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At least 343 records · Page 19

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Abstract Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of this vision will transform plant systems science and ripple outwards through society and across the globe. Beyond deepening our biological understanding, we envision entirely new applications. We further anticipate a wave of diversification of plant systems practitioners while stimulating community engagement, underpinning increasing entrepreneurship. This surge of engagement and knowledge will help satisfy and stoke people's natural curiosity about the future, and their desire to prepare for it, as they seek fuller information about food, health, climate and ecological systems.

59 BASIC BIOLOGICAL SCIENCES↗

Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles

Extracellular vesicles (EVs) are membrane-bound particles secreted by cells, playing crucial roles in intercellular communication. The composition of EVs can undergo changes in response to stress and disease conditions, making them excellent biomarker candidates. However, extracting protein information from EVs can be challenging due to their low abundance in complex biofluids and copurification with contaminant proteins and particles. Techniques to enrich EVs have their strengths and limitations, without one being able to purify EVs to complete homogeneity. This can lead to compromised recovery rates and increased complexity, making data interpretation difficult. In this viewpoint article, we explore the concept that better characterization of EV composition, followed by quantification of EV proteins in complex samples, might be a more viable route for biomarker development. Mass spectrometers can provide reproducible deep coverage of the EV proteome, despite sample impurities. This paradigm shift presents opportunities to integrate advanced bioinformatics tools to refine the EV proteome landscape, identify novel biomarkers, and streamline validation processes in biomarker development. By focusing on leveraging technology rather than achieving absolute purity, this approach can transform current practices and open opportunities for robust biomarker discovery. Herein, we highlight not only such opportunities but also challenges to implement this concept.

Dakup, Panshak P. [Pacific Northwest National Labo↗

Development of transparent, particle‐loaded photoresins for volumetric additive manufacturing of silica glass

Abstract Additive manufacturing of glass aims to change the paradigm of glass manufacturing by allowing for improved customization coupled with lower energy and post‐processing needs. Fabrication of glass via volumetric additive manufacturing (VAM) involves printing in a silica‐loaded photopolymer resin with subsequent thermal processing and adds additional advantages by allowing for rapid printing of parts with smooth surfaces and no supports. Previous work in glass VAM has demonstrated fabrication of optical quality microoptics with overall dimensions on the scale of tens of cubic millimeters. For applications requiring glass printed on the scale of cubic centimeters the rheology, scattering, and green part strength must be controlled via resin formulation. Here, we present insight into a novel glass photopolymer resin suitable for VAM and in the effect of tuning formulation on the ability to produce dense glass parts with volumes on the scale of cubic centimeters.

Myers, Luke A.↗

The basics of quantum computing for chemists

The rapid and successful strides in quantum chemistry in the past decades can be largely credited to a conspicuous synergy between theoretical and computational advancements. However, the architectural computer archetype that enabled such a progress is approaching a state of more stagnant development. One of the most promising technological avenues for the continuing progress of quantum chemistry is the emerging quantum computing paradigm. This revolutionary proposal comes with several challenges, which span a wide array of disciplines. In chemistry, it implies, among other things, a need to reformulate some of its long established cornerstones in order to adjust to the operational demands and constraints of quantum computers. Due to its relatively recent emergence, much of quantum computing may still seem fairly nebulous and largely unknown to most chemists. It is in this context that here we review and illustrate the basic aspects of quantum information and their relation to quantum computing insofar as enabling simulations of quantum chemistry. As a result, we consider some of the most relevant developments in light of these aspects and discuss the current landscape when of relevance to quantum chemical simulations in quantum computers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid Quantum–Classical Graph Transformers for Efficient Sentiment Analysis

Quantum Machine Learning (QML) offers a promising paradigm that leverages quantum computing principles to develop efficient and expressive models for learning from complex and structured data. Recent advances in natural language processing (NLP) and artificial intelligence (AI) have demonstrated capabilities in understanding, generating, and reasoning over linguistic and multimodal information. In this work, we present the Quantum Graph Transformer (QGT), a hybrid quantum–classical architecture that extends graph transformer capabilities through quantum self-attention. The QGT models variable-length sentences as token graphs, where both the embedding encoding and the self-attention mechanisms are implemented using parameterized quantum circuits (PQCs), enabling efficient contextual learning with significantly fewer trainable parameters. We train QGT using both fully connected and 𝑘 -nearest-neighbor graph structures and evaluate it on five benchmark sentiment-classification datasets. Experimental results show that QGT consistently achieves higher or comparable accuracy to existing quantum NLP models and outperforms a Classical Graph Transformer (CGT) baseline with identical architecture, achieving 29.4 × fewer parameters while requiring 3–5 × fewer samples to reach comparable performance. These findings highlight the potential of graph-based quantum models as scalable and data-efficient architectures for natural language understanding.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

