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A perspective on the redox properties of tetrapyrrole macrocycles

Tetrapyrrole macrocycles serve a multitude of roles in biological systems, including oxygen transport by heme and light harvesting and charge separation by chlorophylls and bacteriochlorophylls. Synthetic tetrapyrroles are utilized in diverse applications ranging from solar-energy conversion to photomedicine. Nevertheless, students beginning tetrapyrrole research, as well as established practitioners, are often puzzled when comparing properties of related tetrapyrroles. Questions arise as to why optical spectra of two tetrapyrroles often shift in wavelength/energy in a direction opposite to that predicted by common chemical intuition based on the size of a π-electron system. Gouterman's four-orbital model provides a framework for understanding these optical properties. Similarly, it can be puzzling as to why the oxidation potentials differ significantly when comparing two related tetrapyrroles, yet the reduction potentials change very little or shift in the opposite direction. In order to understand these redox properties, it must be recognized that structural/electronic alterations affect the four frontier molecular orbitals (HOMO, LUMO, HOMO-1 and LUMO+1) unequally and in many cases the LUMO+1, and not the LUMO, may track the HOMO in energy. This perspective presents a fundamental framework concerning tetrapyrrole electronic properties that should provide a foundation for rational molecular design in tetrapyrrole science.

chlorophyll↗

Development of an Assessment Methodology That Enables the Nuclear Industry to Evaluate Adoption of Advanced Automation

Nuclear power has a crucial role in providing safe, reliable, and economical carbon-free electricity for today and the future. For continued operation, many of the existing United States nuclear power plants will begin the subsequent license renewal process for extending their operating license periods. As plants extend their expected operating lifetimes, there is a significant opportunity to modernize. These plants have a much stronger business case with these extended mission periods to modernize and significantly enhance their economic viability in current and future energy markets by implementing digital technologies that support innovation, efficiency gains, and business-model transformation. Ensuring continued safety and reliability is crucial. Transformative digital technologies—including automation—that fundamentally change the concept of operation for the nuclear power plant operating model requires a critical focus on the human and technology integration element. Further, the nuclear industry has historically been reluctant to modernize due to having a risk adverse culture and lack of clarity for a transformative new state vision (Joe & Remer, 2019; Thomas et al., 2020). Common barriers include (1) the perceived value and return on investment (ROI) of digital technology, (2) the perceived risk associated with licensing, regulatory, and cybersecurity, and (3) insufficient guidance for performing digital modifications to power generation systems. This work presents a methodology to address these barriers and support the industry in adopting advanced automation and digital technology through developing a transformative vision and implementation strategy that will address the human and technology integration element. This research leverages previous LWRS Program and industry results. It draws specifically on previous LWRS Program research in the areas of advanced alarm systems, computer-based procedures, model informed decision support, and advanced human-system interface displays (e.g., overviews and task-based). The modernization methodology can be used to guide transformative thinking when integrating a set of vendor-specific capabilities to support a new concept of operations and a utility’s end-state vision. The results of this research are organized into six major sections: - Section 1 introduces the need for supporting large-scale digital modifications that will renew the technology base for extended operating life beyond 60 years - Section 2 describes the challenges that the nuclear industry is enduring with modernizing. - Section 3 summarizes the primary standards and guidance. - Section 4 presents earlier work from the LWRS Program regarding the development of a transformative conceptual design for an advanced control room of a hybrid plants. - Section 5 presents a methodology that is designed at addressing the challenges in the industry today in achieving a transformative new state vision and concept of operations. - Conclusions and next steps of this research are provided in Section 6.

99 GENERAL AND MISCELLANEOUS↗

Using cloud radar to investigate the effect of rainfall on migratory insect flight

The fate of migrating insects that encounter rainfall in flight is a critical consideration when modelling insect movement, but few field observations of this common phenomenon have ever been collected due to the logistical challenges of witnessing these encounters. Operational cloud radars have been deployed around the world by meteorological agencies to study precipitation physics, and as a byproduct, provide a rich database of insect observations that is freely available to researchers. Although considered unwanted ‘clutter’ by the meteorologists who collect the data, the analysis method presented here enables ecologists to delineate co-occurring signals from insects and raindrops. We present a method that uses image processing techniques on cloud radar velocity spectra to examine the fate of migrating insects when they encounter precipitation. By analysing velocity spectra, we can distinguish flying insects from falling rain and compare the relative density of insects in flight before, during and after the rainfall. We demonstrate the method on a case of insect migration in Oklahoma, USA. Using this method, we show the first reconstructed images of migrating insect layers in flight during rainfall. Our analysis shows that mild to moderate rainfall diminishes the number of insects aloft but does not cause full termination of migratory flight, as has previously been suggested. We hope this technique will spur further investigations of how changing weather conditions impact insect migration, and enable some of the first of such studies in regions of the world that are underrepresented in the literature.

