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At least 1,315 records · Page 73

A New Method for Ice-Ice Aggregation in the Adaptive Habit Model

In this paper, a novel methodology for modeling ice-ice aggregation is presented. This methodology combines a modified hydrodynamic collection algorithm with bulk aggregate characteristic information from an offline simulator that collects ice particles, namely, the Ice Particle and Aggregate Simulator, and has been implemented into the Adaptive Habit Microphysics scheme in the Weather Research and Forecasting Model. Aggregates, or snow, are formed via collection of cloud ice particles, where initial ice characteristics and the resulting geometry determine aggregate characteristics. Upon implementation, idealized squall-line simulations are performed to examine the new methodology in comparison with commonly used bulk microphysics schemes. It is found that the adaptive habit aggregation parameterization develops snow and reduces ice mass and number concentrations compared to other schemes. The development of aggregates through the new methodology cascades into other interesting effects, including enhancements in ice and snow growth, as well as homogeneous freezing. Further microphysical analyses reveal varying sensitivities, where snow processes are most sensitive to the new parameterization, followed by ice, then cloud, rain, and graupel processes. Further, the new scheme results in enhancements in surface precipitation due to the persistence of snow at lower altitudes. This persistence is a result of shape-dependent melting and sublimation, increasing the residence time. Moreover, these low-level enhancements are reflected in increases in radar reflectivity at the surface and its spatial distribution. Finally, the ability to predict snow shape and density allows for the simulation of polarimetric radar quantities, resulting in signature enhancements compared to schemes that do not consider spatial and temporal variations in snow shape and density.

54 ENVIRONMENTAL SCIENCES↗

A simple hydride model for cerium ejecta particles

Cerium ejecta particles form after a shock wave impacts a cerium plate with a known roughness or prescribed surface perturbation. When these particles are ejected into hydrogen or deuterium gas the material reacts exothermically and raises the temperature of the particle relative to the gas. A simple model is developed, assuming that the particle remains intact and spherical, to capture the heat and mass transfer that occurs during this process. Model performance is evaluated by comparing with cerium ejecta experiments where the particles are ejected into deuterium gas at initial pressures of 4 and 8 atm. Overall, the model is able to capture the approximately 400 K increase in particle temperature above the surrounding gas temperature.

36 MATERIALS SCIENCE↗

Acceleration of Thermochimica Calculations in Bison

The performance of the open-source thermochemical software library Thermochimica has been enhanced by developing a re-initialization algorithm to make use of data from previous calculations to reduce the number of convergence steps in the Gibbs energy minimization procedure. This algorithm has been tested in the context of stand-alone Thermochimica calculations, and speedups in the range of 2x-3x achieved for cases with chemistries resembling those of irradiated nuclear fuels. Routines to make use of this re-initialization procedure have been implemented in Bison, in which each node uses the results of the previous calculation at that node as the initial conditions for the following Thermochimica call. Examples based on calculating the diffusion of oxygen in UO$_2$ LWR fuel in 1D and 3D have been tested, with speedups up to 7.38x demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

In Situ Cloud Measurements at AMF3 Field Campaign Report

This campaign is a follow-up project to the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility field campaign entitled Cloud Droplet Measurement System for TBS that was focused on integration of the Mesa Photonics' cloud droplet measurement system (CDMS) into the DOE ARM tethered balloon system (TBS) and its initial field testing at ARM’s Southern Great Plains (SGP) atmospheric observatory in February–March 2020. The CDMS performs in situ measurement of droplet size distribution function and droplet number density in clouds. These characteristics are important cloud microphysical properties that are critical input parameters for atmospheric models and are also useful for proper calibration and validation of performance of other atmospheric measurement instrumentation. The overall goals of this campaign were to deploy the CDMS on the DOE ARM TBS, test its compatibility with the TBS under relevant conditions, and perform a series of in-cloud measurements at the third ARM Mobile Facility (AMF3) at Oliktok Point, Alaska. The TBS flights were conducted on November 12–19, 2020.