In Situ MOF Pyrolysis Construction of Hierarchical Porous Co‐Nanoparticles/Carbon Cloth Composites for Enhanced Electromagnetic Wave Shielding and Absorption

The development of high-performance electromagnetic protection materials integrating broadband absorption and effective shielding capabilities is hindered by challenges in simultaneously optimizing multiple electromagnetic properties through conventional material designs. This study pioneers a hierarchical porous Co nanoparticle/carbon cloth (Co/CC) composite via controlled annealing of a Co-MOF precursor on carbon cloth. The Co-MOF served a dual role as both magnetic source and pore-forming agent, enabling in situ generation of uniformly dispersed Co nanoparticles and creation of abundant pores/interfaces on the CC fibers during pyrolysis. This unique architecture synergistically enhanced dielectric loss (via interfacial/dipolar polarization) and magnetic loss (via natural resonance, exchange interactions, and eddy currents), significantly improving impedance matching. The hierarchical pores further functioned as integrated “absorption–reflection” units for efficient electromagnetic energy attenuation. Consequently, the Co/CC composite annealed at 800°C (Co/CC-800) achieves minimum reflection loss (−40.69 dB) and 120% effective absorption bandwidth extension (6.16 GHz) as a filler, and exhibits superior electromagnetic interference shielding effectiveness (46.66 dB) as an integrated component. Significantly, Co/CC-800 demonstrated robust photothermal and electrothermal conversion capabilities, ensuring operational stability in ice-covered and humid harsh environments. This work pioneers a pore-structure-mediated strategy to harmonize dielectric–magnetic synergy, providing a new paradigm for designing advanced multifunctional electromagnetic protection materials.

dielectric‐magnetic synergy↗

Superatoms as Superior Catalysts: ZrO versus Pd

Abstract Single‐atom catalysts are the focus of studies for over a decade due to their enhanced reactivity at smaller sizes. However, they have limitations as they offer only one active site, which may not be sufficient for reactions requiring the co‐adsorption of multiple reactants. Additionally, atoms can migrate on a substrate and coalesce, resulting in decreased reactivity. Here, an alternate path, a single‐superatom catalyst is provided. Superatoms are clusters of atoms that mimic the chemistry of atoms even if they do not contain a single atom whose chemistry they mimic. Motivated by an experimental paper on the photoelectron‐spectroscopy of negatively charged ions where ZrO is found to mimic properties of a Pd atom, first the reaction of Pd and ZrO with small molecules in the gas‐phase is studied and found that ZrO not only mimics the chemistry of Pd, but is able to activate these molecules more strongly than Pd. A detailed first‐principles study of CO 2 reduction (CO 2 ‐RR) and hydrogen evolution reactions (HER) on Pd and ZrO supported on graphene, Au(111), and Cu(111) surfaces shows that superatoms are indeed superior catalysts. The ability to design numerous superatoms by varying size and composition offers a promising new paradigm for catalyst design and synthesis.

Chemistry↗

Rigidity‐Driven Structural Isomers in the NaCl–Ga 2 S 3 System: Implications for Energy Storage

Alternative energy sources require the search for innovative materials with promising functionalities. Systems with unusual chemical properties represent an insufficiently explored domain, concealing unexpected features. Using diffraction and Raman spectroscopy over a wide temperature range, supported by first‐principles simulations, a rare phenomenon is unveiled: phase‐dependent chemical interactions between binary components in the NaCl–Ga 2 S 3 system. In this unique occurrence, previously intact binary crystalline species transform upon melting into mixed liquid structural isomers, forming bonds with new partners. The chemical combinatorics appears to be fully reversible for stable crystals and liquids. Despite this, rapidly frozen glasses out of thermodynamic equilibrium remain in a metastable isomeric state, offering remarkable properties, particularly a high room‐temperature Na + conductivity, comparable to the best sodium halide superionic conductors and therefore encouraging for sodium solid‐state batteries and energy applications. A rigidity paradigm is responsible for the observed phenomenon, as the extremely constrained Ga 2 S 3 crystal lattice does not survive viscous flow, breaking up at a short‐range level. The removal of rigidity constraints and dense packing leads to a significant increase in empty space, which is the origin of high sodium diffusivity. Broadly, the rigidity‐driven structural isomerism opens up an inspiring path to the discovery of atypical materials.

