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At least 127 records · Page 7

Bacterial–fungal interactions: ecology, mechanisms and challenges

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial–fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial–fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Lastly, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

59 BASIC BIOLOGICAL SCIENCES↗

Synopsis of the Oak Ridge Radiation Protection Research Needs Workshop

Radiation protection is foundational to harnessing the societal benefits of radiation in nuclear energy, security, and medicine applications. Significant challenges in radiation protection remain unaddressed for the nuclear fuel cycle, nuclear medicine, emergency response, national defense, and space exploration, as the United States is lacking a coherent research strategy prioritizing radiation protection mission needs and gaps in scientific knowledge to meet these needs. Research and development in the field of radiation protection calls for cooperation among governmental agencies, emergency responders, research organizations, and the academic community. Amidst atrophying national expertise in radiation protection, the Radiation Protection Research Needs Workshop was spearheaded by the Oak Ridge Associated Universities, Oak Ridge National Laboratory, and the Health Physics Society. This workshop facilitated critical dialogue among radiation stakeholders in the governmental and scientific communities, including national laboratories, academic institutions, and industry partners. The workshop featured presentations representing 12 federal agencies and breakout sessions involving the identification of scientific drivers by subject matter experts in each of the following areas: new fuel cycles/reactors, dosimetry, medical physics, instrumentation and operations, decontamination and decommissioning, space radiation, national defense, emergency response, environmental modeling, and low-dose effects. The goal of this workshop was to seek stakeholder input toward the development of a national strategic research agenda in the field of radiation protection. Consequently, the Health Physics Society has established a Special Task Force on Health Physics Research Needs, tasked with the prioritization of scientific drivers in radiation protection for the development of a national strategic research agenda.

61 RADIATION PROTECTION AND DOSIMETRY↗

Ant-Based Cyber Security

We describe a swarming-agent-based, mixed-initiative approach to infrastructure defense where teams of humans and software agents defend cooperating organizations in tandem by sharing insights and solutions without violating proprietary boundaries. The system places human administrators at the appropriate level where they provide system guidance while lower-level agents carry out tasks humans are unable to perform quickly enough to mitigate today’s security threats. Cooperative Infrastructure Defense (CID) uses our ant-based approach to enable dialogue between humans and agents to foster a collaborative problem-solving environment, increase human situational awareness and influence using visualization and shared control. We discuss theoretical implementation characteristics along with results from recent proof-of-concept implementations.

99 GENERAL AND MISCELLANEOUS↗

Ecosystems for Scientific Computing in the Age of AI

Scientific computing is at an inflection point. Artificial intelligence (AI) is reshaping how scientific software is developed, how teams collaborate, how projects are governed, and how the next generation is trained. Drawing on insights from a 2025 workshop report, this article argues that the future of discovery will depend on agile, robust ecosystems built through socio-technical co-design—the intentional integration of technical and human systems. This perspective is essential for ensuring that future scientific computing remains trustworthy, sustainable, and scalable. It combines advances in AI, high-performance computing, and software with new models for cross-disciplinary collaboration, education, and workforce development. Key recommendations include building modular, trustworthy AI-enabled software ecosystems; enabling teams to integrate AI into scientific workflows while preserving human creativity, integrity, and rigor; and developing adaptive training pathways that keep pace with rapid technological change. By sharing these perspectives, we hope to stimulate broader community dialogue and encourage coordinated action.

AI↗

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon-climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool-based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool-based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. In this study, we propose a novel conceptual framework to explore controls on belowground carbon cycling: Probabilistic Representation of Organic Matter Interactions within the Soil Environment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

54 ENVIRONMENTAL SCIENCES↗

Trust and consequences: Role of community science, perceptions, values, and environmental justice in risk communication

