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At least 91 records · Page 5

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗

Compositional Reasoning for Hierarchical State Machines

Harel statecharts and its derivatives are popular graphical languages for specifying discrete control systems via hierarchical state machines. Separately, there has been a long line of work on specifying concurrent systems with process calculi which come equipped with an algebraic theory, the ability reason compositionally about various temporal properties, and strong type systems. While these two approaches to modeling systems are tantalizingly similar, the integrated reasoning principles that exist for process calculi have not been demonstrated in hierarchical state machines. A key issue is that operational theories for process calculi do not behave like control systems, and thus, there is virtually no tool support for modeling control systems with such languages. For a control system designer, bringing the integrated, more scalable reasoning from the process calculi to state-machine languages would enable the specification of more complex systems and a more modular systems development process. Our insight is that we can recover many important results from the process calculi in hierarchical state machines with local scope. We employ a structural operational semantics, which is ubiquitous in process and 𝜆-calculi but uncommon in hierarchical statemachine formalizations, to enable inductive reasoning about behavior. Taking inspiration from the structure of process calculi metatheories, we define a calculus of refinement and equivalence that we prove sound with respect to local notion of (bi)simulation. Furthermore, we prove that the calculus preserves the behavioral properties of reactivity, observational determinism, traces, and linear temporal properties. Our results are mechanized in the Rocq proof assistant.

97 MATHEMATICS AND COMPUTING↗

Role of Electron Correlation beyond the Active Space in Achieving Quantitative Predictions of Spin-Phonon Relaxation

Single-molecule magnets (SMMs) are promising candidates for molecular-scale data storage and processing due to their strong magnetic anisotropy and long spin relaxation times. However, as temperature rises, interactions between electronic states and lattice vibrations accelerate spin relaxation, significantly limiting their practical applications. Recently, ab initio simulations have made it possible to advance our understanding of phonon-induced magnetic relaxation, but significant deviations from experiments have often been observed. The description of molecules’ electronic structure has been mostly based on complete active space self-consistent field (CASSCF) calculations, and the impact of electron correlation beyond the active space remains largely unexplored. In this study, we provide the first systematic investigation of spin-phonon relaxation in SMMs with post-CASSCF multiconfigurational methods, specifically CAS followed by second-order perturbation theory and multiconfiguration pair-density functional theory. Taking Co(II)- and Dy(III)-based SMMs as case studies, we analyze how electron correlation influences spin-phonon relaxation rates across a range of temperatures, comparing theoretical predictions with experimental observations. Our findings demonstrate that post-CASSCF treatments make it possible to achieve quantitative predictions for Co(II)-based SMMs. For Dy(III)-based systems, however, accurate predictions require consideration of additional effects, underscoring the urgent necessity of further advancing the study of the effects of electronic correlation in these complex systems.

Energy↗

One-shot learning for solution operators of partial differential equations

Learning and solving governing equations of a physical system, represented by partial differential equations (PDEs), from data is a central challenge in many areas of science and engineering. Traditional numerical methods can be computationally expensive for complex systems and require complete governing equations. Existing data-driven machine learning methods require large datasets to learn a surrogate solution operator, which could be impractical. Here, we propose a solution operator learning method that requires only one PDE solution, i.e., one-shot learning, along with suitable initial and boundary conditions. Leveraging the locality of derivatives, we define a local solution operator in small local domains, train it using a neural network, and use it to predict solutions of new input functions via mesh-based fixed-point iteration or meshfree neural-network based approaches. We test our method on various PDEs, complex geometries, and a practical spatial infection spread application, demonstrating its effectiveness and generalization capabilities.

97 MATHEMATICS AND COMPUTING↗

Forecasting high-dimensional spatio-temporal systems from sparse measurements

This paper introduces a new neural network architecture designed to forecast high-dimensional spatio-temporal data using only sparse measurements. The architecture uses a two-stage end-to-end framework that combines neural ordinary differential equations (NODEs) with vision transformers. Initially, our approach models the underlying dynamics of complex systems within a low-dimensional space; and then it reconstructs the corresponding high-dimensional spatial fields. Many traditional methods involve decoding high-dimensional spatial fields before modeling the dynamics, while some other methods use an encoder to transition from high-dimensional observations to a latent space for dynamic modeling. In contrast, our approach directly uses sparse measurements to model the dynamics, bypassing the need for an encoder. This direct approach simplifies the modeling process, reduces computational complexity, and enhances the efficiency and scalability of the method for large datasets. We demonstrate the effectiveness of our framework through applications to various spatio-temporal systems, including fluid flows and global weather patterns. Although sparse measurements have limitations, our experiments reveal that they are sufficient to forecast system dynamics accurately over long time horizons. Our results also indicate that the performance of our proposed method remains robust across different sensor placement strategies, with further improvements as the number of sensors increases. This robustness underscores the flexibility of our architecture, particularly in real-world scenarios where sensor data is often sparse and unevenly distributed.

