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At least 37 records · Page 2

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗

Aircraft Icing Severity Evaluation

Aircraft icing refers to the ice buildup on the surface of an aircraft flying in icing conditions. The ice accretion on the aircraft alters the original aerodynamic configuration and degrades the aerodynamic performances and may lead to unsafe flight conditions. Evaluating the flow structure, icing mechanism and consequences is of great importance to the development of an anti/deicing technique. Studies have shown computational fluid dynamics (CFD) and machine learning (ML) to be effective in predicting the ice shape and icing severity under different flight conditions. CFD solves a set of partial differential equations to obtain the air flow fields, water droplets trajectories and ice shape. ML is a branch of artificial intelligence and, based on the data, the self-improved computer algorithms can be effective in finding the nonlinear mapping relationship between the input flight conditions and the output aircraft icing severity features.

Li, Sibo (ORCID:000000021705844X)↗

Deep Learning-based Surrogate Model for Efficient Reservoir Simulation in Large-scale Geological Carbon Storage: Application in IBDP Dataset

This project introduces an advanced deep learning (DL)-based surrogate modeling approach to enhance the efficiency and accuracy of large-scale geological carbon storage (GCS) simulations. Using the Illinois Basin Decatur Project (IBDP) dataset as training data, the study employs a residual U-Net architecture to predict critical state variables such as pressure and CO₂ saturation, as well as CO₂ plume migration. By incorporating key geological parameters (e.g., porosity, permeability, and rock facies) and physics-informed inputs like the diffusive time of flight and time step, the DL model effectively reduces computational complexity while maintaining robust physical constraints. Compared to traditional simulators like Eclipse, the DL model achieves remarkable accuracy, with a root mean square error (RMSE) of 1.57 psi for pressure and 0.007 for saturation, and dramatically reduces computational time from hours to just 69.9 seconds for 50-step simulations. These results demonstrate the potential of innovative DL methodologies to improve the predictivity and operational efficiency of GCS simulations, providing a reliable foundation for decision-making in CCS operations. Supported by the SMART initiative, this project underscores the success of leveraging computational innovations to advance CCS technologies.

advanced deep learning↗

Exploring OpenSNAPI Use Cases and Evolving Requirements [Slides]

Emerging system architectures are rapidly transforming in order to meet shifting requirements. Motivated by expanding data volumes, energy efficiency concerns, and the omnipresent need to improve performance, architectures are increasingly adopting a data-centric approach. At the core of this concept is the goal of minimizing data motion and instead processing data in-situ to the greatest degree possible. Therefore, data-centric designs, in contrast to conventional CPU-centric models, typically distribute compute capabilities throughout the architecture. As part of this paradigm shift, a novel class of devices known as data processing units (DPUs), alongside CPUs and GPUs, are quickly forming a third pillar of data-centric systems. These devices, which include smart network adapters and switches, seek to offload computation on data at the network edge as well as in-flight within the network fabric. The Open Smart Network API (OpenSNAPI) project seeks to develop a unified API for DPU devices. In our previous talks, we introduced the OpenSNAPI project and detailed our investigations regarding the viability of offloading compute intensive kernels to BlueField DPUs. In contrast, in this talk we detail our efforts to offload application-level file I/O to the DPU. We also discuss plans and early efforts to explore in-network compute capabilities. Finally, we describe our observations with respect to the evolving design of OpenSNAPI.

97 MATHEMATICS AND COMPUTING↗

Model reduction for hypersonic aerodynamics via conservative LSPG projection and hyper-reduction

High-speed aerospace engineering applications rely heavily on computational fluid dynamics (CFD) models for design and analysis due to the expense and difficulty of flight tests and experiments. This reliance on CFD models necessitates performing accurate and reliable uncertainty quantification (UQ) of the CFD models. However, it is very computationally expensive to run CFD for hypersonic flows due to the fine grid resolution required to capture the strong shocks and large gradients that are typically present. Furthermore, UQ approaches are “many-query” problems requiring many runs with a wide range of input parameters. One way to enable computationally expensive models to be used in such many-query problems is to employ projection-based reduced-order models (ROMs) in lieu of the (high-fidelity) full-order model. In particular, the least-squares Petrov–Galerkin (LSPG) ROM (equipped with hyper-reduction) has demonstrated the ability to significantly reduce simulation costs while retaining high levels of accuracy on a range of problems including subsonic CFD applications. This allows computationally inexpensive LSPG ROM simulations to replace the full-order model simulations in UQ studies, which makes this many-query task tractable, even for large-scale CFD models. This work presents the first application of LSPG to a hypersonic CFD application. In particular, we present results for LSPG ROMs of the HIFiRE-1 in a three-dimensional, turbulent Mach 7.1 flow, showcasing the ability of the ROM to significantly reduce computational costs while maintaining high levels of accuracy in computed quantities of interest.

