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At least 523 records · Page 29

Lighting up yeast: overview of optogenetics in yeast and their applications to yeast biotechnology

Abstract Optogenetics is an empowering technology that uses light-responsive proteins to control biological processes. Because of its genetic tractability, abundance of genetic tools, and robust culturing conditions, Saccharomyces cerevisiae has served for many years as an ideal platform in which to study, develop, and apply a wide range of optogenetic systems. In many instances, yeast has been used as a steppingstone in which to characterize and optimize optogenetic tools to later be deployed in higher eukaryotes. More recently, however, optogenetic tools have been developed and deployed in yeast specifically for biotechnological applications, including in nonconventional yeasts. In this review, we summarize various optogenetic systems responding to different wavelengths of light that have been demonstrated in diverse yeast species. We then describe various applications of these optogenetic tools in yeast, particularly in metabolic engineering and recombinant protein production. Finally, we discuss emerging applications in yeast cybergenetics—the interfacing of yeast and computers for closed-loop controls of yeast bioprocesses—and the potential impact of optogenetics in other future biotechnological applications.

Biotechnology & Applied Microbiology↗

Enhanced Weathering May Benefit From Co‐Application With Organic Amendments

Abstract Enhanced weathering has emerged as a promising natural climate solution that has the potential to remove billions of tons of carbon from the atmosphere if widely adopted in agricultural settings. Despite this potential, few field trials have been published that verify the carbon dioxide removal (CDR) potential of enhanced weathering in croplands and, until now, none had been published in grazing lands. Anthony et al. (2025, https://doi.org/10.1029/2024AV001480 ) conducted the first trial of enhanced weathering in a California rangeland and showed weathering of ground silicate rocks despite drought conditions in an already dry climate. Co‐application of inorganic (silicate rocks) with organic (biochar and compost) amendments revealed not just additive, but synergistic effects whereby organic amendments increased rates of weathering. This is important because field CDR rates were <10% of the theoretical maximum (i.e., the rate if basalt was completely weathered); thus, methods to improve weathering rates will be necessary for this practice to scale in a meaningful way. Multi‐carbon pool measurements revealed not only how co‐application of soil amendments heightened net carbon benefits, but also how soil amendments complemented each other to produce net benefits for soil carbon, biomass growth, and greenhouse gas emission reductions. Anthony et al. (2025, https://doi.org/10.1029/2024AV001480 ) produce new insights toward our understanding of enhanced weathering as well as introduce paths for future research concerning combined amendment applications, synergistic mechanisms for carbon storage, and deployment in various agricultural contexts. While questions remain about the fate of weathering products in arid regions, Anthony et al. (2025, https://doi.org/10.1029/2024AV001480 ) present novel findings on the potential for significant weathering to occur even under suboptimal conditions.

Almaraz, Maya [Yale Center for Natural Carbon Capt↗

High entropy ceramics for applications in extreme environments

Abstract Compositionally complex materials have demonstrated extraordinary promise for structural robustness in extreme environments. Of these, the most commonly thought of are high entropy alloys, where chemical complexity grants uncommon combinations of hardness, ductility, and thermal resilience. In contrast to these metal–metal bonded systems, the addition of ionic and covalent bonding has led to the discovery of high entropy ceramics (HECs). These materials also possess outstanding structural, thermal, and chemical robustness but with a far greater variety of functional properties which enable access to continuously controllable magnetic, electronic, and optical phenomena. In this experimentally focused perspective, we outline the potential for HECs in functional applications under extreme environments, where intrinsic stability may provide a new path toward inherently hardened device design. Current works on high entropy carbides, actinide bearing ceramics, and high entropy oxides are reviewed in the areas of radiation, high temperature, and corrosion tolerance where the role of local disorder is shown to create pathways toward self-healing and structural robustness. In this context, new strategies for creating future electronic, magnetic, and optical devices to be operated in harsh environments are outlined.

