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At least 397 records · Page 22

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗

Particle flow reconstruction for the CMS Phase-II Level-1 Trigger

The upgrade of the CMS detector for the high-luminosity LHC will include trackfinding for the first time in the Level-1 trigger, enabling Particle Flow reconstruction of every event in addition to comprehensive pileup mitigation. The Correlator trigger will reconstruct isolated leptons and photons, hadronic jets, and energy sums, assisted in many cases by machine learning to benefit from the complete particle-level event record. Here, we present the logic of these algorithms, possible implementations using large FPGAs and their demonstration in prototype hardware, in addition to the expected physics performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Case Study: Hybrid Carbon Conversion Using Low-Carbon Energy Sources in Coal-Producing States

The demand for more carbon efficient power sources and a decrease in natural gas prices has decreased the desire for coal power. This decrease in demand has led to massive job losses in coal mining regions over the past decade. The purpose of this project is to develop a hybrid energy system utilizing both a coal power plant and advanced reactor, which is competitive with natural gas by improving on profitability and decreasing carbon emissions. This report details the problem with a summary of the impact on the coal industry and the availability of renewable energy sources in the Appalachian region. Because of the geography of the region, variable renewable energy sources are not available without significant size and siting restrictions. However, biomass in the form of wood waste is abundant and can be used as a carbon neutral energy source. Combining biomass and coal processing, in addition to thermal power plants, can increase system profits and efficiency by providing peaking power and conversion opportunities for secondary markets. The electric load is based on publicly available demand data from Appalachian Power, which services the western Virginia and southern West Virginia in the Appalachian region. The demand information is combined by service, normalized, and scaled to an average demand of 1000 kW, which will be the basis for sizing the hybrid energy system. A traditional screening curve analysis for a coal plant and advanced reactor shows that the least cost design varies significantly based on the assumed discount rate and capital recovery period. An optimization program to size the design in TEAL based on the load curve gives 10 optimal designs, all with a negative resulting net present value (NPV) and a coal plant capacity of less than 15%. Including profits from selling captured carbon at a flat rate results in a positive NPV; however, the coal capacity factor only increases to about 40%. There are limitations with this optimization as well since the price of CO2 is likely to decrease as more is sold to the conversion market. The suggested design will combine coal power, an advanced reactor, and coal and biomass coprocessing to produce a variety of products that can be sold to the conversion market while increasing system efficiency. The analysis of conversion pathways for coal and biomass reveals that multiple options will need to be included in the analysis to produce the optimal system design. Three systems will be optimized and compared to determine the best design based on the figures of merit of total NPV and cost of carbon avoided. The first system will include a coal power plant and an advanced reactor that will sell electricity to the grid to meet demand and sell captured carbon to the conversion market. The second system adds a high-temperature steam electrolysis plant, which will utilize electricity during times of low demand to produce hydrogen and sell it to the conversion market. The third system adds biomass and coal processing with options for hydrocarbon oils, syngas to be produced for the conversion market, and electricity generation to power components within the system or provide peaking power. This analysis will be based on a new approach that combines traditional screening curve methods with a dispatch algorithm that optimizes the system based on the opportunity cost of different production options. The resulting optimization algorithm should provide results with less processing time than HERON’s decision tree method. The results from this analysis will determine an optimal design and reinforce the benefits of coal power when used in a hybrid energy system. The initial results show that the addition of a secondary market for carbon sales could result in a positive NPV and increases the capacity factor of the coal plant as compared to a design with only sales to the electricity market. The addition of more markets and additional coal consumption from biomass coprocessing could increase NPV further, replace carbon in other markets through the sale of biomass-derived hydrocarbons, and demonstrate the value of coal power technology.