Risk communication is often viewed as imparting information and perhaps as a two-way dialogue. Risk communication inadequacies on the part of both “communicator” and “community members” can lead to adverse consequences and amplify environmental justice disparities. The paper suggests a transformational approach where risk communicators must learn to trust community experts and their knowledge base (and act upon it), where risk information imparted by risk communicators addresses what communities are most concerned about (as well as risk from specific chemicals or radionuclides), and where risk information and assessments address underlying issues and disparities, as well as cultural traditions (among others). Providing risk probabilities is no longer sufficient; western science may not be enough, and community and native scientific knowledge is needed. Risk communication (or information transfer) for environmental risks that are ongoing usually applies to low-income, minority communities—people living in dense inner cities, rural communities, Native American communities—or to people living near a risky facility. Communication within this context requires mutual trust, listening and respect, as well as acceptance of indigenous and community knowledge as equally valuable. Examples are given to illustrate a community perspective.

97 MATHEMATICS AND COMPUTING↗

The dynamic nature of risk in DOE facilities in the surveillance and maintenance program–with observations for risk communications

Here, we explore three case studies of facilities at two US Department of Energy (DOE) former nuclear weapons research and production sites—the Oak Ridge National Laboratory and the Hanford site—whose risk profiles have changed during their long-term management under the DOE's surveillance and maintenance (S&M) program. These case studies provide examples of the challenges faced in communicating to external stakeholders, such as federal and state regulators, local communities surrounding the site, as well as the general public, the circumstances surrounding unexpected events or the emergence/discovery of new risk-important information at historically high-risk sites. We identify common topics of importance from these case studies and suggest a taxonomy for risk communicators to use in informing the dialogues with individuals and organizations that may not be technically oriented or fully informed on the subject matter. The taxonomy is based on technical insights from the quintessential definition of risk known as the Kaplan–Garrick “risk triplet” as well as insights from regulatory guidance documents on risk communication with external stakeholders originally developed for the commercial nuclear power industry.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

The best of both worlds – entering the nursing profession with support of a transition programme

Abstract Background Transition into clinical practice for newly graduated nurses is a difficult time, with high stress levels defined by a demanding period of personal and professional acclimatisation. Transitions are complicated and multi‐dimensional, and to understand this process, it is crucial to identify the factors that facilitate or stand in the way of a healthy transition. Aim The phenomenological study aimed to describe newly graduated nurses’ expectations of transitioning into the nursing profession at the start of a clinical nursing introduction programme, including education, supervision, and critical reflection with peers. Method The study was based on seven group interviews with newly graduated nurses. The interviews utilised open‐ended and follow‐up questions and were carried out as a dialogue to enable reflection on the phenomenon of interest. This was explored and illuminated using the reflective lifeworld research approach, based on phenomenological epistemology. Findings “Expectations of transition into the nursing profession via the Clinical Nursing Introduction Programme” is signified by an oscillating movement between uncertainty, security, challenge, and growth on the threshold of a new identity. The phenomenon is constituted by the courage to grow, responsibility and fear, belonging and vulnerability, and support and challenge. Conclusion Transitioning into the nursing profession via the Clinical Nursing Introduction Programme means having the best of both worlds. Newly graduated nurses have the opportunity to receive education and structured support at the same time as they work independently in clinical practice.

Berglund, Mia↗

The perspective awareness model - Eliciting multiple perspectives to formulate high quality decisions

A great deal of attention is given to the importance of communication in environmental remediation and radioactive waste management. However, very little attention is given to eliciting multiple perspectives so as to formulate high quality decisions. Plans that are based on a limited number of perspectives tend to be narrowly focused whereas those that are based on a wide variety of perspectives tend to be comprehensive, higher quality, and more apt to be put into application. In addition, existing methods of dialogue have built-in limitations in that they typically draw from the predominant thinking patterns which focus in some areas but ignore others. This can result in clarity but a lack of comprehensiveness. This paper presents a Perspective Awareness Model which helps groups such as partnering teams, interagency teams, steering committees, and working groups elicit a wide net of perspectives and viewpoints. The paper begins by describing five factors that makes cooperation among such groups challenging. Next, a Perspective Awareness Model that makes it possible to manage these five factors is presented. The two primary components of this model --- the eight 'Thinking Directions' and the 'Shared Documentation' --- are described in detail. Several examples are given to illustrate how the Perspective Awareness Model can be used to elicit multiple perspectives to formulate high quality decisions in the area of environmental remediation and radioactive waste management. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Radioactive waste management: the relation between geological disposal and advanced nuclear technologies