54 ENVIRONMENTAL SCIENCES↗

A simple hydride model for cerium ejecta particles

Cerium ejecta particles form after a shock wave impacts a cerium plate with a known roughness or prescribed surface perturbation. When these particles are ejected into hydrogen or deuterium gas the material reacts exothermically and raises the temperature of the particle relative to the gas. A simple model is developed, assuming that the particle remains intact and spherical, to capture the heat and mass transfer that occurs during this process. Model performance is evaluated by comparing with cerium ejecta experiments where the particles are ejected into deuterium gas at initial pressures of 4 and 8 atm. Overall, the model is able to capture the approximately 400 K increase in particle temperature above the surrounding gas temperature.

36 MATERIALS SCIENCE↗

Start-up Operation Experience with a Liquid Fluoride Salt Forced Convection Loop

A liquid fluoride salt forced convection test loop was constructed at Oak Ridge National Laboratory. Its unique features include a pebble bed test section, high-temperature instrumentation, a noncontact rotating gas seal for the pump, a silicon carbide flow tube, and a unique inductive heating technique. Initial startup and shake-down testing has been completed. This paper describes how several of the systems performed, highlights those that worked well, and discusses issues that arose during the start-up process. This discussion should be of interest to those who intend to develop molten salt technologies and who are interested in some of the specific techniques used in this experiment.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

2023 Critical Materials Strategy

The global effort to curb carbon emissions is accelerating demand for clean energy technologies and the materials they rely on. Demand for these materials will only continue to grow, especially as some nations aim to achieve net zero emissions by 2050. While some major materials like steel, copper, and aluminum are already powering the fossil fuel economy, others are more minor materials with potential supply risks. These risks could jeopardize the ability to reduce greenhouse gas emissions within the desirable timeframe to avoid significant climate change. In some cases, it may be necessary to take action to improve the resilience of material supply chains and mitigate supply risks. Understanding the importance of individual materials to clean energy and the supply risks associated with them is necessary to identify which materials may serve as potential roadblocks to a clean energy future. The U.S. Department of Energy (DOE) issued a series of 13 supply chain deep dive assessment reports on various energy technologies in 2022 in response to President Biden’s Executive Order on America’s Supply Chains (E.O. 14017). These reports emphasized that supply chain bottlenecks can occur at any stage of the value chain from mining and refining to component and even sub-system manufacturing. The bottlenecks are a combination of factors such as material availability, equipment availability, work force availability and quality, logistics, regulatory framework, and market conditions. These bottlenecks were worsened during the global Covid-19 pandemic. Its lingering impacts have hindered capacity expansion for material supply chains and prevented product lead-time recovery. One approach to reduce supply chain risks for the United States is to have a strong domestic manufacturing sector with a diverse set of producers. Boosting responsible domestic production would require leveraging the latest science not only in material extraction but also in developing substitutes, recycling, reuse, and remanufacturing. This report is an updated analysis of previous Critical Materials Strategy (CMS) reports published by the DOE in 2010, 2011, and 2019 based on national and global priorities, technology advancement, and technology adoption trends. Like the CMS reports, this analysis presents the results of a formal material criticality assessment to identify which materials are critical to the continued deployment of clean energy technologies globally. The analysis in this report leveraged the DOE supply chain deep dive assessments to develop the initial list of materials to evaluate. This DOE Critical Materials Assessment (CMA) is conducted independently of criticality assessments performed by other U.S. government agencies, such as that conducted by the U.S. Geological Survey (USGS). This analysis complements the USGS critical minerals determination in three aspects. First, the DOE assessment is performed from a global perspective, while the USGS analysis focusses on the importance of minerals to the U.S. economy. Second, this report focuses on the importance of materials to clean energy technologies, rather than to the economy in general. Lastly, this study is forward looking to 2035 based on clean energy deployment scenarios, whereas the USGS assessment is retrospective. Materials evaluated in this report that do not appear in the USGS Critical Minerals List include copper, uranium, electrical steel, and SiC. A draft version of this report received ~80 public comments related to supporting data and methodological improvement. Those comments have been incorporated as much as possible where appropriate. Highlights of findings from this 2023 CMA include: Rare earth materials (neodymium, praseodymium, dysprosium, and terbium) used in magnets in electric vehicle (EV) motors and wind turbine generators continue to be critical. While dysprosium (Dy) and terbium (Tb) are both heavy rare earth elements that serve the same function in magnets, the criticality of Tb is slightly lower than that for Dy in the short term due to the widespread use of Dy in high-grade magnets and Tb’s present role as a substitute. Similarly, praseodymium (Pr) is critical in the medium term but only near critical in the short term because it is more substitutable in magnets than neodymium (Nd); Materials used in batteries for EVs and stationary storage are now considered to be critical. While cobalt (Co) was found to be critical in this and previous reports, lithium (Li) becomes critical in the medium term due to its broader use in various battery chemistries and the rampant growth of the EV industry. Natural graphite is a new addition in this assessment and is also found to be critical; Platinum group metals used in hydrogen electrolyzers, such as platinum (Pr) and iridium (Ir), are critical due to an increased focus on hydrogen technologies to achieve net zero carbon emissions, while those used in catalytic converters, such as rhodium (Rh) and palladium (Pd), were screened out due to the decreased importance of catalytic converters in the medium term; Gallium (Ga) continues to be critical due to its use in light-emitting diodes (LEDs). In addition, the use of Ga has increased in magnet manufacturing and in semiconductor in forms such as gallium arsenide (GaAs) or gallium nitride (GaN); Major materials like Aluminum (Al), copper (Cu), nickel (Ni), and silicon (Si) move from noncritical in the short term to near critical in the medium term due to their importance in electrification; Electrical steel is near critical due to its use in transformers for the grid and electric motors in EVs.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Homomorphic Encryption for Electrical Metering Aggregation: Protecting the Privacy of Building Tenants