54 ENVIRONMENTAL SCIENCES↗

Parallel-in-Time Multigrid Methods for Hyperbolic Problems, with a Focus on the Shallow Water Equations

The coming massive parallelism of exascale computing presents a pressing challenge for the many DOE simulations of time-dependent partial differential equations, which typically use traditional sequential time stepping methods. Since this traditional approach is inherently serial, it presents a sequential bottleneck when moving to exascale computing, because future performance gains will come through greater concurrency, not faster clock speeds. Thus, the goal of this work is to research parallelism in time, i.e., methods that compute multiple time values simultaneously, not sequentially. The focus will be on hyperbolic problems of programmatic interest to DOE, with the goal of enabling scalable simulations of time-dependent hyperbolic problems on future architectures. The difficulty lies in the fact that hyperbolic problems are well-known to be difficult for parallel-in-time methods, with the most common parallel-in-time method, Parareal, diverging in many cases. Here, the chosen methodology for scalably solving these hyperbolic space-time equations is multigrid-reductionin-time (MGRIT), because multigrid (when it works) is a powerful, optimal, and scalable solver for discretized PDEs. To further research in this area, this project will explore a model hyperbolic problem (the shallow water equations) in the context of recent advances (e.g., by Wingate and Haut) in constructing improved coarse time-grid time-propagators by using the slow asymptotic structure of the equations. In particular, we will investigate if such coarse time-propagators offer significant advantages in an MGRIT setting, and explore any broader insights gained into parallel-in-time for hyperbolic problems.

97 MATHEMATICS AND COMPUTING↗

Reducing uncertainty of polar to midlatitude linkages using DOE’s E3SM in a coordinated model-experiment setting

This project brought DOE’s climate modeling effort with the Energy Exascale Earth System Model into the Polar Amplification Model Intercomparison Project (PAMIP), which is part of the sixth and latest Coupled Model Intercomparison Project, CMIP6. PAMIP examines the causes and consequences of polar amplification, when external forcing results in a larger temperature increase in high latitudes than the global average, in a coordinated set of model experiments with a common modeling protocol. Our teams from UC Irvine and the University of Toronto have designed, carried out, analyzed, and disseminated PAMIP output from the Energy Exascale Earth System Model (E3SM) and the Community Earth System Model (CESM). PAMIP’s ongoing stream of significant new results have advanced progress in the community’s understanding and led to new outstanding research questions that have motivated further work. PAMIP has led to improved consensus on the atmospheric response to sea ice loss. The important finding is that for a similar sea ice anomaly forcing, the simulated atmospheric response in the troposphere is remarkably consistent among the 16 models’ runs analyzed. The zonal-mean tropospheric response consists of a very robust equatorward shift of the westerly flow in mid-latitudes. However, while the multi-model mean response is robust, it has a weak amplitude relative to internal variability. We identified a weakness in the models (including E3SM) in terms of their response to sea-ice forcing that is related to eddy forcing (or nonlinear dynamical effects) at mid- to high latitudes. In fact, E3SM is an outlier in terms of the models participating, and in that sense, it turned out to be a vital participant model. We found that reductions in energy transport due sea-ice loss and involving dry air only are compensated by increases in moist energy transport from warmer sea surface temperature in midlatitudes. This leads to a large spread in energy transport into the Arctic and is a potential source of spread in Arctic amplification. We identified an important role that climate modes, including tropical modes of variability (El Nino and the Southern Oscillation (ENSO); the Quasi-biennial Oscillation (QBO)) play in the response to sea-ice anomalies, including in ocean coupled experiments. Similarly, we identified and quantified the contribution of sea-ice thickness to the atmospheric response compared to the response to sea-ice extent only. We found that it is important to run large ensembles and even with an ensemble size of 100 simulations the response is largely influenced by internal variability. We demonstrated convincingly that Ural blocking, not sea-ice loss, provides the weakening of the stratospheric polar vortex in fall/early winter and a negative phase of the North Atlantic Oscillation that can last for up to two months. However, sea-ice anomalies can influence the background flow so that the response to Ural blocking is more persistent under low sea-ice conditions in the Barents/Kara Sea than high sea ice Atmospheric model hierarchies that progressively add individual processes have a long history in providing dynamical insight for modeling the atmosphere. Similarly, coupled model hierarchies that progressively add individual ocean processes can provide insights into the workings of the coupled climate system, however such hierarchies have not been available except for a non-dynamical slab ocean model. Because of the missing processes, surface flux corrections must be added to produce a target climate. In this project, we managed to overcome this problem and develop a globally coupled ocean model hierarchy in CESM that can turn on and off the processes of mixed-layer entrainment and Ekman flow. We used the hierarchy to study the impact of Arctic sea-ice loss on the climate system. We find that the effect of mixed-layer entrainment on ocean heat uptake influences the atmospheric circulation by shifting the latitudinal positions of the mid-latitude westerly jet and the Intertropical Convergence Zone (ITCZ). In quadrupled CO 2 experiments, we studied how air-sea coupling affects the response of tropical rainfall under global warming. In order to identify the importance of individual ocean processes, we used the hierarchy of ocean models to separate the effects of seasonal mixed-layer entrainment, wind-driven Ekman flows, and frictional flows. We showed that including Ekman and frictional flows allows our simulation to produce the Pacific Ocean's enhanced equatorial warming pattern and equatorward ITCZ contraction noted in previous climate simulations. We also showed that the frictional flow, which has yet to receive much attention, is as important as the Ekman flow in generating equatorial heat convergence.