36 MATERIALS SCIENCE↗

A review of artificial intelligence applications in manufacturing operations

Abstract Artificial intelligence (AI) and machine learning (ML) can improve manufacturing efficiency, productivity, and sustainability. However, using AI in manufacturing also presents several challenges, including issues with data acquisition and management, human resources, infrastructure, as well as security risks, trust, and implementation challenges. For example, getting the data needed to train AI models can be difficult for rare events or costly for large datasets that need labeling. AI models can also pose security risks when integrated into industrial control systems. In addition, some industry players may be hesitant to use AI due to a lack of trust or understanding of how it works. Despite these challenges, AI has the potential to be extremely helpful in manufacturing, particularly in applications such as predictive maintenance, quality assurance, and process optimization. It is important to consider the specific needs and capabilities of each manufacturing scenario when deciding whether and how to use AI in manufacturing. This review identifies current developments, challenges, and future directions in AI/ML relevant to manufacturing, with the goal of improving understanding of AI/ML technologies available for solving manufacturing problems, providing decision‐support for prioritizing and selecting appropriate AI/ML technologies, and identifying areas where further research can yield transformational returns for the industry. Early experience suggests that AI/ML can have significant cost and efficiency benefits in manufacturing, especially when combined with the ability to capture enormous amounts of data from manufacturing systems.

Plathottam, Siby Jose↗

On the Power of Abstract Interpretation

Increasingly sophisticated applications of static analysis place increased burden on the reliability of the analysis techniques. Often, the failure of the analysis technique to detect some information my mean that the time or space complexity of the generated code would be altered. Thus, it is important to precisely characterize the power of static analysis techniques. We follow the approach of Selur et. al. who studied the power of strictness analysis techniques. Their result can be summarized by saying 'strictness analysis is perfect up to variations in constants.' In other words, strictness analysis is as good as it could be, short of actually distinguishing between concrete values. We use this approach to characterize a broad class of analysis techniques based on abstract interpretation including, but not limited to, strictness analysis. For the first-order case, we consider abstract interpretations where the abstract domain for data values is totally ordered. This condition is satisfied by Mycroft's strictness analysis that of Sekar et. al. and Wadler's analysis of list-strictness. For such abstract interpretations, we show that the analysis is complete in the sense that, short of actually distinguishing between concrete values with the same abstraction, it gives the best possible information. We further generalize these results to typed lambda calculus with pairs and higher-order functions. Note that products and function spaces over totally ordered domains are not totally ordered. In fact, the notion of completeness used in the first-order case fails if product domains or function spaces are added. We formulate a weaker notion of completeness based on observability of values. Two values (including pairs and functions) are considered indistinguishable if their observable components are indistinguishable. We show that abstract interpretation of typed lambda calculus programs is complete up to this notion of indistinguishability. We use denotationally-oriented arguments instead of the detailed operational arguments used by Selur et. al.. Hence, our proofs are much simpler. They should be useful for further future improvements.

Reddy, Uday S.↗

Melt compounding of spray-dried cellulose nanofibrils/polypropylene and their application in 3D printing

Abstract Micro- and nano-scale cellulosic fillers exhibit excellent dispersion and distribution within a thermoplastic matrix during the process of melt compounding or injection molding. In this study, spray-dried cellulose nanofiber (SDCNF) powders were manufactured using a pilot-scale rotating disk atomizer spray dryer. Bleached Kraft pulp (BKP), unbleached Kraft pulp (UKP), and old corrugated cardboard pulp (OCC) fibrillated at a fines level of 90% were used as feedstock materials for spray-drying. BKP-, UKP-, and OCC- SDCNFs were compounded with polypropylene using a twin screw co-rotating extruder. Maleic anhydride grafted polypropylene (MAPP) was used as a coupling agent in the composite formulations. The tensile, flexural, and impact properties of SDCNF-filled PP composites increased at 10 wt% SDCNF loading. The presence of SDCNFs in the PP matrix resulted in faster crystallization and a 12% reduction in the degree of crystallinity of the neat PP. The coefficient of thermal expansion (CTE) of neat PP was reduced by up to 31% attributable to the presence of the SDCNFs. Application of the SDCNF-reinforced PP composites in 3D printing reduced the shrinkage rate of the printed neat PP by 39%, and the printability of the PP was significantly improved with the addition of the SDCNFs.