Electrical meters are devices that measure consumer electricity usage. The data collected by these meters is necessary for utility billing and electrical grid management but can also be used to assess the environmental impact of buildings. Prior research has found that unprotected metering data could potentially be used to infer some information about the behaviors of building tenants by detecting changes in electricity usage. For example, a period of low electricity usage could suggest that the tenants are not in the building. As smart metering becomes more common, there is a growing need for data privacy protections for metering data that do not negatively impact the quality and availability of data used for energy management and billing applications. To identify potential solutions, we developed a Python-based data aggregation platform to analyze the potential efficacy of privacy-enhancing technologies for energy metering applications. This platform aggregates groups of metering sites into virtual buildings, which could potentially detach changes in electrical activity from individual tenants, making it more difficult to track the activity of a specific tenant. To further protect data during analysis, this project utilizes homomorphic encryption as part of its initial approach. Homomorphic encryption offers a means of protecting energy consumption data while permitting mathematical operations to be performed without the need to know the data contents. This allows for data to be processed into usable statistics without revealing energy consumption information. A series of homomorphic encryption libraries were evaluated to determine their applicability and limitations in the context of metering data. The use of these techniques may help to reassure consumers and encourage further adoption of smart grid infrastructure.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Precursor Analysis Report: Industroyer2 and Wiper Malware Targeting Ukrainian Energy Provider 2022

