto solid density targets as laser wavelength is varied. Scaling laws for the hot electron temperature, T hot ⁠, and the maximum ion energy, E max ⁠, are recast as a function of laser wavelength. These predictions are compared to results from particle-in-cell computer simulations in a variety of geometries, including cases where realistic plasma density profiles as determined by a radiation hydrodynamics code are used. It is found that the wavelength dependence observed in simulation is less pronounced than what is predicted from the well-established scaling laws. An assessment of how switching to longer laser wavelengths, specifically 2 μm Tm:YLF technology, would impact current high energy density science applications and diagnostics is made.

Electromagnetism

Detailed Characterization of CZT Detector Response for Improved Coded-Aperture Imaging Performance

Gamma-ray imaging is a powerful method for locating and quantifying sources of radiation. The coded-aperture technique demonstrates superior angular resolution in comparison to other methods (e.g., Compton reconstruction). In this method, a mask constructed of highly attenuating material encodes the scene as a shadow pattern on a position-sensitive detector; this pattern can then be used to recreate the origin(s) of incident radiation. This is typically done through convolution of the mask and shadow patterns. Iterative methods which attempt to reconstruct the observed shadow pattern using a weighted combination of simulated patterns may also be employed. In either case, errors in event position reconstruction due to detector imperfections alter the shadow pattern and will therefore degrade system performance and may introduce imaging artifacts. These effects can be mitigated with a detailed understanding of such errors – allowing for the generation of representative simulations that include the errors and/or correction of raw imager data to remove the errors. We present a calibration process for a commercially available cadmium zinc telluride (CZT) gamma imager which provides a comprehensive characterization of the spatial and energy dependence of event reconstruction. By illuminating a mask featuring a regular grid of pinholes with a calibration source, the localized response of the detector can be measured with fine granularity. These local responses are combined to generate a full detector response map which can be used to distort simulations in a manner that is representative of the observed detector data. Details of the calibration procedure and an assessment of the impact of its end products on the performance of iterative imaging methods will be presented.

Ziock, Klaus-Peter

A Bulk versus Nanoscale Hydrogen Storage Paradox Revealed by Material-System Co-Design

Metal hydrides are serious contenders for materials-based hydrogen storage to overcome constraints associated with compressed or liquefied H 2 . Their ultimate performance is usually evaluated using intrinsic material properties without considering a systems design perspective. An illustrative case with startling implications is (LiNH 2 +2LiH). Using models that simulate the storage system and associated fuel cell of a light-duty vehicle (LDV), the performance of the bulk hydrides is compared with a nanoscaled version in porous carbon (PC), (LiNH 2 +2LiH)@(6-nm PC). Using experimental material properties, the simulations show that (LiNH 2 +2LiH)@(6-nm PC) counterintuitively has higher usable gravimetric and volumetric capacities than the bulk counterpart on a system basis despite having lower capacities on a materials-only basis. Nanoscaling increases the thermal conductivity and lowers the desorption enthalpy, which consequently increases heat management efficiency. In a simulated drive cycle for fuel cell-powered LDV, the fuel cell is inoperable using bulk (LiNH 2 +2LiH) as the storage material but completes the drive cycle using the nanoscale material. Further, these results challenge the notion that nanoscaling incurs mass and volume penalties. Instead, the synergistic nanoporous host-hydride interaction can favorably modulate chemical and heat transfer properties. Moreover, a co-design approach considering application-specific tradeoffs is essential to accurately assess a material's potential for real-world hydrogen storage.

08 HYDROGEN

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

DFTB+ is a flexible, open-source software package developed by its community, designed for fast and efficient atomistic quantum mechanical simulations. It employs various methods that approximate density functional theory (DFT), such as density functional-based tight binding (DFTB) and the extended tight binding (xTB) approach allowing simulations of large systems over extended time scales with reasonable accuracy, while being significantly faster than traditional ab initio methods. In recent years, several new extensions of the DFTB method have been developed and implemented in the DFTB+ program package in order to improve the accuracy and generality of the available simulation results. In this paper, we review those enhancements, show several use case examples and discuss the strengths and limitations of its features.

36 MATERIALS SCIENCE

Testbed Demonstration of a Microgrid Building Block Prototype

With the adoption of ambitious climate action goals, the penetration level of distributed energy resources (DERs) is rapidly increasing. Microgrids are an efficient way to integrate these DERs, facilitating their operation and control. Additionally, microgrids enhance the overall resilience of the distribution system by serving critical loads both within and outside their boundaries. However, the need for substantial customized engineering leads to a high cost of development, installation and maintenance of microgrids. To address this challenge, Microgrid Building Blocks (MBB) are proposed to reduce the deployment cost of microgrids through modular, standardized design and implementation. This work presents a testbed demonstrating the integrated power conversion, control, and communication functionalities of an MBB. The testbed is formed by a real-time electromagnetic transient (EMT) simulation combined with a hardware and software prototype of MBB. The use cases supported by the MBB testbed are enumerated. The islanded operation, voltage regulation, and optimal dispatch capabilities of an MBB-based microgrid controller are validated through a case study.