25 ENERGY STORAGE↗

AEcroscopy: A Software–Hardware Framework Empowering Microscopy Toward Automated and Autonomous Experimentation

Microscopy has been pivotal in improving the understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most characterization labs. However, traditional microscopy operations are still limited largely by a human-centric click-and-go paradigm utilizing vendor-provided software, which limits the scope, utility, efficiency, effectiveness, and at times reproducibility of microscopy experiments. Here, in this work, a coupled software–hardware platform is developed that consists of a software package termed AEcroscopy (short for Automated Experiments in Microscopy), along with a field-programmable-gate-array device with LabView-built customized acquisition scripts, which overcome these limitations and provide the necessary abstractions toward full automation of microscopy platforms. The platform works across multiple vendor devices on scanning probe microscopes and electron microscopes. It enables customized scan trajectories, processing functions that can be triggered locally or remotely on processing servers, user-defined excitation waveforms, standardization of data models, and completely seamless operation through simple Python commands to enable a plethora of microscopy experiments to be performed in a reproducible, automated manner. This platform can be readily coupled with existing machine-learning libraries and simulations, to provide automated decision-making and active theory-experiment optimization to turn microscopes from characterization tools to instruments capable of autonomous model refinement and physics discovery.

47 OTHER INSTRUMENTATION↗

Three practical workflow schedulers for easy maximum parallelism

Runtime scheduling and workflow systems are an increasingly popular algorithmic component in HPC because they allow full system utilization with relaxed synchronization requirements. There are so many special-purpose tools for task scheduling, one might wonder why more are needed. Use cases seen on the Summit supercomputer needed better integration with MPI and greater flexibility in job launch configurations. Preparation, execution, and analysis of computational chemistry simulations at the scale of tens of thousands of processors revealed three distinct workflow patterns. A separate job scheduler was implemented for each one using extremely simple and robust designs: file-based, task-list based, and bulk-synchronous. Comparing to existing methods shows unique benefits of this work, including simplicity of design, suitability for HPC centers, short startup time, and well-understood per-task overhead. All three new tools have been shown to scale to full utilization of Summit, and have been made publicly available with tests and documentation. This work presents a complete characterization of the minimum effective task granularity for efficient scheduler usage scenarios. Here, these schedulers have the same bottlenecks, and hence similar task granularities as those reported for existing tools following comparable paradigms.

97 MATHEMATICS AND COMPUTING↗

Demographic and genetic consequences of a steelhead supplementation program

Abstract Objective Supplementation of naturally spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. Our objective was to evaluate whether the use of a juvenile captive broodstock and an integrated paradigm could increase returns of steelhead, the anadromous form of Rainbow Trout Oncorhynchus mykiss, while avoiding negative genetic impacts commonly associated with hatchery propagation. Methods We analyzed 291 genetic markers in adult steelhead returning to an integrated population in southwest Washington over the course of 15 years. Reproductive success (RS) of fish spawning in the natural environment was evaluated by origin (hatchery versus natural) and return year. Data were then pooled over years to maximize sample sizes for comparing RS estimates among groups (i.e., estimation of relative reproductive success [RRS]). Result We observed a weak relationship between RS and origin (male p = 0.347; female p = 0.066), but a significant relationship between RS and return year (male p < 0.001, η2 = 0.896; female p ⟨ 0.001, η2 = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Estimates of RRS for fish spawned in the hatchery ranged from 2.4 to 6.4, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. Estimates of RRS were ⟨1.0 for hatchery-origin fish spawning in the natural environment, but the difference was nonsignificant for males and marginally significant for females. Hatchery-origin fish exhibited reduced genetic diversity as well as evidence of increased temporal population structure. Conclusion We conclude that the program was successful in achieving an increase in adult returns but not in avoiding negative genetic effects on the population and that any lasting impacts of supplementation remain to be determined.