Fluid Dynamics↗

High-throughput terahertz imaging: progress and challenges

Abstract Many exciting terahertz imaging applications, such as non-destructive evaluation, biomedical diagnosis, and security screening, have been historically limited in practical usage due to the raster-scanning requirement of imaging systems, which impose very low imaging speeds. However, recent advancements in terahertz imaging systems have greatly increased the imaging throughput and brought the promising potential of terahertz radiation from research laboratories closer to real-world applications. Here, we review the development of terahertz imaging technologies from both hardware and computational imaging perspectives. We introduce and compare different types of hardware enabling frequency-domain and time-domain imaging using various thermal, photon, and field image sensor arrays. We discuss how different imaging hardware and computational imaging algorithms provide opportunities for capturing time-of-flight, spectroscopic, phase, and intensity image data at high throughputs. Furthermore, the new prospects and challenges for the development of future high-throughput terahertz imaging systems are briefly introduced.

36 MATERIALS SCIENCE↗

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

Quantifying Turbine-Level Risk to Golden Eagles Using a High-Fidelity Updraft Model and a Stochastic Behavioral Model

To minimize the effects of wind farms on Golden Eagle (Aquila chrysaetos) populations while enabling sustainable development of renewable energy resources, it is important to understand how eagles interact with atmospheric flows, terrain features, and anthropogenic structures. Models that predict migratory flight paths provide one tool that helps us grasp how the location of wind farms may influence interactions and impacts on migrating Golden Eagles. The current state-of-the-art in predicting migratory flight paths uses a deterministic fluid-flow analogy to predict eagle trajectory using only an orographic updraft potential computed from topographical features. This model does not take into account variables, such as thermal updrafts and time varying atmospheric conditions that are known to influence migratory behavior. In this work, we improve on the model with the objective of developing tools that advance our understanding of how atmospheric flows and terrain features affect migratory eagle behavior and their interactions with wind farms. Specifically, we 1) incorporate both orographic and thermal updraft information in simulating eagle flight paths; 2) incorporate stochasticity into eagle travel patterns to better capture the influence of exogenous factors on, and the inherent stochasticity of eagle behavior; 3) consider spatio-temporal atmospheric data at wind-farm-scale when computing updraft potential; and 4) account for how atmospheric conditions and the direction of migration change seasonally and how these changes affect eagle migratory flight behavior. We tested the model using a 50km by 50km region with 50 m resolution in the western United States. We simulated 900 independent, probabilistic eagle tracks during southerly and northerly migration, assuming eagles solely rely on orographic updrafts. The preliminary results indicate that the inclusion of finer resolution atmospheric data allows for the inclusion of realistic conditions that an eagle experiences. The stochasticity in eagle tracks provides a platform to include uncertainty in eagle decision making and help produce robust eagle presence maps. We will deploy updraft and downdraft velocities computed using a high-fidelity, wind farm scale, computational fluid dynamics solver under development at National Renewable Energy Laboratory. This work is a first step in the development of a predictive and generalizable eagle behavior model at the wind farm scale that does not rely on empirical data collection. Although the current model is intended for migratory eagles, we will extend and refine this model to inform the development of additional behavioral modes, including resident eagle behavior. This modeling approach improves our ability to understand eagle use of the landscape at a fine scale, and it is our hope that this work will ultimately help advance strategies that minimize the impact of wind development on Golden Eagle populations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

Autonomous aerial flight path inspection using advanced manufacturing techniques

Robotic systems have shown capabilities to perform inspection tasks in dangerous and difficult-to-access environments, such as those found in different components of power plants. However, most of the current robotic inspection technology is designed for specific components. Aerial robots, commonly termed as Drones, have raised an option to inspect a wider range of structural components. Nevertheless, current aerial inspecting technology still relies on a human pilot with limited line of sight, field of view and a reduced perception as the drone flies away, which prevents performing close-quarter inspection in intricate, structurally complex and GPS-denied environments. This work introduces offline inspection path generation methods based on robotics-integrated to manufacturing techniques. One method uses computer-aided manufacturing (CAM) techniques and the other an additive manufacturing (AM) approach to generate the flight path. That is to say, the drone would fly along the path described by a 3D (Three Dimensional) printer’s extruder or a CNC (Computer Numerical Control) machining tool, enabling to fly very close the structure even in physical structures with a complex geometry. Once the trajectories are generated, they are introduced for its validation in the Gazebo robotics simulator. Simulation results demonstrate the proper performance of the method and confirm that this approach can be used for close inspection of structural components.