97 MATHEMATICS AND COMPUTING↗

The tensor-train stochastic finite volume method for uncertainty quantification

The stochastic finite volume method offers an efficient one-pass approach for assessing uncertainty in hyperbolic conservation laws. Still, it struggles with the curse of dimensionality when dealing with multiple stochastic variables. Here, we introduce the stochastic finite volume method within the tensor-train framework to counteract this limitation. This integration, however, comes with its own set of difficulties, mainly due to the propensity for shock formation in hyperbolic systems. To overcome these issues, we have developed a tensor-train-adapted stochastic finite volume method that employs a global WENO reconstruction, making it suitable for such complex systems. This approach represents the first step in designing tensor-train techniques for hyperbolic systems and conservation laws involving shocks.

97 MATHEMATICS AND COMPUTING↗

Testing convolutional neural network based deep learning systems: a statistical metamorphic approach

Machine learning technology spans many areas and today plays a significant role in addressing a wide range of problems in critical domains,i.e., healthcare, autonomous driving, finance, manufacturing, cybersecurity,etc. Metamorphic testing (MT) is considered a simple but very powerful approach in testing such computationally complex systems for which either an oracle is not available or is available but difficult to apply. Conventional metamorphic testing techniques have certain limitations in verifying deep learning-based models (i.e., convolutional neural networks (CNNs)) that have a stochastic nature (because of randomly initializing the network weights) in their training. In this article, we attempt to address this problem by using a statistical metamorphic testing (SMT) technique that does not require software testers to worry about fixing the random seeds (to get deterministic results) to verify the metamorphic relations (MRs). We propose seven MRs combined with different statistical methods to statistically verify whether the program under test adheres to the relation(s) specified in the MR(s). We further use mutation testing techniques to show the usefulness of the proposed approach in the healthcare space and test two CNN-based deep learning models (used for pneumonia detection among patients). The empirical results show that our proposed approach uncovers 85.71% of the implementation faults in the classifiers under test (CUT). Furthermore, we also propose an MRs minimization algorithm for the CUT, thus saving computational costs and organizational testing resources.

Computer Science↗

A multidimensional approach to quantum state tomography of photoelectron wavepackets

There is a growing interest in reconstructing the density matrix of photoelectron wavepackets, in particular in complex systems where decoherence can be introduced either by a partial measurement of the system or through coupling with a stochastic environment. To this end, several methods to reconstruct the density matrix, quantum state tomography protocols, have been developed and tested on photoelectrons ejected from noble gases following absorption of extreme ultraviolet (XUV) photons from attosecond pulses. It remains a challenge to obtain model-free, single scan protocols that can reconstruct the density matrix with high fidelities. Current methods require extensive measurements or involve complex fitting of the signal. Efficient single-scan reconstructions would be of great help to increase the number of systems that can be studied. We propose a new and more efficient protocol that is able to reconstruct the continuous variable density matrix of a photoelectron in a single time delay scan. It is based on measuring the coherences of a photoelectron created by absorption of an XUV pulse using a broadband infrared (IR) probe that is scanned in time and a narrowband IR reference that is temporally fixed to the XUV pulse. We illustrate its performance for a Fano resonance in He as well as mixed states in Ar arising from spin-orbit splitting. We show that the protocol results in excellent fidelities and near-perfect estimation of the purity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Preparing MPICH for exascale

The advent of exascale supercomputers heralds a new era of scientific discovery, yet it introduces significant architectural challenges that must be overcome for MPI applications to fully exploit its potential. Among these challenges is the adoption of heterogeneous architectures, particularly the integration of GPUs to accelerate computation. Additionally, the complexity of multithreaded programming models has also become a critical factor in achieving performance at scale. The efficient utilization of hardware acceleration for communication, provided by modern NICs, is also essential for achieving low latency and high throughput communication in such complex systems. In response to these challenges, the MPICH library, a high-performance and widely used Message Passing Interface (MPI) implementation, has undergone significant enhancements. Here, this paper presents four major contributions that prepare MPICH for the exascale transition. First, we describe a lightweight communication stack that leverages the advanced features of modern NICs to maximize hardware acceleration. Second, our work showcases a highly scalable multithreaded communication model that addresses the complexities of concurrent environments. Third, we introduce GPU-aware communication capabilities that optimize data movement in GPU-integrated systems. Finally, we present a new datatype engine aimed at accelerating the use of MPI derived datatypes on GPUs. These improvements in the MPICH library not only address the immediate needs of exascale computing architectures but also set a foundation for exploiting future innovations in high-performance computing. By embracing these new designs and approaches, MPICH-derived libraries from HPE Cray and Intel were able to achieve real exascale performance on OLCF Frontier and ALCF Aurora respectively.