Throughout this paper we aim to scope the most pregnant themes, issues and research questions concerning the relation between geological disposal and advanced nuclear technologies in the broad context of radioactive waste management. Especially from a socio-technical point of view the mutual impacts, divergences and complementarities between both strategies seem to have received limited dedicated examination up until today. Specific attention is paid to the main arguments that seem to underpin both research streams, related to how the issue of radioactive waste is contextualized and which problems and solutions are consequently identified and proposed. Ultimately we aim to encourage scientifically integer communication and constructive dialogue between both fields, to investigate the common possibilities of enhancing radioactive waste management as a whole. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Future Circular Collider Feasibility Study Report

Volume 3 of the FCC Feasibility Report presents studies related to civil engineering, the development of a project implementation scenario, and environmental and sustainability aspects. The report details the iterative improvements made to the civil engineering concepts since 2018, taking into account subsurface conditions, accelerator and experiment requirements, and territorial considerations. It outlines a technically feasible and economically viable civil engineering configuration that serves as the baseline for detailed subsurface investigations, construction design, cost estimation, and project implementation planning. Additionally, the report highlights ongoing subsurface investigations in key areas to support the development of an improved 3D subsurface model of the region. The report describes the development of the project scenario based on the ‘avoid-reduce-compensate’ iterative optimisation approach. The reference scenario balances optimal physics performance with territorial compatibility, implementation risks, and costs. Environmental field investigations covering almost 600 hectares of terrain—including numerous urban, economic, social, and technical aspects—confirmed the project’s technical feasibility and contributed to the preparation of essential input documents for the formal project authorisation phase. The summary also highlights the initiation of public dialogue as part of the authorisation process. The results of a comprehensive socio-economic impact assessment, which included significant environmental effects, are presented. Even under the most conservative and stringent conditions, a positive benefit-cost ratio for the FCC-ee is obtained. Finally, the report provides a summary of the studies conducted to document the current state of the environment.

Benedikt, M. [European Organization for Nuclear Re↗

ENERGY INVESTMENTS UNDER CLIMATE POLICY: A COMPARISON OF GLOBAL MODELS

The levels of investment needed to mobilize an energy system transformation and mitigate climate change are not known with certainty. This paper aims to inform the ongoing dialogue and in so doing to guide public policy and strategic corporate decision making. Within the framework of the LIMITS integrated assessment model comparison exercise, we analyze a multi-IAM ensemble of long-term energy and greenhouse gas emissions scenarios. Our study provides insight into several critical but uncertain areas related to the future investment environment, for example in terms of where capital expenditures may need to flow regionally, into which sectors they might be concentrated, and what policies could be helpful in spurring these financial resources. We find that stringent climate policies consistent with a 2°C climate change target would require a considerable upscaling of investments into low-carbon energy and energy efficiency, reaching approximately $45 trillion (range: $30–$75 trillion) cumulative between 2010 and 2050, or about $1.1 trillion annually. This represents an increase of some $30 trillion ($10–$55 trillion), or $0.8 trillion per year, beyond what investments might otherwise be in a reference scenario that assumes the continuation of present and planned emissions-reducing policies throughout the world. In other words, a substantial "clean-energy investment gap" of some $800 billion/yr exists — notably on the same order of magnitude as present-day subsidies for fossil energy and electricity worldwide ($523 billion). Unless the gap is filled rather quickly, the 2°C target could potentially become out of reach.

carbon financing↗

The Plant Microbiome: From Ecology to Reductionism and Beyond

Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. Finally, the next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.