42 ENGINEERING↗

Laser Measurements and Modeling of Shock Tunnel Freestream Velocity and Multispecies Thermal Nonequilibrium

Coherent anti-Stokes Raman scattering (CARS) and nitric oxide molecular tagging velocimetry (NO-MTV) were used to characterize the freestream in Sandia’s Hypersonic Shock Tunnel (HST) using a burst-mode laser operated at 100 kHz. Experiments were performed at nominal freestream velocities of 3 and 4 km/s using both air and N 2 test gas. The CARS diagnostic provides nonequilibrium characterization of the flow by measuring vibrational and rotational temperatures of N 2 and O 2 , which are compared to NO temperatures from separate laser absorption experiments. Simultaneous, collinear freestream velocities were measured using NO MTV along with pitot pressure measurements. Furthermore, this extensive freestream dataset is compared to nonequilibrium CFD that is capable of modeling species-specific, vibrational temperatures throughout the nozzle expansion. Significant nonequilibrium between vibrational and rotational temperatures was measured at each flow condition. N 2 exhibits the most nonequilibrium, followed by O 2 and NO. The CFD model captures this trend, although it consistently overpredicts N 2 and O 2 vibrational temperatures. At 3 km/s, the modeled NO nonequilibrium is underpredicted, whereas it is overpredicted at 4 km/s. Good agreement is seen between CFD and the velocity and rotational temperature measurements. Experiments with water added to the test gas yielded no discernable difference in vibrational relaxation.

Aerodynamics↗

TRINIDI (Time-of-Flight Resonance Imaging with Neutrons for Isotopic Density Inference)

This software is an open-source Python library that provides tools for processing hyperspectral neutron time-of-flight radiography data. This type of data allows material decomposed reconstructions to be generated with the use of material characteristic spectral responses and the algorithms provided in this code library. The software library will contain tools for pre-processing the neutron measurement data, estimating measurement system parameters, reconstructing material decomposed radiographs, and computing material decomposed computed tomography (CT). Furthermore, it will have capability to generate and process simulated neutron time-of-flight data with the goal of benchmarking and demonstrating the tools that are provided. The software will include thorough documentation and application examples.

Balke, Thilo↗

Improving SGP4 Orbit Determination with New State Estimation Algorithm

The Simplified General Perturbations 4 Model (SGP4) is a well-known tool for performing satellite orbit determination. However, uncertainties and inaccuracies in the initial state inputs (required by SGP4) degrade the performance of the propagator. We present a new state estimation algorithm that allows for independent computation of these initial inputs using Unscented Kalman Filtering and GPS data from a satellite. The algorithm is tested on real flight data and demonstrates a notable performance improvement over the standard method of orbit determination using SGP4.

97 MATHEMATICS AND COMPUTING↗

ATDM AD projects to ECP Report (Q3 FY2020)

The SPARC team has completed much of the workflow development needed for the coupled and uncoupled analyses needed to support our flight test validation work. The SPARC team has continued to make progress on development activities to support unsteady, full reentry vehicle aero analysis, which have focused on turbulence modeling, uniform mesh refinement, in-situ visualization (with the Paraview/Catalyst team), and performance analysis. The SPARC team is making solid progress towards our Q4 goal of demonstrating an improved Wall Modeled Large Eddy Simulation (WMLES) capability for standard geometries using high-order finite difference, discontinuous Galerkin, and low-dissipation finite volume methods. The SPARC team has met the minimum completion criteria for parts of the L1, including documenting performance and scaling of SPARC on Trinity, Sierra and Astra, and performing runs for the flight test validation case.

97 MATHEMATICS AND COMPUTING↗

Pathways to a Sustainable Aviation Ecosystem: Flight DNA: An Anonymized Aviation Data Tool and Repository

The National Renewable Energy Laboratory (NREL) has deep experience developing secure, national data repositories, which it augments with analysis, technology and market expertise, high-performance computing, and innovative data visualization. By adapting the architecture of existing mobility databases (i.e., Fleet DNA, the Transportation Secure Data Center, the National Fuel Cell Technology Evaluation Center), NREL can build a powerful aviation data clearinghouse - Flight DNA - that helps stakeholders navigate the web of pitfalls and possibilities generated by new aviation technologies.