01 COAL, LIGNITE, AND PEAT↗

Generating Massive Scale-free Networks: Novel Parallel Algorithms using the Preferential Attachment Model

Recently, there has been substantial interest in the study of various random networks as mathematical models of complex systems. As real-life complex systems grow larger, the ability to generate progressively large random networks becomes all the more important. This motivates the need for efficient parallel algorithms for generating such networks. Naïve parallelization of sequential algorithms for generating random networks is inefficient due to inherent dependencies among the edges and the possibility of creating duplicate (parallel) edges. In this article, we present message passing interface-based distributed memory parallel algorithms for generating random scale-free networks using the preferential-attachment model. Our algorithms are experimentally verified to scale very well to a large number of processing elements (PEs), providing near-linear speedups. The algorithms have been exercised with regard to scale and speed to generate scale-free networks with one trillion edges in 6 minutes using 1,000 PEs.

97 MATHEMATICS AND COMPUTING↗

Multi-physics Topology OPtimization and Additive Manufacturing for High-temperature Heat Exchangers

This research significantly advances the understanding of high-temperature heat exchanger design through an integrated approach that combines topology optimization (TO), triply periodic minimal surface (TPMS) structures, additive manufacturing (AM) and thermohydraulic testing. Each of these components contributes uniquely to a unified, high-performance design, fabrication and testing workflow. Topology optimization serves as the foundation of the design methodology by providing a systematic way to determine the most effective material layout for separating hot and cold fluids while maximizing thermal performance. The researchers introduced a novel three-material optimization framework using two density fields to represent hot fluid, cold fluid, and solid domains. This approach enables automated discovery of optimal shapes and flow paths that cannot be intuitively designed, especially under constraints imposed by manufacturing technologies. Furthermore, constraints such as minimal wall thickness and overhang angles were embedded into the optimization process, ensuring that resulting designs are not only thermally efficient but also manufacturable using modern additive techniques. In parallel, the study delves into the use of Gyroid-based TPMS geometries for constructing the core of the heat exchanger. TPMS structures are known for their high surface area, excellent fluid mixing capabilities, and minimal pressure drop characteristics. The researchers applied a data-driven modeling framework using Heteroscedastic Sparse Gaussian Process Regression (HSGPR) combined with genetic algorithms. This allowed for the rapid evaluation and optimization of key geometric parameters such as frequency, iso-value, and phase shift. The result was a set of Gyroid structures tailored for high heat transfer and low flow resistance, demonstrating clear improvements over conventional straight-channel designs. After the designing process, additive manufacturing played a critical role by turning these highly complex, optimized geometries into physical components. Utilizing Laser Powder Bed Fusion (LPBF) with Haynes 282, the study demonstrated the feasibility of fabricating these heat exchangers at high precision. Post-processing methods, including dilation-erosion operations, were applied to ensure local features adhered to self-supporting constraints. The fabricated structures were then subjected to thermohydraulic testing under conditions representative of supercritical CO 2 Brayton cycles, validating the predicted performance and confirming the viability of the full design-to-fabrication pipeline. Finally, thermohydraulic testing across the above studies served as a crucial experimental validation of advanced heat exchanger. Under consistent high-temperature and high-pressure conditions using supercritical CO 2 , the testing demonstrated that both TO and Gyroid-based TPMS designs significantly outperformed conventional straight-channel HXs. The TO design achieved a 115% increase in UA and NTU and a 27.6% boost in gravimetric power density, while the data-driven optimized Gyroid design delivered a 166% increase in UA and NTU and improved effectiveness from 68.7% to 86.1%. These results validate the simulation models, confirm the manufacturability of complex geometries under AM constraints, and provide key insights into design-performance trade-offs, thereby advancing the development of high-efficiency, compact heat exchangers for extreme environments.

36 MATERIALS SCIENCE↗

Classical and quantum compression for edge computing: the ubiquitous data dimensionality reduction

Edge computing aims to address the challenges associated with communicating and transferring large amounts of data generated remotely to a data center in a timely and efficient manner. A central pillar of edge computing is local (i.e., at- or near-source) data processing capability so that data transfer to a data center for processing can be minimized. Data compression at the edge is therefore a natural component of edge workflows. Here we present a survey of data compression algorithms with a focus on edge computing. Not all compression algorithms can accommodate the data type heterogeneity, tight processing and communication time constraints, or energy efficiency requirement characteristics of edge computing. We discuss specific examples of compression algorithms that are being explored in the context of edge computing. We end our review with a brief survey of emerging quantum compression techniques that are of importance in quantum information processing, including the proposed concept of quantum edge computing.