Materials Science↗

Ginkgo - A math library designed to accelerate Exascale Computing Project science applications

Large-scale simulations require efficient computation across the entire computing hierarchy. A challenge of the Exascale Computing Project (ECP) was to reconcile highly heterogeneous hardware with the myriad of applications that were required to run on these supercomputers. Mathematical software forms the backbone of almost all scientific applications, providing efficient abstractions and operations that are crucial to harness the performance of computing systems. Ginkgo is one such mathematical software library, nurtured by ECP, providing high-performance, user-friendly, and performance portable interfaces for applications in ECP and beyond. In this paper, we elaborate on Ginkgo’s philosophy of high-performance software that is sustainable, reproducible, and easy to use. We showcase the wide feature set of solvers and preconditioners available in Ginkgo and the central concepts involved in their design. We elaborate on four different ECP software integrations: MFEM, PeleLM + SUNDIALS, XGC, and ExaSGD that use Ginkgo to accelerate their science runs. Performance studies of different problems from these applications highlight the effectiveness of Ginkgo and the benefits incurred by these ECP applications.

Cojean, Terry↗

Scenario Complexity for Unmanned Aircraft System Traffic

This work introduces an approach to estimate the complexity of a low-altitude air traffic scenario involving multiple UASs using mathematical programming. Given a set of multi-point UAS flight trajectories, vehicle dynamics, and a conflict resolution algorithm, an abstract model is developed such that it can be solved quickly using a mathematical programming optimization software without running high-fidelity simulations that can be computationally expensive and may not suit real-time applications. In the abstract model, each vehicle is represented by a time-varied vector associated with position, speed, and heading information. The total extra distance that aircraft need to divert from their original routes to avoid collisions is computed and used to setup a quadratic programming formula. The metrics including the number of conflicts and extra distances travelled by all vehicles are then utilized to estimate the complexity of a given UAS flight scenario. Results and verification against high-fidelity simulations will be provided in the final draft.

UTM↗

A Bispectral Composite Threshold Approach for Automatic Cloud Detection in VIIRS Imagery

The detection of clouds in satellite imagery has a number of important applications in weather and climate studies. The presence of clouds can alter the energy budget of the Earth‐atmosphere system through scattering and absorption of shortwave radiation and the absorption and re‐emission of infrared radiation at longer wavelengths. The scattering and absorption characteristics of clouds vary with the microphysical properties of clouds, hence the cloud type. Thus, detecting the presence of clouds over a region in satellite imagery is important in order to derive atmospheric or surface parameters that give insight into weather and climate processes. For many applications however, clouds are a contaminant whose presence interferes with retrieving atmosphere or surface information. In these cases, is important to isolate cloud‐free pixels, used to retrieve atmospheric thermodynamic information or surface geophysical parameters, from cloudy ones. This abstract describes an application of a two‐channel bispectral composite threshold (BCT) approach applied to VIIRS imagery. The simplified BCT approach uses only the 10.76 and 3.75 micrometer spectral channels from VIIRS in two spectral tests; a straight‐forward infrared threshold test with the longwave channel and a shortwave - longwave channel difference test. The key to the success of this approach as demonstrated in past applications to GOES and MODIS data is the generation of temporally and spatially dependent thresholds used in the tests from a previous number of days at similar observations to the current data. The paper and subsequent presentation will present an overview of the approach and intercomparison results with other satellites, methods, and against verification data.