aviation↗

Autonomous Aerial Power Plant Inspection in GPS-denied Environments

Inspection of coal-fired power plants is frequently dangerous, includes difficult places to reach, and can turn expensive due to the downtimes and cost of inspection crew. Robotic systems have shown capabilities to address some of these issues, but most of the current robotic inspection technology in power plants is designed for specific components. Conversely, recent advances in machine vision have empowered aerial platforms for long-range, remotely-controlled, GPS-based inspections of industrial plants. This capability has led to wide spread utilization of aerial robots (commonly termed Drones, UVS or UAS) platforms for inspection in less challenging environments where both collision avoidance, and GPS reception are not significant issues. The challenge in adapting airborne technology for power plant inspection lies in internal structures and the complex network of piping, and distribution systems, which impose significant risks for collision and can hinder the reception and transmission of GPS signals. The current state of the art in aerial inspection technology within the energy sector is controlled via radio control, and utilizes GPS-based navigation, for inspection of large-scale plants such as offshore platforms and wind turbine parks. Nevertheless, close-range and autonomous inspection in the GPS-denied environments of power plants has not yet been achieved, as it requires precise guidance and navigation with real-time situational awareness and obstacle avoidance capabilities. This endeavor introduced the use of rotary wing flying robots, due to their station keeping and vertical take-off capabilities for power plant components inspection. To enable close quarter inspection two methods were used. One method uses the 3D CAD (Three-dimensional Computer-Aided Design) model of the asset to inspect to generate the UAV’s inspection path. To acquire, analyze and process the 3D model, first, the STL file is produced to obtain surface points and vectors normal to the surface. Later, by introducing other variables such as wall offset and a controlled trajectory between each outline and each subsequent layer, the flight path is generated. The proposed framework will generate a path that will pass as close as desired from the surface and navigate in intricate environments. A second method, use advanced manufacturing techniques such as CNC (Computer Numerical Control) and additive manufacturing. Once the inspection flight path is obtained, vision-based navigation systems are employed to have the UAV autonomously tracking the provided trajectory. Finally, Artificial Intelligence-enabled developments are in charge of detecting cracks and corrosion in structural components of power plants. The proposed methods are validated in simulations, laboratory and industrial setups, where it is shown that the developed systems acting together enable close-quarter autonomous aerial inspection and mapping in power plant assets. The system can be further improved by adding more sensors to navigate in different GPS-denied environments, with non-homogeneous lighting conditions, dust and in general situations where vision-based systems may fail.

01 COAL, LIGNITE, AND PEAT↗

SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.

97 MATHEMATICS AND COMPUTING↗

The Computational Analysis of a Generic Hypersonic Store Separation

Many current hypersonic vehicles involve a main vehicle from which components separate during flight and presents simulation challenges such as shock-shock interactions, highly nonlinear interactions, and shock wave boundary layer interactions. These aerodynamic phenomena influence the attitude and trajectory of each object, which needs to be understood before large-scale experiments can be run. To gain a generic understanding of the process, high-fidelity Reynolds-averaged Navier-Stokes solutions are performed on a conical vehicle geometry passing through an oblique shock wave that is representative of different configurations and scenarios. Trajectory and applied forces are tracked and show the vehicle’s dynamics are predominantly the result of differential flow incidence angles causing a strong shock; this leads to a large pressure increase over a fraction of the vehicle, which influences pitch. The vehicle appears to follow conventional stability theory with detached eddy simulation and small disturbances in initial attitude shown to have minimal influence on the scenario.

Savery, Ryan↗

NASA analysis of space mission options for the 2025 planetary defense conference hypothetical asteroid impact threat scenario

The 2025 Planetary Defense Conference (PDC) hypothetical asteroid impact threat exercise is being conducted in coordination with the United Nations-endorsed Space Mission Planning Advisory Group (SMPAG), exercising SMPAG's processes for assessing space mission options and communicating to decision makers. Here, in this paper, we describe the work performed by our NASA-led team and present the results we contributed to the SMPAG effort for the exercise. Our NASA-led team assessed mission options for asteroid reconnaissance (flyby and rendezvous), deflection, and robust disruption using several viable techniques: kinetic impactors, ion beam deflection, and nuclear explosive devices. Our simulations and analyses considered how much change-in-velocity an asteroid can tolerate before fragmentation onset, and we worked towards establishing requirements for robustly disrupting an asteroid. Heuristics informed by the simulation results are incorporated into optimization of deflection and disruption mission campaign options. Finally, we make some observations about useful generalizations from these results with potential applicability to any planetary defense scenario.

Asteroid deflection↗