54 ENVIRONMENTAL SCIENCES↗

Experiments and Simulations to Describe Alkalinity Release from Particle-Containing Oil-in-Water Emulsions and Particle Suspensions

Among the most common amendments added to groundwater during site remediation are compounds used to adjust or maintain the pH. This research describes an approach to encapsulate mineral particles (MgO and CaCO 3 ) within oil droplets suspended within an aqueous phase for the purpose of delivery to the subsurface environment. A series of batch experiments was combined with mathematical modeling to illustrate the encapsulation and understand the influence of particle encapsulation on rates and extents of alkalinity release. The encapsulation of the alkalinity-releasing particles results in slower rates of amendment release as compared to rates obtained using suspensions of bare mineral particles, allowing for the possibility of control as a function of the pH. The results indicate that the alkalinity release from particle suspensions followed a mineral dissolution mechanism that could not explain the rate of the alkalinity release of the encapsulated particles. The reduction in mineral dissolution rates observed with the encapsulated particles was found to result from a mass transfer limitation. This limitation was well described using a linear driving force expression to account for the resistance to mass transfer at the oil–water interface.

EVO↗

HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency

Many workflows in high-energy-physics (HEP) stand to benefit from recent advances in transformer-based large language models (LLMs). While early applications of LLMs focused on text generation and code completion, modern LLMs now support orchestrated agency: the coordinated execution of complex, multi-step tasks through tool use, structured context, and iterative reasoning. We introduce the HEP Toolkit for Agentic Planning, Orchestration, and Deployment (HEPTAPOD), an orchestration framework designed to bring this emerging paradigm to HEP pipelines. The framework enables LLMs to interface with domain-specific tools, construct and manage simulation workflows, and assist in common utility and data analysis tasks through schema-validated operations and run-card-driven configuration. To demonstrate these capabilities, we consider a representative Beyond the Standard Model (BSM) Monte Carlo validation pipeline that spans model generation, event simulation, and downstream analysis within a unified, reproducible workflow. HEPTAPOD provides a structured and auditable layer between human researchers, LLMs, and computational infrastructure, establishing a foundation for transparent, human-in-the-loop systems.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

Development of a BlueCRAB/MELCOR Framework for Supporting Realistic Mechanistic Source Term Calculations in Microreactors