Smith, Christian T. (ORCID:0000000240522669)↗

Mind the gaps! Climate scientists should heed lessons in collaborative storytelling from William Shakespeare

Abstract To co‐produce locally relevant climate knowledge, climate scientists are engaging in new collaborations—with stakeholders and with scholars in the humanities, arts, and social sciences. In our work as a Shakespeare scholar‐turned‐public‐humanist and a climate scientist, we have created a methodology that allows researchers and communities to co‐produce knowledge by co‐producing narratives. We combine principles from emerging climate “storylines” research with collaborative storytelling inspired by William Shakespeare's plays and theatrical practices. Shakespeare's plays spark collaborations and interpretations, in part, because of how Shakespeare leaves gaps in the narrative. These gaps allow others to enter as collaborators, creating a “cognitive ecology” that fosters knowledge and action among all engaged. Integrating these methods into climate storyline‐making offers a radical paradigm: it upends the scientist's role as the focal storyteller and expert, and fosters, instead, partnership, equity, and a co‐exploration of multiple uncertainties. It is time for researchers to cede control to a cognitive ecology of collaborative action. This article is categorized under: Trans‐Disciplinary Perspectives > Humanities and the Creative Arts

54 ENVIRONMENTAL SCIENCES↗

ChemML : A machine learning and informatics program package for the analysis, mining, and modeling of chemical and materials data

ChemML is an open machine learning (ML) and informatics program suite that is designed to support and advance the data-driven research paradigm that is currently emerging in the chemical and materials domain. ChemML allows its users to perform various data science tasks and execute ML workflows that are adapted specifically for the chemical and materials context. Key features are automation, general-purpose utility, versatility, and user-friendliness in order to make the application of modern data science a viable and widely accessible proposition in the broader chemistry and materials community. Finally, ChemML is also designed to facilitate methodological innovation, and it is one of the cornerstones of the software ecosystem for data-driven in silico research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Addressing technical challenges in 100% variable inverter-based renewable energy power systems

Rapidly increasing levels of variable inverter-based renewable energy sources are quickly changing electric power systems and prompting questions about how the systems will be operated when renewable generation becomes the dominant technologies. Here, we review the status of this shifting paradigm in power systems throughout the world. We then review the implications of this shift, focusing on the rising challenges, and we provide an overview and technology-readiness classifications of some proposed mitigation strategies. Finally, we highlight outstanding questions that will require solutions to reach these ultrahigh shares of variable inverter-based renewable energy sources.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Diversity in Photoprotection and Energy Balancing in Terrestrial and Aquatic Phototrophs

The evolution of oxygenic photosynthesis enabled organisms to use sunlight as an energy source, allowing them to colonize new niches. At the same time, life (as we know it) places severe constraints on photosynthesis. For example, the initial reactions of photosynthesis involve highly energetic intermediates that, if not controlled, can generate highly toxic side products (especially reactive oxygen species, ROS), that can damage other essential components of the organisms it powers. Photosynthesis must therefore be tightly regulated to balance the need for efficient energy conversion with the necessity of avoiding photodamage (Gust D, Kramer D, Moore A, Moore T, Vermaas W, Mater Res Bull 33:383–389, 2008). A related constraint on photosynthesis is the need to precisely balance how much energy is stored in ATP and NADPH to precisely meet biochemical demands. If this balancing does not occur, the system will fail, leading to photodamage (Kramer DM, Evans JR, Plant Physiol 155:70–78, 2011). Consideration of these requirements is essential for efforts to improve the efficiency of photosynthesis by introducing CO 2 concentrating mechanisms, altering metabolism or biosynthetic pathways to shunt energy to alternative products (Kramer DM, Evans JR, Plant Physiol 155:70–78, 2011). These balancing processes must be extremely robust to contend with the rapid and unpredictable fluctuations in environmental conditions and metabolic demands that occur in nature. A large body of work has come from model systems, especially terrestrial higher plants and the green alga Chlamydomonas reinhardtii, leading to a model for the regulation of light reactions that involves 1) sensing of the pH gradient component of the thylakoid proton motive force (pmf), and 2) the redox state of the plastoquinone- and stromal pools. Over the short term, these sensors trigger regulation of light capture by altering the activity of ATP synthase leading to adjustments in lumen pH, which fine tunes light capture through nonphotochemical quenching (NPQ) and control of electron flow by adjusting the rate of PQH 2 oxidation at the b 6 f complex. Simultaneously, this system controls the balance of ATP/NADPH by adjusting electron flux to linear and cyclic electron flow pathways to balance ATP/NADPH. This integrated “pmf paradigm” model explains much of the existing data on plants and green algae, but may not extend to other diverse organisms. This review considers how advances in our understanding of photosynthesis over the past 7–8 years, particularly in the discoveries of diverse biochemical/biophysical mechanisms in aquatic photosynthetic species, affects the view of energy balance, including the shunting of electrons to O 2 through the flavodiiron proteins (FLV), the plastid terminal oxidase, the dissipation of electric field by ion movements, and the activation of alternative electron sinks. Furthermore, we will introduce the basic model that has been developed for higher plant chloroplasts, then contrast these with selected aquatic systems, focusing on how the differences impact the needs to re-balance both energy input and its partitioning into energy currencies.