Guo, Yanfei [Argonne National Laboratory (ANL), Ar↗

Detecting Anomalies for Fire Prevention in Distribution Systems: Challenges and Analytical Techniques

Electric utilities in California have historically been linked to up to 10% of wildfires. To mitigate this risk, Southern California Edison has invested significantly in wildfire prevention strategies, including undergrounding cables and enhancing equipment inspections. This article explores a novel approach to fire prevention by detecting anomalies in the distribution system that may indicate potential fire hazards. The focus is on identifying arcing conditions through high-resolution point-on-wave (POW) measurements. Arcing, a precursor to fires, is challenging to detect due to its subtle transients and complex system topology. The article discusses the use of advanced signal processing and machine learning techniques, such as spectral correlation function and discrete wavelet transform, to extract features from POW data and accurately identify arcing events. The study demonstrates a high accuracy rate in detecting arcing, paving the way for improved fire prevention measures in electric distribution systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Boundary Layer Exploration of Aerosols and Clouds ON Ships (BEACONS)

BEACONS aims to demonstrate autonomous deployment of a shipborne system that routinely observes atmospheric, cloud, and aerosol properties. These observations enable scientists to study aerosol-cloud interactions, advancing energy resilience and the Department of Energy's mission to improve model prediction. Key Project Outcomes Autonomous deployment of aerosol and cloud measurement systems aboard a Pasha Hawaii Marjorie C commercial ship. Six-month campaign for continuous, high-resolution aerosol and cloud data collection with minimal crew intervention. Development and testing of instruments in two phases, advancing from essential to complex systems. AI-ready processed data on the BEACONS Data Platform for near-real-time data access. Validation of aerosol-cloud interaction hypotheses for improved modeling. Establishment of best practices for instrument deployment in marine environments. Scientific collaboration to support the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) mission.

54 ENVIRONMENTAL SCIENCES↗

FTL: Transfer Learning Nonlinear Plasma Dynamic Transitions in Low Dimensional Embeddings (FTL) v1.0

Fusion Transfer Learning (FTL) model provides a new paradigm to study high-dimensional dynamical behaviors, such as those in fusion plasma systems. The knowledge transfer process leverages a pre-trained neural encoder-decoder network, initially trained on linear simulations, to effectively capture nonlinear dynamics. The low-dimensional embeddings extract the coherent structures of interest, while preserving the inherent dynamics of the complex system. Experimental results highlight FTL's capacity to capture transitional behaviors and dynamical features in plasma dynamics -- a task often challenging for conventional methods. The model developed in this study is generalizable and can be extended broadly through transfer learning to address various magnetohydrodynamics (MHD) modes.

Bai, Zhe↗

Existing Methods for Grid Strength Assessment and Role of Hydropower in Future Grids

The power system is undergoing rapid evolution with increasing penetration of inverter-based resources (IBRs), large loads, microgrids, and power electronic devices. Ensuring reliable and stable operation of the modern power grid is a multi-faceted challenge that requires detailed understanding of this complex system. Dynamic stability is a major concern in maintaining the security of power grids as the generation mixes and large loads transitions to include high shares of power electronic devices. The operation of IBRs in regions with low system strength and higher grid impedances has been found to be the main reason behind many of the power system instabilities that manifest themselves in various types of oscillations and interactions that, if not properly addressed and damped, can jeopardize the reliable operation of the power system. Weak grid conditions compound such stability problems, particularly when many IBRs operate in proximity to and connect to weak power grids. Therefore, it is important to assess grid strength for planning, integration and operation of IBRs for a given power system. In this report, we aim to understand and classify existing methodologies for grid strength assessment, along with their limitations and future needs. Further, we aim to utilize the huge untapped potential in utilizing hydro energy resources in addressing some of the pertinent challenges of grid strength and reliable operation of modern power systems. Hydropower, historically valued for its flexibility and dispatchability, now faces new constraints due to reduced share of synchronous machines in the generation mix and seasonal variability of available water resources. Yet, these same plants present untapped potential beyond energy generation - notably, as providers of critical grid services. This report explores how hydropower plants, particularly through operation as synchronous condensers, can play a pivotal role in strengthening the grid amid evolving system dynamics.