97 MATHEMATICS AND COMPUTING↗

Roadmap for unconventional computing with nanotechnology

Abstract In the ‘Beyond Moore’s Law’ era, with increasing edge intelligence, domain-specific computing embracing unconventional approaches will become increasingly prevalent. At the same time, adopting a variety of nanotechnologies will offer benefits in energy cost, computational speed, reduced footprint, cyber resilience, and processing power. The time is ripe for a roadmap for unconventional computing with nanotechnologies to guide future research, and this collection aims to fill that need. The authors provide a comprehensive roadmap for neuromorphic computing using electron spins, memristive devices, two-dimensional nanomaterials, nanomagnets, and various dynamical systems. They also address other paradigms such as Ising machines, Bayesian inference engines, probabilistic computing with p-bits, processing in memory, quantum memories and algorithms, computing with skyrmions and spin waves, and brain-inspired computing for incremental learning and problem-solving in severely resource-constrained environments. These approaches have advantages over traditional Boolean computing based on von Neumann architecture. As the computational requirements for artificial intelligence grow 50 times faster than Moore’s Law for electronics, more unconventional approaches to computing and signal processing will appear on the horizon, and this roadmap will help identify future needs and challenges. In a very fertile field, experts in the field aim to present some of the dominant and most promising technologies for unconventional computing that will be around for some time to come. Within a holistic approach, the goal is to provide pathways for solidifying the field and guiding future impactful discoveries.

Finocchio, Giovanni (ORCID:0000000210433876)↗

Distinguishing isotropic and anisotropic signals for X-ray total scattering using machine learning

Understanding structure–property relationships is essential for advancing technologies based on thin films. X-ray pair distribution function (PDF) analysis can access relevant atomic structure details spanning local-, mid- and long-range structure. While X-ray PDF has been adapted for thin films on amorphous substrates, measurements on single-crystal substrates are necessary to accurately determine structure origins for some thin film materials, especially those for which the substrate changes the accessible structure and properties. However, when measuring films on single-crystal substrates, high-intensity anisotropic Bragg spots saturate 2D detector images, overshadowing the thin films' isotropic scattering signal. This renders previous data processing methods for films on amorphous substrates unsuitable for films on single-crystal substrates. To address this measurement need, we developed IsoDAT2D, an innovative data processing approach using unsupervised machine learning algorithms. The program combines dimensionality reduction and clustering algorithms to separate thin film and single-crystal substrate X-ray scattering signals. We use SimDAT2D , a program we developed to generate simulated thin film data, to validate IsoDAT2D . Here we also use IsoDAT2D to isolate X-ray total scattering signal from a thin film on a single-crystal substrate. The resulting PDF data are compared with similar data processed using previous methods, especially substrate subtraction for single-crystal and amorphous substrates. PDF data from IsoDAT2D -identified X-ray total scattering data are significantly better than from single-crystal substrate subtraction, but not as reliable as PDF data from amorphous substrate subtraction. With IsoDAT2D , there are new opportunities to expand PDF to a wider variety of thin films, including those on single-crystal substrates, with which new structure–property relationships can be elucidated to enable fundamental understanding and technological advances.