Somda, Baza [Virginia Tech]

Case Study: Leveraging GenAI to Build AI-based Surrogates and Regressors for Modeling Radio Frequency Heating in Fusion Energy Science

This work presents a detailed case study on using Generative AI (GenAI) to develop AI surrogates for simulation models in fusion energy research. The scope includes the methodology, implementation, and results of using GenAI to assist in model development and optimization, comparing these results with previous manually developed models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

CMS Storage Performance with RNTuple

CMS is transitioning to use ROOT’s new RNTuple data storage format for the files CMS will write in the HL-LHC era. Based on initial tests, CMS expects faster I/O and smaller files compared to the present TTree storage format. This contribution will show a comprehensive performance comparison between RNTuple and TTree I/O using CMS AOD and MiniAOD data formats as test cases for both simulation and collision data corresponding to similar data taking conditions of LHC Run 3. Quantities such as the resulting file size, the memory usage of the I/O components, and the rate of events being read from a file or written to a file will be measured. CMS’ data processing relies heavily on reading files over the local or wide area networks. The file read patterns are important because the latencies have been seen to influence the total production job times. Therefore a study on the file read patterns will be conducted by recording traces of the offset, size, and timestamp of each read request for both RNTuple and TTree. The behavior of network reads will be mimicked by reading local files where artificial latency will be added to the read requests. The effect of different latency values on the job times will be studied.

Jones, Christopher D. [Fermilab]

Surrogate modelling for urban building energy simulation based on the bidirectional long short-term memory model

Here, the urban microclimate is essential for accurate simulation-based urban building energy modelling (UBEM). However, a high spatial-resolution microclimate can increase the computational resources demands of UBEM. Surrogate modelling is one of the promising approaches for fast UBEM. This study proposes a bidirectional Long Short-Term Memory (LSTM)-based approach for simulation-based UBEM surrogate modelling. The estimations are aggregated into census tracts using total building floor area. A case study using UBEM to estimate annual hourly building energy use and anthropogenic heat from all existing buildings in Los Angeles County found that most of the surrogate models can complete the annual hourly simulation within 90 minutes with a normalized mean absolute error lower than 10%, and that the bidirectional LSTM outperforms the standard LSTM in accuracy. This study demonstrates the advantages of bidirectional RNN architecture in building energy surrogate modelling and is expected to promote long-term and high-resolution UBEM with detailed microclimates.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

High-Throughput Computing: Case Study of Medical Image Processing Applications

HPC is designed for large-scale simulations using monolithic codes of tightly coupled processes highly optimized to deliver decreased time to solution. Medical image processing is not a traditional field of HPC. Similar to AI applications, medical image processing parses large datasets, typically multiple times, to support a variety of studies for classification, diagnosis or monitoring purposes. The convergence of AI, HPC and Big Data encouraged more fields using image processing to transition to HPC. However, not all applications benefit from the same optimizations. In this paper we focus on high throughput medical image processing applications that analyze a huge dataset of small MRI images and that require HPC systems to decrease the time of parsing the entire dataset and not individual MRIs. We show in this research the performance of running SLANT, an image processing application for a whole brain segmentation, on large-scale systems and highlight performance limitations. We present optimizations prioritizing throughput that exhibit a 3.5x speed-up on the Summit Supercomputer that can be used as a baseline for building a high-throughput execution framework for other HPC systems.

Predescu, Maria

Designing an Optimal Sensor Network via Minimizing Information Loss

Optimal experimental design is a classic topic in statistics, with many well-studied problems, applications, and solutions. The design problem we study is the placement of sensors to monitor spatiotemporal processes, explicitly accounting for the temporal dimension in our modeling and optimization. We observe that recent advancements in computational sciences often yield large datasets based on physics-based simulations, which are rarely leveraged in experimental design. We introduce a novel model-based sensor placement criterion, along with a highly-efficient optimization algorithm, which integrates physics-based simulations and Bayesian experimental design principles to identify sensor networks that “minimize information loss” from simulated data. Our technique relies on sparse variational inference and (separable) Gauss-Markov priors, and thus may adapt many techniques from Bayesian experimental design. We validate our method through a case study monitoring air temperature in Phoenix, Arizona, using state-of-the-art physics-based simulations. Our results show our framework to be superior to random or quasi-random sampling, particularly with a limited number of sensors. We conclude by discussing practical considerations and implications of our framework, including more complex modeling tools and real-world deployments.

54 ENVIRONMENTAL SCIENCES