59 BASIC BIOLOGICAL SCIENCES↗

matsim-agents v1.0

matsim-agents is a multi-agent AI framework for atomistic materials simulation and discovery. It orchestrates large language models (LLMs), machine-learned interatomic potentials (MLIPs), and DFT codes into a single agentic loop running on laptops and DOE leadership-class supercomputers. MULTI-AGENT ORCHESTRATION A LangGraph state machine with three nodes: a Planner that converts a natural-language research objective into structured tasks; an Executor that dispatches atomistic tools and loops until the queue is empty; and an Analyst that summarizes results into a human-readable report. State is checkpointed after every step and human-in-the-loop gates can be inserted at any edge. HYPOTHESIS-DRIVEN DISCOVERY CHAT An interactive REPL (matsim-agents chat) that couples LLM dialogue with atomistic simulation. Chemical formulas are automatically detected in conversation turns and trigger a full crystal-phase exploration: structure generation → relaxation → stability scoring → result injection back into the conversation, creating a closed hypothesis-refinement loop. CRYSTAL PHASE ENUMERATION Given a composition, the phase explorer enumerates prototypes by stoichiometry: elemental (fcc/bcc/hcp/sc/diamond), binary 1:1 (rocksalt/CsCl/zincblende/ wurtzite/fluorite/rutile), ternary 1:1:3 (cubic perovskite), ternary 1:2:4 (perovskite + spinel), quaternary 1:1:2:6 (Fm-3m double perovskite). 2-D prototypes (graphene, h-BN, MoS2 2H/1T) and multilayer stacking are also supported via --include-2d and --num-layers. SUPERCELL GENERATION AND SITE DECORATION Auto-tiling to a minimum atom count (--min-atoms), explicit NxNxN tiling (--supercell), symmetry-distinct site decorations (--n-orderings), and isotropic lattice-scale sweeps (--lattice-scales) for volume bracketing. MLFF RELAXATION AND STABILITY SCORING HydraGNN (multi-headed GNN) drives structure relaxation via ASE with FIRE, BFGS, or BFGSLineSearch. Stability output: delta-E/atom ranking across phases and a max-residual-force dynamical-stability proxy. Other MLIPs (MACE, NequIP, Orb) can be plugged in through the same interface. DFT BACKENDS Quantum ESPRESSO pw.x and VASP 6.6 are first-class labellers. Both have validated GPU builds and SLURM/PBS launchers for three DOE platforms: Frontier (AMD MI250X, ROCm), Aurora (Intel PVC, oneAPI), Perlmutter (NVIDIA A100, CUDA). QE produces ~100 binaries (pw.x, ph.x, epw.x, ...). VASP supports scf, relax, vc-relax, and vc-relax-shape run types. ACTIVE-LEARNING LOOP matsim-agents al run CONFIG.yaml drives an iterative HydraGNN-DFT loop: MD generates candidates → ensemble/MC-dropout uncertainty selects the most informative → DFT labels them in parallel inside one allocation → dataset grows → HydraGNN retrains → repeat. DFT backend is a single YAML toggle (dft.backend: vasp | qe). LLM-generated seed structures are supported (no curated POSCAR library needed). Config uses ${VAR}, ${VAR:-default}, ${VAR:?msg} shell-style substitution for cross-user/cross-site portability. LLM BACKENDS Ollama (local, default), vLLM (HPC multi-GPU serving), OpenAI, Anthropic, HuggingFace Transformers+Accelerate. Selected at runtime via flag or env var with no code changes. HPC PORTABILITY Same Python entry points run on Frontier (ROCm 7.2), Aurora (oneAPI), and Perlmutter (CUDA 12). DFT and ML stacks are never co-loaded in the same shell; they couple through the scheduler and filesystem. Advanced multi-node launchers (serve, discovery-chat, single-relaxation, active-learning, QE warm-start) are provided for all three platforms. CODABENCH COMPETITION BUNDLE A self-contained benchmark: 159 atomistic test structures across 11 material classes, 5 tasks (formation energy, forces, ML relaxation, AI-DFT relaxation, phase stability ranking), public/private leaderboard split (30/70), and four ready-to-run baselines: MACE-MP-0, HydraGNN, UMA, AllScAIP.