Efforts are currently underway to deploy microreactor modeling and simulation tools to better support vendors and regulatory authorities in submitting and reviewing licensing applications. In particular, the Nuclear Regulatory Commission is expected to rely on the Comprehensive Reactor Analysis Bundle (BlueCRAB) multiphysics toolset in performing design- and beyond-design-basis accident analyses. In addition, the Nuclear Regulatory Commission has been using the MELCOR code to estimate mechanistic source terms during accidents. As MELCOR relies on isotopic inventory and reactor temperature/power evolution profiles during accident conditions—all of which can theoretically be obtained from BlueCRAB—the ultimate goal of this activity is to establish a common BlueCRAB-MELCOR framework. However, prior to the present research, BlueCRAB had never been used to calculate such quantities of interest at the full-core level. While there are many Monte Carlo (MC) codes capable of computing such quantities of interest, they are unable to readily account for multiphysics feedback. BlueCRAB allows for the coupling of different physics codes together to perform multiphysics-informed calculations. Therefore, the purpose of this fiscal year 2023 work is to investigate the feasibility and challenges of performing such calculations within BlueCRAB so as to generate the data that MELCOR relies on. To demonstrate the methodology, the proposed workflow was applied to a prototypical heat pipe-cooled microreactor model. To predict isotopic concentrations (taking into account the ac- cumulation of fission products during operation), the necessary microscopic cross sections were generated via OpenMC and tabulated with respect to temperature and burnup. Next, a recently developed capability in Griffin (the reactor physics application in BlueCRAB) was used to convert the OpenMC output format into the ISOXML format used by Griffin. A multiphysics microscopic depletion calculation that involved performing a coupled full-core, heterogeneous neutron trans- port and thermal calculation at each depletion step was conducted to deplete the core to end of life (EOL) conditions so as to provide both isotopics and the initial condition for the transient calculation. Following a brief null-transient to verify that the initial condition had been properly restarted and was indeed in thermal equilibrium, a heat pipe failure transient was simulated. Thus, the entire workflow of using BlueCRAB to generate MELCOR inputs, from cross-section generation to producing isotopic inventory and power/temperature evolution profiles during transients, is demonstrated. This report also details the identified gaps in the workflow and how they were (for the most part) addressed. Future work should focus on directly including MEL- COR into the workflow by performing a MELCOR calculation using the BlueCRAB-generated input data. In addition, the heat pipe reactor design should be improved so as to reflect more prototypical burnup characteristics at EOL.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Impact of Varying Dark Energy on Future Large-Scale Structure Studies

The cosmos withholds multiple mysteries such as dark forms of matter and energy that are yet beyond human comprehension. In the standard cosmological model, $\Lambda$CDM, the cosmological constant $\Lambda$ is thought to be responsible for the late accelerated expansion of the Universe. However, recent results from the Dark Energy Spectroscopic Instrument (DESI) suggest the possibility of evolving dark energy, which warrants further exploration. Future surveys such as the Rubin Observatory Legacy Survey of Space and Time (LSST) will map the large-scale structure (LSS) with unprecedented precision, giving us valuable statistical information about the cosmos. The goal of this research is to investigate the potential impact of an evolving dark energy scenario on cosmological parameters constrained by LSS probes, as will be mapped by the LSST. For this, we examine the power spectra of lens galaxies, source galaxies, and cross-power spectra between lens galaxies and source galaxies. The combination of these statistics is commonly referred to as '3 $\times$ 2 points'. For this investigation, we created a set of simulations resembling LSST data and used them to perform cosmological parameter inference in two scenarios: one in which the simulated data is based on the fiducial model and another on evolving dark energy. We then examined the degeneracy between the cosmological parameters and checked for potential shifts in the parametric space when the data contains dynamical dark energy but the modeling assumes $\Lambda$CDM. Our findings indicate that mismodeling the dark energy equation of state can significantly impact parameter inference, particularly affecting the total matter density, $\Omega_m$, and the growth of structures, as represented by the $S_8$ parameter. These results highlight the importance of further exploring extensions of the $\Lambda$CDM model in future LSS studies.

Yaman Acharya, A.↗

State-of-the-art on research and applications of machine learning in the building life cycle

Fueled by big data, powerful and affordable computing resources, and advanced algorithms, machine learning has been explored and applied to buildings research for the past decades and has demonstrated its potential to enhance building performance. This study systematically surveyed how machine learning has been applied at different stages of building life cycle. By conducting a literature search on the Web of Knowledge platform, we found 9579 papers in this field and selected 153 papers for an in-depth review. The number of published papers is increasing year by year, with a focus on building design, operation, and control. However, no study was found using machine learning in building commissioning. There are successful pilot studies on fault detection and diagnosis of HVAC equipment and systems, load prediction, energy baseline estimate, load shape clustering, occupancy prediction, and learning occupant behaviors and energy use patterns. None of the existing studies were adopted broadly by the building industry, due to common challenges including (1) lack of large scale labeled data to train and validate the model, (2) lack of model transferability, which limits a model trained with one data-rich building to be used in another building with limited data, (3) lack of strong justification of costs and benefits of deploying machine learning, and (4) the performance might not be reliable and robust for the stated goals, as the method might work for some buildings but could not be generalized to others. Finally, findings from the study can inform future machine learning research to improve occupant comfort, energy efficiency, demand flexibility, and resilience of buildings, as well as to inspire young researchers in the field to explore multidisciplinary approaches that integrate building science, computing science, data science, and social science.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Modeling batch melting: Roles of heat transfer and reaction kinetics