LaFontaine Frank J.↗

Pincers with diverse donors and their interconversion: application to Ni(II)

Abstract A pincer ligand composed of a pyridine with ortho positions substituted by a bulky phosphine arm and a pyrazole arm (PNNH) is installed on nickel(II) to yield the diamagnetic planar complex [(PNNH)NiCl]Cl. The chloride anion can be replaced by BPh 4 − by a metathesis. The acidic pyrazole proton can be removed with LiN(SiMe 3 ) 2 to yield the square planar neutral molecule (PNN − )NiCl. The coordinated chloride can be metathetically replaced by azide to yield diamagnetic (PNN − )Ni(N 3 ). To evaluate changing the phosphine donor for a phosphine sulfide, the corresponding pincer ligand SPNNH was synthesized and installed on NiBr 2 . The reduced steric bulk from the more distant phosphorous keeps both halides coordinated in the paramagnetic molecular species (SPNNH)NiBr 2 . Several attempts to dehydrobrominate this species result in synthesis and characterization of two unexpected products. One effort revealed that the electrophilic character of P(V) leaves the phosphorus atom in (SPNNH)NiBr 2 vulnerable to nucleophilic attack, resulting in a P/C cleavage product which was characterized.

Cabelof, Alyssa C.↗

Timescales and Processes of Methane Hydrate Formation and Breakdown, With Application to Geologic Systems

Abstract Gas hydrate is an ice‐like form of water and low molecular weight gas stable at temperatures of roughly −10°C to 25°C and pressures of ~3 to 30 MPa in geologic systems. Natural gas hydrates sequester an estimated one sixth of Earth's methane and are found primarily in deepwater marine sediments on continental margins, but also in permafrost areas and under continental ice sheets. When gas hydrate is removed from its stability field, its breakdown has implications for the global carbon cycle, ocean chemistry, marine geohazards, and interactions between the geosphere and the ocean‐atmosphere system. Gas hydrate breakdown can also be artificially driven as a component of studies assessing the resource potential of these deposits. Furthermore, geologic processes and perturbations to the ocean‐atmosphere system (e.g., warming temperatures) can cause not only dissociation, but also more widespread dissolution of hydrate or even formation of new hydrate in reservoirs. Linkages between gas hydrate and disparate aspects of Earth's near‐surface physical, chemical, and biological systems render an assessment of the rates and processes affecting the persistence of gas hydrate an appropriate Centennial Grand Challenge. This paper reviews the thermodynamic controls on methane hydrate stability and then describes the relative importance of kinetic, mass transfer, and heat transfer processes in the formation and breakdown (dissociation and dissolution) of gas hydrate. Results from numerical modeling, laboratory, and some field studies are used to summarize the rates of hydrate formation and breakdown, followed by an extensive treatment of hydrate dynamics in marine and cryospheric gas hydrate systems.

58 GEOSCIENCES↗

Understanding the metal-to-insulator transition in La1−xSrxCoO3−δ and its applications for neuromorphic computing

Abstract Transition metal oxides that exhibit a metal-to-insulator transition (MIT) as a function of oxygen vacancy concentration are promising systems to realize energy-efficient platforms for neuromorphic computing. However, the current lack of understanding of the microscopic mechanism driving the MIT hinders the realization of effective and stable devices. Here we investigate defective cobaltites and we unravel the structural, electronic, and magnetic changes responsible for the MIT when oxygen vacancies are introduced in the material. We show that, contrary to accepted views, cooperative structural distortions instead of local bonding changes are responsible for the MIT, and we describe the subtle interdependence of structural and magnetic transitions. Finally, we present a model, based on first principles, to predict the required electric bias to drive the transition, showing good agreement with available measurements and providing a paradigm to establish design rules for low-energy cost devices.