36 MATERIALS SCIENCE↗

Coupling Remote Sensing With a Process Model for the Simulation of Rangeland Carbon Dynamics

Rangelands provide significant environmental benefits through many ecosystem services, which may include soil organic carbon (SOC) sequestration. However, quantifying SOC stocks and monitoring carbon (C) fluxes in rangelands are challenging due to the considerable spatial and temporal variability tied to rangeland C dynamics as well as limited data availability. We developed the Rangeland Carbon Tracking and Management (RCTM) system to track long-term changes in SOC and ecosystem C fluxes by leveraging remote sensing inputs and environmental variable data sets with algorithms representing terrestrial C-cycle processes. Bayesian calibration was conducted using quality-controlled C flux data sets obtained from 61 Ameriflux and NEON flux tower sites from Western and Midwestern US rangelands to parameterize the model according to dominant vegetation classes (perennial and/or annual grass, grass-shrub mixture, and grass-tree mixture). The resulting RCTM system produced higher model accuracy for estimating annual cumulative gross primary productivity (GPP) (R 2 > 0.6, RMSE <390 g C m -2 ) relative to net ecosystem exchange of CO 2 (NEE) (R 2 > 0.4, RMSE <180 g C m -2 ). Model performance in estimating rangeland C fluxes varied by season and vegetation type. The RCTM captured the spatial variability of SOC stocks with R 2 = 0.6 when validated against SOC measurements across 13 NEON sites. Model simulations indicated slightly enhanced SOC stocks for the flux tower sites during the past decade, which is mainly driven by an increase in precipitation. Future efforts to refine the RCTM system will benefit from long-term network-based monitoring of vegetation biomass, C fluxes, and SOC stocks.

54 ENVIRONMENTAL SCIENCES↗

Streaming Readout and Data-Stream Processing With ERSAP

With the exponential growth in the volume and complexity of data generated at high-energy physics and nuclear physics research facilities, there is an imperative demand for innovative strategies to process this data in real or near-real-time. Given the surge in the requirement for high-performance computing, it becomes pivotal to reassess the adaptability of current data processing architectures in integrating new technologies and managing streaming data. This paper introduces the ERSAP framework, a modern solution that synergizes flow-based programming with the reactive actor model, paving the way for distributed, reactive, and high performance in data stream processing applications. Additionally, we unveil a novel algorithm focused on time-based clustering and event identification in data streams. The efficacy of this approach is further exemplified through the data-stream processing outcomes obtained from the recent beam tests of the EIC prototype calorimeter at DESY.

Vardan, Gyurjyan↗

CSISAR--Complete System Integrated SAR

The CSISAR tool is GUI based and very simple to use. The algorithms are robust, and the unique processing flows, that the user is stepped through, virtually eliminate the possibility of error in GEOINT production. An integrated data manager is a key part of the CSISAR system. This data manager keeps track of the data available to a user and informs the user of what data is available and what can be done with that data. This keeps the user from having to be trained in the nuances of the algorithms. CSISAR also has an integrated product manager, which helps the user identify, view and manage previously made products. CSISAR was originally developed in 2010-2011 as a Windows based system. It was updated in 2015 to be a Linux based system. This SAND report is intended to make the Product Description and User’s Guide for CSISAR (originally included within the software) more widely available. New is a brief addition of Linux-specific installation details.

97 MATHEMATICS AND COMPUTING↗

An uncertainty-aware strategy for plasma mechanism reduction with directed weighted graphs

In this work, we present a framework for the analysis and reduction of plasma mechanisms by means of weighted directed graphs, in which reactions and species are both treated as nodes. The methodology consists of two distinct analyses. The first, which is qualitative, relies on graph spatializations via force-directed algorithms to discover the predominant global patterns in the chemical model. The second ranks the reactions based on their shortest paths' lengths from/to the species of interest and their relative contributions to the power balance. Further, this quantitative investigation enables a strategy for mechanism reduction that is fully automatized, as it does not require any expert knowledge, highly effective, as it generates reduced mechanisms that are highly accurate while relying on a small number of processes, and easily interpretable, as the algorithm justifies the importance of the retained reactions by outputting their related chemical pathways. Additionally, the work proposes a methodology extension that employs ensembles of graphs to improve the robustness of the reduced mechanism to reaction parameter uncertainties. The approach, here tested for steady-state predictions of a plasma system characterizing negative hydrogen ion sources, is general and can be used in a wide variety of applications outside the particular nuclear fusion context demonstrated in this work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Particle-in-cell Simulations of Relativistic Magnetic Reconnection with Advanced Maxwell Solver Algorithms