The Industroyer2 and Wiper Malware Targeting Ukrainian Energy Provider 2022 Precursor Analysis Report leverages publicly available information about the Industroyer2 cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. An adversary attempted to cause a blackout in Ukraine in April 2022 by using the Industroyer2 malware against a regional Ukrainian energy provider. The adversary targeted eight high-voltage electrical substations and utilized the malware in tandem with disk wipers for Windows, Linux, and Solaris operating systems in an attempt to make response and recovery efforts more difficult. The adversary reused a piece of the original Industroyer malware designed to open circuit breakers and de-energize target substations. The adversary gained initial access to the victim’s enterprise network through unknown means in February 2022 and was able to perform reconnaissance, pivot to the operations network, and reside in the system for at least 51 days. This gave the adversary a detailed understanding of the environment and allowed them to customize the Industroyer2 malware to the victim’s operations network. However, defenders detected and stopped the attack before the adversary could achieve their intended impact. Had the Industroyer2 attack been successful, it could have caused a blackout for more than two million people during the early stages of Russia’s invasion of Ukraine. Researchers and analysts identified 22 unique techniques (used in a sequence of 31 steps) utilized during the attack with a total of 297 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Twenty-three of the identified techniques used during the Industroyer2 cyber attack were precursors to the triggering event. Analysis identified 224 observables associated with these precursor techniques, 122 of which were assessed to have an increased likelihood of being perceived in the 51 days preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Robust Polymer Electrolytes For Flexible Energy Storage (CRADA Final Report)

As part of the Cyclotron Road program, Anthro Energy investigated the formulation, synthesis, and application of advanced supramolecular compounds for lithium-ion batteries. Anthro Energy developed and tested formulations and chemistries to create polymeric materials with improved mechanical strength, safety, and electrochemical performance. These materials were explored for use in next-generation batteries with a variety of form factors. Initially, Anthro Energy tested these materials to create flexible and deformable batteries, which are in high demand for the wearable/flexible electronics industry. In future work, Anthro Energy’s materials may be applied to create rigid structural batteries, or to enable novel chemistries such as silicon anodes or lithium metal anodes. In the process of testing the company’s unique lithium-ion cells, Anthro Energy explored the development and utilization of novel cell components, cell architectures, and testing protocols. These next-generation flexible and structural batteries may eventually enable new categories of electronic devices.

25 ENERGY STORAGE↗

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

Ultrathin, conductive and fouling-resistant zwitterionic polymer films

Disclosed are methods of preparing antifouling coatings on reverse osmosis membranes with initiated vapor deposition or oxidative vapor deposition. The coatings enhance the stability and lifetime of membranes without sacrificing performance characteristics, such as permeability or salt retention.

36 MATERIALS SCIENCE↗

Temperature-based reactive flow model for TATB plastic bonded explosives

A new reactive flow model is presented for TATB-based plastic bonded explosives, applicable to shock initiation and detonation problems of differing initial temperature. Temperature disequilibrium is assumed between unreacted explosive, material in the vicinity of compressed defects (called hot spots), and detonation products. The model incorporates temperature-dependent decomposition reaction rates. Arrhenius model parameters were derived from subscale quantum-based molecular dynamics simulations of shock-induced TATB decomposition. Further, a model of detonation carbon aggregation is incorporated, describing the late-time slow release of energy inherent to detonation in TATB-based materials. The predictive ability of the model in the shock initiation regime is tested against recent thin pulse experiments on PBX 9502. Here, the model is found to perform equally well in predicting the size effect curve of ambient, cold, and hot PBX 9502 rate sticks.

Chemistry - Chemical explosives↗

Targeting tissues via dynamic human systems modeling in generative design

Drug discovery is a complex, costly process with high failure rates. A successful drug should bind to a target, be deliverable to an intended site of activity, and promote a desired pharmacological effect without causing toxicity. Typically, these factors are evaluated in series over the course of a pipeline where the number of candidates is sequentially whittled down from a very large initial pool. One promise of AI-driven discovery is the opportunity to evaluate multiple facets of drug performance in parallel. However, despite ML-driven advancements, current models for pharmacological property prediction are exclusively trained to predict molecular properties, ignoring important, dynamic biodistribution and bioactivity effects. Here, we present our progress towards incorporating quantitative systems physiology models into an AI-enabled drug design and molecular generation pipeline. Within a genetic algorithm, we include human-relevant physiologically based pharmacokinetic (PBPK) models. These PBPK models leverage properties that are predicted by a fine-tuned molecular language model. Together, these models will aid in capturing the mapping between molecules and therapeutic outcomes that is necessary to accelerate the drug discovery process.