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

Advances in the Application and Utility of Subseasonal-to-Seasonal Predictions

The subseasonal-to-seasonal (S2S) predictive time scale, encompassing lead times ranging from 2 weeks to a season, is at the frontier of forecasting science. Forecasts on this time scale provide opportunities for enhanced application-focused capabilities to complement existing weather and climate services and products. There is, however, a “knowledge–value” gap, where a lack of evidence and awareness of the potential socioeconomic benefits of S2S forecasts limits their wider uptake. To address this gap, here we present the first global community effort at summarizing relevant applications of S2S forecasts to guide further decision-making and support the continued development of S2S forecasts and related services. Focusing on 12 sectoral case studies spanning public health, agriculture, water resource management, renewable energy and utilities, and emergency management and response, we draw on recent advancements to explore their application and utility. These case studies mark a significant step forward in moving from potential to actual S2S forecasting applications. We show that by placing user needs at the forefront of S2S forecast development—demonstrating both skill and utility across sectors—this dialogue can be used to help promote and accelerate the awareness, value, and cogeneration of S2S forecasts. We also highlight that while S2S forecasts are increasingly gaining interest among users, incorporating probabilistic S2S forecasts into existing decision-making operations is not trivial. Nevertheless, S2S forecasting represents a significant opportunity to generate useful, usable, and actionable forecast applications for and with users that will increasingly unlock the potential of this forecasting time scale.

54 ENVIRONMENTAL SCIENCES↗

Science Applications of Phased Array Radars

Phased array radars (PARs) are a promising observing technology, at the cusp of being available to the broader meteorological community. PARs offer near instantaneous sampling of the atmosphere with flexible beam forming, multi-functionality, low operational and maintenance costs, and without mechanical inertia limitations. These PAR features are transformative compared to those offered by our current reflector-based meteorological radars. The integration of PARs into meteorological research has the potential to revolutionize the way we observe the atmosphere. The rate of adoption of PARs in research will depend on many factors including i) the need to continue educating the scientific community on the full technical capabilities and trade-offs of PARs through an engaging dialogue with the science and engineering communities and ii) the need to communicate the breadth of scientific bottlenecks that PARs can overcome in atmospheric measurements and the new research avenues that are now possible using PARs in concert with other measurement systems. The former is the subject of a companion article that focuses on PAR technology while the latter is the objective here.

54 ENVIRONMENTAL SCIENCES↗

Impact of Tropical and Extratropical Cyclones on Future U.S. Offshore Wind Energy

Over 60 participants, including government officials, regulators, certification bodies, national laboratory researchers, academia, and industry representatives, gathered in person twice for a comprehensive discussion on the impacts of extreme weather on large-scale deployment of offshore wind energy for the U.S. The dialogue focused on addressing modeling challenges, the need for detailed observational data, refining risk assessment methodologies, and understanding the implications of climate change.

14 SOLAR ENERGY↗

Climate Change and National Security

Climate change is increasingly recognized as having national security implications, which has prompted dialogue between the climate change and national security communities – with resultant advantages and differences. Climate change research has proven useful to the national security community sponsors in several ways. It has opened security discussions to consider climate as well as political factors in studies of the future. It has encouraged factoring in the stresses placed on societies by climate changes (of any kind) to help assess the potential for state stability. And it has shown that, changes such as increased heat, more intense storms, longer periods without rain, and earlier spring onset call for building climate resilience as part of building stability. For the climate change research community, studies from a national security point of view have revealed research lacunae, for example, such as the lack of usable migration studies. This has also pushed the research community to consider second- and third-order impacts of climate change, such as migration and state stability, which broadens discussion of future impacts beyond temperature increases, severe storms, and sea level rise; and affirms the importance of governance in responding to these changes. The increasing emphasis in climate change science toward research in vulnerability, resilience, and adaptation also frames what the intelligence and defense communities need to know, including where there are dependencies and weaknesses that may allow climate change impacts to result in security threats and where social and economic interventions can prevent climate change impacts and other stressors from resulting in social and political instability or collapse.

Malone, Elizabeth L↗