Kanazawa, Atsuko↗

Scalable Data-Intensive Geocomputation: A Design for Real-Time Continental Flood Inundation Mapping

The convergence of data-intensive and extreme-scale computing enables an integrated software and data ecosystem for scientific discovery. Developments in this realm will fuel transformative research in data-driven interdisciplinary domains. Geocomputation provides computing paradigms in Geographic Information Systems (GIS) for interactive computing of geographic data, processes, models, and maps. Because GIS is data-driven, the computational scalability of a geocomputation workflow is directly related to the scale of the GIS data layers, their resolution and extent, as well as the velocity of the geo-located data streams to be processed. Unique in high user interactivity and low end-to-end latency requirements, geocomputation applications will dramatically benefit from the convergence of high-end data analytics (HDA) and high-performance computing (HPC). The application level challenge, however, is to identify and eliminate computational bottlenecks that arise along a geocomputation workflow. Indeed, poor scalability at any of the workflow components is detrimental to the entire end-to-end pipeline. Here, we study a large geocomputation use case in flood inundation mapping that handles multiple national-scale geospatial datasets and targets low end-to-end latency. We discuss benefits and challenges for harnessing both HDA and HPC for data-intensive geospatial data processing and intensive numerical modeling of geographic processes. We propose an HDA+HPC geocomputation architecture design that couples HDA (e.g., Spark)-based spatial data handling and HPC-based parallel data modeling. Key techniques for coupling HDA and HPC to bridge the two different software stacks are reviewed and discussed.

Liu, Yan↗

Machine-Learning Accelerated Studies of Materials with High Performance and Edge Computing

In the studies of materials, experimental measurements often serve as the reference to verify physics theory and modeling; while theory and modeling provide a fundamental understanding of the physics and principles behind. However, the interactions and cross validation between them have long been a challenge even to-date. Not only that inferring a physics model from experimental data is itself a difficult inverse problem, another major challenge is the orders-of-magnitude longer wall-clock time required to carry out high-fidelity computer modeling to match the timescale of experiments. We envisage that by combining high performance computing, data science, and edge computing technology, the current predicament can be alleviated, and a new paradigm of data-driven physics research will open up. For example, we can accelerate computer simulations by first performing the large-scale modeling on high performance computers and train a machine-learned surrogate model. This computationally inexpensive surrogate model can then be transferred to the computing units residing closely to the experimental facilities to perform high-fidelity simulations at a much higher throughout. The model will also be more amenable to analyzing and validating experimental observations in comparable time scales at a much lower computational cost. Further integration of these accelerated computer simulations with an outer machine learning loop can also inform and direct future experiments, while making the inverse problem of physics model inference more tractable. We will demonstrate a proof-of-concept by using a quantum Monte Carlo application, Dynamical Cluster Approximation (DCA++), to machine-learn a surrogate model and accelerate the study of quantum correlated materials.

Li, Ying Wai↗

Evolution of Intent and Social Influence Networks and Their Significance in Detecting COVID-19 Disinformation Actors on Social Media

Online disinformation actors are those individuals or bots who disseminate false or misleading information over social media, with the intent to sway public opinion in the information domain towards harmful social outcomes. Quantification of the degree to which users post or respond intentionally versus under social influence, remains a challenge, as individuals or organizations operating the profile are foreshadowed by their online persona. However, social influence has been shown to be measurable in the paradigm of information theory. In this paper, we introduce an information theoretic measure to quantify social media user intent, and then investigate the corroboration of intent with evolution of the social network and detection of disinformation actors related to COVID-19 discussions on Twitter. Our measurement of user intent utilizes an existing time series analysis technique for estimation of social influence using transfer entropy among the considered users. We have analyzed 4.7 million tweets originating from several countries of interest, during a 5 month period when the arrival of the first dose of COVID vaccinations were announced. Our key findings include evidence that: (i) a significant correspondence between intent and social influence; (ii) ranking over users by intent and social influence is unstable over time with evidence of shifts in the hierarchical structure; and (iii) both user intent and social influence are important when distinguishing disinformation actors from non-disinformation actors.

Gunaratne, Chathika↗