Abstract Relativistic magnetic reconnection is a nonideal plasma process that is a source of nonthermal particle acceleration in many high-energy astrophysical systems. Particle-in-cell (PIC) methods are commonly used for simulating reconnection from first principles. While much progress has been made in understanding the physics of reconnection, especially in 2D, the adoption of advanced algorithms and numerical techniques for efficiently modeling such systems has been limited. With the GPU-accelerated PIC code WarpX, we explore the accuracy and potential performance benefits of two advanced Maxwell solver algorithms: a nonstandard finite-difference scheme (CKC) and an ultrahigh-order pseudo-spectral method (PSATD). We find that, for the relativistic reconnection problem, CKC and PSATD qualitatively and quantitatively match the standard Yee-grid finite-difference method. CKC and PSATD both admit a time step that is 40% longer than that of Yee, resulting in a ∼40% faster time to solution for CKC, but no performance benefit for PSATD when using a current deposition scheme that satisfies Gauss’s law. Relaxing this constraint maintains accuracy and yields a 30% speedup. Unlike Yee and CKC, PSATD is numerically stable at any time step, allowing for a larger time step than with the finite-difference methods. We found that increasing the time step 2.4–3 times over the standard Yee step still yields accurate results, but it only translates to modest performance improvements over CKC, due to the current deposition scheme used with PSATD. Further optimization of this scheme will likely improve the effective performance of PSATD.

79 ASTRONOMY AND ASTROPHYSICS↗

Statistical Learning for Nonlinear Model Reduction from Local Simulations of Stochastic and Particle- and Agent-Based Systems

Stochastic physical systems across the sciences that have very high-dimensional state spaces, with a large number of fast degrees of freedom that force direct simulators to proceed by integration steps that are orders of magnitude smaller than events of interests (e.g., particle collisions). Examples range from molecular motion to dynamics of large populations of cells. A grand challenge in the simulation and understanding of such systems is the systematic construction of accurate, interpretable, reduced models, enabling faster simulations, revealing fundamental properties of the dynamics, and predicting phenomena of interest that the original simulator could not reached with sufficient accuracy or within a given computational budget. In this projected we developed novel statistical estimation/machine learning techniques for analyzing and building empirical reduced models for important families of high-dimensional stochastic systems, in particular: - we developed techniques for estimating interaction kernels in interacting particle- and agent-based systems, which are ubiquitous in Physics, Biology and many other sciences, given observed trajectories of the system; - we developed techniques for nonlinear model reduction for high-dimensional stochastic systems that have a small number of unknown, nonlinear slow variables, and a large number of fast modes, that are possibly of large magnitude, given observed short trajectories of the system in the form of bursts of trajectories from different initial conditions; - we developed novel techniques for estimating linear dynamical systems on graphs when both the dynamics and the underlying graph are unknown, and we have a sparse set of space-time observations; - we considered the problem of estimating an unknown nonlinear observation function of a standard process (e.g. Brownian motion), so that we can recognized if an observed dynamics is "just" a nonlinear version of a known dynamics; we also developed benchmarks for learning algorithms aimed at learning and classifying diffusion processes.

97 MATHEMATICS AND COMPUTING↗

Snowmass Computational Frontier: Topical Group Report on Experimental Algorithm Parallelization