36 MATERIALS SCIENCE↗

Design, construction, and validation of an in-situ groundwater trace element analyzer with applications in carbon storage

Abstract It is estimated that carbon emissions should reach net-zero by 2050 to meet important climate targets. Carbon capture is likely necessary to reach these targets, requiring a long-term storage solution such as geological carbon sequestration. However, as with any subsurface activity, leakage can occur, potentially impacting groundwater quality near the storage site. Rapid detection is essential to mitigate damage to this resource. Since CO 2 will acidify groundwater, the concentrations of acid soluble minerals and associated cations will increase. Thus, an in-situ, real-time element analysis system based on laser-induced breakdown spectroscopy (LIBS) is under development to monitor these elements. The system splits the traditional LIBS system into a miniature, all-optical sensor head built around a passively Q-switch laser fiber coupled to a control unit. Previous work has validated the LIBS technique for use at high pressure as well as the split system design. In this work, a fieldable prototype sensor is developed and tested in an onsite monitoring well where trace elements concentrations (approx. 0–3 ppm) were tracked over 20 days. These concentrations varied in response to local rainfall, diluting with increased rain, demonstrating the ability of a LIBS-based sensor to track trace elements under real-world conditions.

54 ENVIRONMENTAL SCIENCES↗

Contrasting the characteristics of atmospheric pressure plasma jets operated with single and double dielectric material: physicochemical characteristics and application to bacterial killing

Abstract This study reports an experimental comparison of two types of atmospheric pressure plasma jets in terms of their fundamental plasma characteristics and efficacy in bacterial sterilization. The plasma jets are fabricated by inserting a high voltage electrode inside a one-end closed (double DBD plasma jet) or both ends open (single DBD plasma jet) quartz tubes which are further enclosed inside a second quartz tube containing a ground electrode. Both plasma jets are operated in contact with water surface by using a unipolar pulsed DC power supply with helium as the working gas. Results from electrical and time-resolved imaging show that the single DBD configuration induces 3–4 times higher accumulation of charges onto the water surface with significantly faster propagation of plasma bullets. These results are accompanied by the higher discharge intensity as well as stronger emissions from short-lived reactive species which were analyzed through optical emission spectroscopy at the plasma-water interface. The rotational temperature for the single DBD configuration was observed to be higher making it unsafe for direct treatments of sensitive biological targets. These characteristics of the single DBD configuration result in the production of more than two times higher concentration of H 2 O 2 in plasma activated water. Shielding of the HV electrode reduces the plasma potential which in turn reduces the electric field & electron energy at the plasma-water interface. The reduced electric field for the double DBD configuration was lower by ≈463 Td than the single DBD configuration. The bactericidal efficacy of the two configurations of the plasma jets were tested against Escherichia coli , a well studied Gram-negative bacterium that can be commensal and pathogenic in human body. Our results demonstrate that although single DBD plasma jet result in stronger antibacterial effects, the double DBD configuration could be safer.

Physics↗

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗

Numerical simulations of colliding jets in an external wind: application to 3C 75

ABSTRACT The radio galaxy 3C 75 is remarkable because it contains a pair of radio-loud active galaxies, each of which produces a two-sided jet, with the jet beams appearing to collide and merge to the west of the galaxies. Motivated by 3C 75, we have conducted three-dimensional hydrodynamic simulations of jet collisions. We have extended previous studies by modelling the physical properties of the cluster atmosphere, including an external wind, and using realistic jet powers obtained from observational data. We are able to produce a morphology similar to that of 3C 75. The simulations imply that direct contact between the bulk jet flows on the west of the source is required to produce a morphology consistent with 3C 75. We quantify how the merging jets decelerate, how the wind deflects the jets and cocoons, the entrainment of intra-cluster material into the cocoons, the cocoon energetics, and how the jet interactions generate enstrophy. By comparing simulations of pairs of two-sided jets with those of single two-sided sources, we determine how the interaction between two bipolar jets changes their evolution. The unprecedented sensitivity and angular resolution of upcoming observatories will lead to the detection of many more complex sources at high redshift, where interacting jets are expected to be more numerous. The morphology of these complex sources can provide significant insight into the conditions in their environments.

Musoke, G.↗