Development of mathematical models of heat and mass transfer in glass-melting furnaces began in the 1970s and progressed rapidly with advances in sophisticated experimental/numerical techniques and increasing computational power. Today, practically all newly built or rebuilt furnaces are optimized with these models to meet stringent quality requirements, reduce the unit costs of manufacturing, or control emissions. One remaining hurdle is to model the batch-to-glass conversion accurately enough to reliably assess the glass production rate. This article summarizes two key aspects of the batch-conversion modeling—the heat transfer and the kinetics of conversion—and reviews the current state-of-the-art approaches to simulating them. We critically examine the advantages of the commonly used heat transfer approach, but also explain that its predictive capabilities are significantly restricted by the dependence of batch thermal properties on the time-temperature history. We argue that kinetic approaches to the batch-conversion modeling would offer a significant improvement when coupled with the heat transfer approach. Finally, we summarize key areas requiring further research on the way toward a realistic model of the batch blanket.

Pokorny, Richard↗

Residential Building Energy Efficiency Field Studies: Low-Rise Multifamily

In recent years, the U.S. Department of Energy (DOE) has conducted a series of research studies to validate energy efficient building technologies in the field. Much of the work has focused on single-family construction, and some has also addressed commercial energy codes. The work detailed in this DOE-funded study (EE0007616) focuses on low-rise multifamily buildings (three stories or fewer above grade) in various regions of the United States, and reports on how state-level building codes are being implemented, both in terms of observed characteristics and also in terms of estimated energy impacts. Nearly 100 buildings across four states—Illinois, Minnesota, Oregon, and Washington—were sampled, which represent a range of climate types from mild temperature to very cold continental. Both common entry and outdoor entry buildings were included, and a parallel research project evaluated envelope air tightness and current still-evolving air tightness testing methods. Finally, a set of structured interviews of building designers and other relevant professionals was carried to out to gain more insight into this market. To the greatest extent possible, the methodology developed under the project for low-rise multifamily buildings mirrored the approach established by Pacific Northwest National Laboratory (PNNL) for single-family residential buildings (https://www.energy.gov/eere/buildings/downloads/residential-building-energy-code-field-study). This included the general approach to sampling, recruitment, and data collection, as well as data analysis and presentation. The range of permitting dates for the sites encompassed two energy code cycles in most regions. All states in the study had adopted a variation of the International Energy Conservation Code (IECC) for the structure of their state code. The low-rise multifamily occupancy presents a hybrid building type: most of the building’s conditioned floor area was covered by the residential chapter of the code while portions of the building (such as corridors and common spaces) fell under the commercial code chapter. The key items assessed in this work were: Building Shell—exterior wall insulation, ceiling insulation, foundation insulation, windows. Common Areas—HVAC and lighting. Living Units—lighting, ventilation. A few items were not assessed in detail, given their relative paucity in this occupancy type; these included duct leakage, pipe insulation, and hot water circulation controls. Building characteristics were collected via a combination of architectural, mechanical, electrical, and plumbing plan reviews and field inspections, and entered into a spreadsheet-based tool that was later queried to build a database. Data went through quality control both upon arrival and via a later semi-automated review and assurance process. Most of the data are presented graphically so that the reader can quickly assess compliance with the applicable energy codes (both by state and by code year). As a final step, EnergyPlus™ simulations were created for all buildings in the study to estimate both the as-found energy use intensity (EUI) and the energy and CO 2 that could be saved if features that were found to not meet code minimums were brought up to code. The savings estimates were tabulated for each of the four states in the study. The research team found that the single-family approach was largely applicable to low-rise multifamily buildings. This applies to both the data collection and the prototype EUI analysis. Most of the occupied space is living units and falls under residential energy codes, and many characteristics use similar envelope construction and relatively straightforward mechanical systems and lighting. One of the most challenging aspects of this work was to build an effective spreadsheet-based data collection instrument that could allow efficient collection of both building plan and field data. The research team is of the view that other methods could be equally effective if the work is done carefully with diligent quality control. The primary findings for the work center around the thermal envelope and mechanical systems and lighting at the sites: For thermal envelope components, the majority of buildings met or were better than the prescriptive code.This suggests that building designers and builders are aware of code requirements. In some cases, surveyed buildings were designed to qualify for energy efficiency certification programs. These buildings made up at least 20% of sampled buildings in each state. Almost all buildings met mechanical system efficiency requirements (for both living units and common areas). In some cases, sites employed systems that were considerably more efficient than required by the applicable energy code. Dwelling units had a majority of high-efficacy lighting, often in excess of the state’s residential code requirements. While high-efficacy fixtures were also typical in common areas (corridors and stairwells), lighting power densities (LPDs) in these areas were sometimes higher than levels dictated by the applicable part of the state commercial energy code. The simulation models run on a series of low-rise multifamily prototypes, informed by a composite of the field data collected, calculated annual EUIs of between 20 and 50 kBtu/ft2-yr, with the range representing the effects of both building characteristics and building location (climate zone). A detailed process (based on simulations of prototype buildings) was used to estimate the amount of avoided energy use that would occur if 100% adherence to energy codes were attained. The results indicated modest savings are attainable for items such as window thermal performance and common area lighting. The result is overall only a modest potential for additional energy savings, averaging about 10% of EUI.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Enabling a Physical Twin for Control Methods Evaluation