The substantial increase in data volume and complexity expected from future experiments will require significant investment to prepare experimental algorithms. These algorithms include physics object reconstruction, calibrations, and processing of observational data. In addition, the changing computing architecture landscape, which will be primarily composed of heterogeneous resources, will continue to pose major challenges with regard to algorithmic migration. Portable tools need to be developed that can be shared among the frontiers (e.g., for code execution on different platforms) and opportunities, such as forums or cross-experimental working groups, need to be provided where experiences and lessons learned can be shared between experiments and frontiers. At the same time, individual experiments also need to invest considerable resources to develop algorithms unique to their needs (e.g., for facilities dedicated to the experiment), and ensure that their specific algorithms will be able to efficiently exploit external heterogeneous computing facilities. Common software tools represent a cost-effective solution, providing ready-to-use software solutions as well as a platform for R&D work. These are particularly important for small experiments which typically do not have dedicated resources needed to face the challenges imposed by the evolving computing technologies. Workforce development is a key concern across frontiers and experiments, and additional support is needed to provide career opportunities for researchers working in the field of experimental algorithm development. Finally, cross-discipline collaborations going beyond high-energy physics are a key ingredient to address the challenges ahead and more support for such collaborations needs to be created. This report targets future experiments, observations and experimental algorithm development for the next 10-15 years.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Optimal Control of Biomass Feedstock Processing System Under Uncertainty in Biomass Quality

Planning of biorefinery operations is complicated by the stochastic nature of physical and chemical characteristics of biomass feedstock, such as, moisture level and carbohydrate content. Biomass characteristics affect the performance of the equipment which feed the reactor and the efficiency of the conversion process in a biorefinery. We propose a stochastic optimization model to identify a blend of feedstocks, inventory levels, and operating conditions of equipment to ensure a continuous flowing of biomass to the reactor while meeting the requirements of the biochemical conversion process. We propose a sample average approximation (SAA) of the model, and develop an efficient algorithm to solve the SAA model. A feedstock preprocessing process consists of two-stage grinding and pelleting is used to develop a case study. Extensive numerical analysis are conducted which lead to a number of observations. Our main observation is that sequencing bales based on moisture level and carbohydrate content leads to robust solutions that improve processing time and processing rate of the reactor. We provide a number of managerial insights that facilitate the implementation of the model proposed. Note to Practitioners—This paper is motivated by the challenges faced in the bioenergy industry. The focus of this paper is on plants which use the biochemical conversion process to generate liquid fuels. It has been observed that variations in biomass characteristics, such as moisture content, cause variations in feeding of the system which lead to under-utilization of equipment. A requirement of biochemical conversion process is to maintain the carbohydrate content of biomass processed by the reactor, larger than a threshold. We propose a model that identifies the inventory levels and operating conditions of equipment to ensure a continuous flowing of biomass to the reactor. The goal is to improve equipment utilization while satisfying the requirements of the conversion process. The model is tested using real-life data. We found out that by sequencing bales based on moisture level and carbohydrate content, a plant can reduce variability in the system leading to improved system reliability, higher processing rates of the reactor, and higher throughput.

09 BIOMASS FUELS↗

Optimizing Perovskite Thin‐Film Parameter Spaces with Machine Learning‐Guided Robotic Platform for High‐Performance Perovskite Solar Cells

Abstract Simultaneously optimizing the processing parameters of functional thin films remains a challenge. The design and utilization of a fully automated platform called SPINBOT is presented for the engineering of solution‐processed functional thin films. The SPINBOT is capable of performing experiments with high sampling variability through the unsupervised processing of hundreds of substrates with exceptional experimental control. Through the iterative optimization process enabled by the Bayesian optimization (BO) algorithm, the SPINBOT explores an intricate parameter space, continuously improving the quality and reproducibility of the produced thin films. This machine learning (ML)‐guided reliable SPINBOT platform enables the acceleration of the optimization process of perovskite solar cells via a simple photoluminescence characterization of films. As a result, this study arrives at an optimal film that, when processed into a solar cell in an ambient atmosphere, immediately yields a champion power conversion efficiency (PCE) of 21.6% with satisfactory performance reproducibility. The unsealed devices retain 90% of their initial efficiency after 1100 h of continuous operation at 60–65 °C under metal‐halide lamps. It is anticipated that the integration of robotic platforms with the intelligent algorithm will facilitate the widespread adoption of effective autonomous experimentation to address the evolving needs and constraints within the materials science research community.

14 SOLAR ENERGY↗