Fox, Zach↗

Competition Between Growth and Removal in Zirconia Nanocrystal-Derived Tribofilms: The Role of Co-additives

Antiwear additives permit energy-efficient lubrication of gearboxes, bearings, and other tribological interfaces. We study zirconia (ZrO 2 ) nanocrystal additives, which readily form protective tribofilms in tribological contacts. Our prior work demonstrated cooperative antiwear performance between ZrO 2 and the S- and P-based co-additives in fully formulated hydrocarbon gear oils. Here, we extend that work by examining the growth kinetics of the ZrO 2 tribofilms, including the influence of the co-additives. In the boundary lubrication regime for mixed rolling-sliding contacts, the initial phase of ZrO 2 tribofilm growth is soon overtaken by removal processes, phenomena whose importance has gone unnoticed in prior work. Tribofilm removal affects the steady-state thickness and morphology of the tribofilm as well as its growth kinetics. The S- and P-based co-additives are incorporated into the ZrO 2 tribofilm, and alter the competition between the growth and removal processes, increasing initial net growth rates per contact cycle and contributing to a more polished final interface. This work highlights the significance of removal processes in determining tribofilm antiwear performance, and suggests several routes for improving tribofilm growth kinetics using co-additives.

Coadditives↗

AI Benchmark Democratization and Carpentry

Benchmarks are a cornerstone of modern machine learning, enabling reproducibility, comparison, and scientific progress. However, AI benchmarks are increasingly complex, requiring dynamic, AI-focused workflows. Rapid evolution in model architectures, scale, datasets, and deployment contexts makes evaluation a moving target. Large language models often memorize static benchmarks, causing a gap between benchmark results and real-world performance. Beyond traditional static benchmarks, continuous adaptive benchmarking frameworks are needed to align scientific assessment with deployment risks. This calls for skills and education in AI Benchmark Carpentry. From our experience with MLCommons, educational initiatives, and programs like the DOE's Trillion Parameter Consortium, key barriers include high resource demands, limited access to specialized hardware, lack of benchmark design expertise, and uncertainty in relating results to application domains. Current benchmarks often emphasize peak performance on top-tier hardware, offering limited guidance for diverse, real-world scenarios. Benchmarking must become dynamic, incorporating evolving models, updated data, and heterogeneous platforms while maintaining transparency, reproducibility, and interpretability. Democratization requires both technical innovation and systematic education across levels, building sustained expertise in benchmark design and use. Benchmarks should support application-relevant comparisons, enabling informed, context-sensitive decisions. Dynamic, inclusive benchmarking will ensure evaluation keeps pace with AI evolution and supports responsible, reproducible, and accessible AI deployment. Community efforts can provide a foundation for AI Benchmark Carpentry.

von Laszewski, Gregor [Virginia U.]↗

Integrating AlphaFold and deep learning for atomistic interpretation of cryo-EM maps

Abstract Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and fitting into cryo-EM maps. In this work, we designed a protein model-building workflow, which combines a deep-learning cryo-EM map feature enhancement tool, CryoFEM (Cryo-EM Feature Enhancement Model) and AlphaFold. A benchmark test using 36 cryo-EM maps shows that CryoFEM achieves state-of-the-art performance in optimizing the Fourier Shell Correlations between the maps and the ground truth models. Furthermore, in a subset of 17 datasets where the initial AlphaFold predictions are less accurate, the workflow significantly improves their model accuracy. Our work demonstrates that the integration of modern deep learning image enhancement and AlphaFold may lead to automated model building and fitting for the atomistic interpretation of cryo-EM maps.

59 BASIC BIOLOGICAL SCIENCES↗