Advanced nuclear reactors play an important role in the energy future of the United States and the rest of the world. They are designed and operated based on a different model than that of the current operating fleet, thus enabling deployment in remote locations and allowing for safe semi-autonomous or autonomous operations. Such characteristics require the development of a new reactor control paradigm. A significant factor in the development of control technologies and methods is integration of the various technologies and methods with each other and with hardware (both reactor system hardware and control hardware). A recent workshop on control of advanced reactors identified the lack of a flexible, expandable software/hardware infrastructure to enable such integration as a key gap. A previous phase of the current effort involved developing and demonstrating the Control and Optimization Modular Modeling Application for Nuclear Deployment (COMMAND) platform, which is capable of integrating autonomous-control-enabling technologies and methods, without the constraints imposed by existing software solutions. This platform will enable advanced reactor developers to deploy and test any developed technologies and methods by employing a common framework, and to couple them with their own models and hardware. The present phase of this effort entails using the Microreactor Automated Control System (MACS) platform, which was developed by the U.S. Department of Energy (DOE) Microreactor Program, to serve as a control method testbed. MACS can be used by advanced reactor developers to integrate their control related research activities with any reactor system. For the present effort, MACS was customized to mirror Idaho National Laboratory (INL)’s Microreactor Applications Research Validation and Evaluation (MARVEL) microreactor, and COMMAND was leveraged to enable MACS to emulate the physics of MARVEL, thus positioning MACS as a physical twin of MARVEL.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective

Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling assisted synthesis of Zr-doped Li 3-x In 1-x Zr x Cl 6 with ultrahigh ionic conductivity for lithium-ion batteries

All-solid-state lithium-ion batteries (ASSLBs) are an important milestone for the future of energy storage because of their capability of impressive energy density and outstanding safety. However, oxide and sulfide solid-state electrolytes (SSEs) suffer from either low ionic conductivity or poor chemical stability. In contrast, halide-based SSEs, are promising as candidate materials owing to high conductivity, good stability, and broad cathode compatibility. Though element doping of the SSEs is an effective and common approach to further improve their electrochemical properties, dopant exploration and optimization through solely experimental trials are both costly and time-consuming. For this aspect, computational simulations for dopant element and concentration screening are adopted in this research and zirconium is selected as a suitable dopant for Li 3 InCl 6 . Further, the synthesized Li 2.75 In 0.75 Zr 0.25 Cl 6 exhibited Li ionic conductivity of 5.82 x 10 -3 Scm -1 at room temperature, which is the highest among reported halide SSEs. The ASSLB formed with Li 2 CoO 2 -Li 2.75 In 0.75 Zr 0.25 Cl 6 -Li/In delivers a high initial capacity of 129.3 mAh∙g -1 . Conclusively, this work provides an effective approach which combines computational modeling and experimental verification for the development of halide SSEs with improved stability and conductivity. The successful design approach and compelling results provide further possibilities and capabilities in future SSE research.