13 HYDRO ENERGY↗

Dynamic Control of Sodium Cold Trap Purification Temperature Using LSTM System Identification

This study investigates the dynamic regulation of the sodium cold trap purification temperature at Argonne National Laboratory’s liquid sodium test facility, employing long short-term memory (LSTM) system identification techniques. The investigation introduces an innovative hybrid approach by integrating model predictive control (MPC) based on first principles dynamic models with a multi-step time–frequency LSTM model in predicting the temperature profiles of a sodium cold trap purification system. The long short-term memory–model predictive controller (LSTM-MPC) model employs a sliding window scheme to gather training samples for multi-step prediction, leveraging historical data to construct predictive models that capture the non-linearities of the complex system dynamics without explicitly modeling the underlying physical processes. The performance of the LSTM-MPC and MPC were evaluated through simulation experiments, where both models were assessed on their capacity to maintain the cold trap temperature within predefined set-points while minimizing deviations and overshoots. Results obtained show how the data-driven LSTM-MPC model demonstrates stability and adaptability. In contrast, the traditional MPC model exhibits irregularities, particularly evident as overshoots around set-point limits, which can potentially compromise its effectiveness over long prediction time intervals. The findings obtained offer valuable insights into integrating data-driven techniques for enhancing real-time monitoring systems.

LSTM-MPC↗

Close roof-mounted system temperature estimation for compliance to IEC TS 63126

When photovoltaic (PV) modules are installed on rooftops, the module temperature depends primarily on the geographic location and the mounting configuration. If the mounting structure does not provide sufficient airflow in a hot environment, the 98th percentile temperature will exceed 70°C, which according to IEC TS 63126 ED. 1, requires higher levels of thermal stability testing. However, there is no clear way to determine the temperature level needed for a particular location and system design. Here, in this work, we identify a relationship between the module standoff to the rooftop and the module temperature and propose methods to describe a minimum standoff for typical PV modules in a simple mounting configuration installed in a given location. For more complex system designs, we show how to determine an equivalent “effective standoff” that can be applied to generic calculations. Lastly, we show measurements and calculations from several systems to demonstrate how this method could work.

14 SOLAR ENERGY↗

High-power test of a C-band linear accelerating structure with an RFSoC-based LLRF system

Normal conducting linear particle accelerators consist of multiple rf stations with accelerating structure cavities. Low-level rf (LLRF) systems are employed to set the phase and amplitude of the field in the accelerating structure and to compensate for the pulse-to-pulse fluctuation of the rf field in the accelerating structures with a feedback loop. The LLRF systems are typically implemented with analog rf mixers, heterodyne-based architectures, and discrete data converters. There are multiple rf signals from each of the rf stations, so the number of rf channels required increases rapidly with multiple rf stations. With a large number of rf channels, the footprint, component cost, and system complexity of the LLRF hardware will increase significantly. To meet the design goals of being compact and affordable for future accelerators, we have designed the next-generation LLRF (NG-LLRF) with a higher integration level based on RFSoC technology. The NG-LLRF system samples rf signals directly and performs rf mixing digitally. Further, the NG-LLRF has been characterized in loopback mode to evaluate the performance of the system and has also been tested with a standing-wave accelerating structure, a prototype for the Cool Copper Collider (C 3 ) with a peak rf power level up to 16.45 MW. The loopback test demonstrated amplitude fluctuation below 0.15% and phase fluctuation below 0.15°, which are considerably better than the requirements of C 3 . The rf signals from the different stages of the accelerating structure at different power levels are measured by the NG-LLRF, which will be critical references for the control algorithm designs. The NG-LLRF also offers flexibility in waveform modulation, so we have used rf pulses with various modulation schemes, which could be useful for controlling some of the rf stations in accelerators. In this paper, the high-power test results at different stages of the test setup will be summarized, analyzed, and discussed.

47 OTHER INSTRUMENTATION↗

Fabricated devices for performing bacterial-fungal interaction experiments across scales

Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.

59 BASIC BIOLOGICAL SCIENCES↗

Progress in $Nb_3Sn$ SRF Technology: Opportunities and Outlook

Nb3Sn superconducting radiofrequency (SRF) cavities can expand performance capabilities of particle accelerators for both the fundamental research and the industrial applications. The technology holds a great appeal especially to small-scale applications, where it can enable a turn-key compact cryocooler operation eliminating the need for complex sub-atmospheric liquid helium cryogenic plants. Since the research into Nb3Sn SRF coatings using vapor diffusion technique restarted in 2009 at Cornell University, there has been a growing number of SRF groups around the world developing this technology with a steady increase in cavity performance and system complexity. In this talk, after a short overview of SRF technology, I will present on some of the recent developments in Nb3Sn SRF cavities, focusing on recent efforts to complete the first-of-its-kind Nb3Sn 2-cavity CEBAF-type cryomodule, which was assembled and tested last year. The talk will conclude with a short overview on some of the ongoing projects and the future possibilities for Nb3Sn cavities in accelerator applications.

43 PARTICLE ACCELERATORS↗