25 ENERGY STORAGE↗

Machine learning in materials research: Developments over the last decade and challenges for the future

The number of studies that apply machine learning (ML) to materials science has been growing at a rate of approximately 1.67 times per year over the past decade. In this review, I examine this growth in various contexts. First, I present an analysis of the most commonly used tools (software, databases, materials science methods, and ML methods) used within papers that apply ML to materials science. The analysis demonstrates that despite the growth of deep learning techniques, the use of classical machine learning is still dominant as a whole. It also demonstrates how new research can effectively build upon past research, particular in the domain of ML models trained on density functional theory calculation data. Next, I present the progression of best scores as a function of time on the matbench materials science benchmark for formation enthalpy prediction. In particular, a dramatic improvement of 7 times reduction in error is obtained when progressing from feature-based methods that use conventional ML (random forest, support vector regression, etc.) to the use of graph neural network techniques. Finally, I provide views on future challenges and opportunities, focusing on data size and complexity, extrapolation, interpretation, access, and relevance.

36 MATERIALS SCIENCE↗

A mixture of grass–legume cover crop species may ameliorate water stress in a changing climate

Climate change models predict increasing precipitation variability in the mid-latitude regions of Earth, generating a need to reduce the negative impacts of these changes on crop production. Despite considerable research on how cover crops support agriculture in a changing climate, understanding is limited of how climate change influences the growth of cover crops. We investigated the early development of two common cover crop species—crimson clover (Trifolium incarnatum) and rye (Secale cereale)—and hypothesized that growing them in the mixture would ameliorate stress from drought or waterlogging. This hypothesis was tested in a 25-day greenhouse experiment, where the two factors (species number and water stress) were fully crossed in randomized blocks, and plant responses were quantified through survival, growth rate, biomass production and root morphology. Water stress negatively influenced the early growth of these two species in contrasting ways: crimson clover was susceptible to drought while rye performed poorly under waterlogging. Per-plant biomass in rye was always greater in mixture than in monoculture, while per-plant biomass of crimson clover was greater in mixture under drought. Both species grew longer roots in mixture than in monoculture under drought, and total biomass of mixtures did not differ significantly from the more-productive monoculture (rye) in any water condition. In the face of increasingly variable precipitation, growing crimson clover and rye together has potential to ameliorate water stress, a possibility that should be further investigated in field experiments.

54 ENVIRONMENTAL SCIENCES↗

Bridging gaps in permafrost-shrub understanding

Permafrost, permanently frozen ground which underlies much of the Arctic and sub-Arctic, is influenced by deciduous shrubs, yet our understanding of permafrost-shrub interactions is limited. This is largely due to a lack of widespread, long-term, high-quality observations across Arctic and sub-Arctic systems, which are difficult to study due to their remote locations. Shrubs are rapidly expanding in many areas of Arctic tundra and can either amplify or inhibit permafrost thaw, making it crucial that we can understand and predict permafrost-shrub interactions. As we have limited time and resources to make observations, we must design our field campaigns to be as impactful as possible. Below we outline the current state of knowledge and give suggestions about how we can maximize our fieldwork’s impact. From field studies conducted around the Arctic, we know that shrubs generally have a cooling effect on permafrost in the summer, largely caused by the shrub canopy shading the soil. However, summertime cooling can be counteracted by a warming effect in winter, caused by the trapping of blowing snow by shrubs, which leads to increased snow depths. In addition to these commonly observed effects, both observations and models show that other local factors such as climate, soil, snow, and disturbances can interact to cause contrasting dominant effects on permafrost temperatures. For example, shrubs that protrude through the snowpack have been observed to cool permafrost in winter via thermal bridging between the air above the snow and the soil below. However, at other research sites, protruding shrubs lower the surface albedo and cause earlier snowmelt in spring, amplifying permafrost thaw by exposing the soil to thawing earlier. Protruding shrubs have also been observed to induce snow melt in autumn, creating ice layers at the snow surface that prevent further snow accumulation and eliminate the ability of shrubs to trap blowing snow, thereby reducing the winter warming effect. While we understand the physical processes that lead to these effects, we cannot explain why we observe different effects between sites.

54 ENVIRONMENTAL SCIENCES↗