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DOE OSTI2025

Visolis Microbial Chemical Intermediate Library Screening (CRADA Final Report)

Visolis is developing a commercial process for the bioproduction of a chemical intermediate, towards the derivative production of a portfolio of bio-based chemicals with large application potential, from drop-in commodity chemicals, to innovative specialty chemical offerings, to materials for multiple end markets and industries, which will ultimately benefit consumers and the public. Visolis already has several variants of a microbe that produce the chemical intermediate at distinct levels (i.e. high, medium, and low). They are currently pursuing transcriptomics analysis for some of these strains, towards a better understanding of the biology behind what makes certain strains perform better than others. There exist genome-scale library approaches for the microbe that could be used to screen gene disruption, overexpression, or repression candidates for perturbations to the production of the chemical intermediate. These approaches often reveal opportunities for further production improvement that are not otherwise accessible using hypothesis-driven metabolic engineering approaches. However, Visolis, while it could generate or procure such genome-scale libraries, does not have the automated strain engineering workflows required to screen thousands of variants, obtaining a production phenotype and a genotype for each. The purpose of this collaboration is to use LBNL and SNL capabilities to enable Visolis to effectively screen thousands of genome-scale library strain variants for phenotype/genotype relationships that will complement Visolis’ transcriptomic investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Theoretical power-law relationship between permeability and formation factor

Permeability k and formation factor F are important petrophysical properties that have broad applications to reservoir engineering. Although well-log analysis has advanced reservoir characterizations, direct measurement of k is still not available. Accordingly, resistivity logs and more particularly formation factor have been frequently used to estimate k. In this study, we present a theoretical framework to relate k to F. We use power-law scaling from continuum percolation theory to develop a theoretic relationship between k and F, which is similar in form to a published power-law equation with empirical coefficients. Our result gives a physical interpretation to this empirical relationship. We also compare power-law scaling laws from percolation theory with data derived from experimental measurements and numerical simulations in the literature. Finally, using the Curve Fitting toolbox of MATLAB, the parameters of the power-law equations are determined, and the significance of the non-universal power laws are discussed.

42 ENGINEERING↗

DOE OSTI2021

A genome-scale phylogeny of the kingdom Fungi

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ~85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Finally, our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Towards the scale-up production of cellulose nanocomposites using melt processing: A critical review on structure-processing-property relationships

Cellulose nanomaterials (CNMs) naturally exist in plant biomass. The success of extraction of CNMs opened up a new era of using plant biomass for innovative industrial applications. Because CNMs are abundant, renewable, biodegradable, transparent, light weight and low in cost, they are ideal materials for large volume applications such as packaging, automotive, building and infrastructure. In many potential application areas, CNM-enable products appear in a composite form, mostly polymer composites. Additionally, the industrial-scale manufacturing of CNM/thermoplastic composites remains as a set of unsolved problems for academia and industry. A prime challenge in applications is the nanoscale dispersion of CNMs in thermoplastic matrices during melt processing. Both bench-scale and pilot-scale studies have been conducted to solve the dispersion issue of CNMs. In this article, research related to the dispersion of CNMs in thermoplastic matrices during melt processing were critically reviewed. All research papers were classified into three groups: chemically-aided dispersion, physically-aided dispersion and mechanically-aided dispersion. Numerous factors affect the CNM dispersion and the mechanical performance of its nanocomposites. There are material-related factors, including CNM types and forms, polymer matrices, surface modification, coupling agents, etc. Furthermore, extrusion processing parameters also play a significant role, covering screw rotation speed, extrusion barrel temperature settings and screw design. In addition, the material-related factors interact with the processing-related factors. Understanding all factors and their interactions are important for moving CNM nanocomposites research a step further towards industrial-relevant production, which is the final ambitious goal of this manuscript.

42 ENGINEERING↗

DOE OSTI2023

Observational study of relationships between entrainment rate, homogeneity of mixing, and cloud droplet relative dispersion

The entrainment–mixing process is key to the cloud’s dynamical and microphysical processes. However, to the best of our knowledge, no study has quantitatively linked entrainment rate and homogeneity of mixing. Additionally, their combined effects on cloud droplet relative dispersion and physical mechanisms are even more unclear. This study analyzed the aircraft measurements of cumulus clouds collected in the Holistic Interactions of Shallow Clouds, Aerosols, and Land-Ecosystems field campaign to identify these relationships. The relationship between the entrainment rate and homogeneous mixing degree was found to be moderately positive, and the underlying mechanisms related to mixing and evaporation time scales and environmental relative humidity were explored. The relationship between relative dispersion and entrainment rate changes from positive to negative with increasing entrainment rate, depending on the dominance of evaporation of large or small droplets. The relative dispersion first increases and then decreases with increasing homogeneous mixing degree, validating the results of previous model simulations. Further, the results shed new light on understanding the interactions between cloud microphysics and cloud dynamics through turbulent entrainment and mixing processes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Interactions Between Clouds and Wind-Driven Surface Heat Exchanges over Land

Earth system model experiments show that increasing horizontal resolution fundamentally alters the simulated soil-moisture-precipitation feedback. Kilometer-scale simulations often produce weaker or even negative feedback compared to coarse-resolution models. A key difference of kilometer-scale models is that they resolve mesoscale secondary circulations, including boundary layer horizontal rolls and cellular structures, in addition to cold pools and downdrafts associated with convective precipitation. However, because the relevant processes occur on yet-smaller scales, these circulations are often poorly resolved. This project demonstrated that boundary layer secondary circulations significantly affect surface heat exchanges and wind gusts, and that current model parameterizations can misrepresent these processes at kilometer-scale resolution. Using DOE Atmospheric Radiation Measurement (ARM) observations and targeted experiments with the DOE Energy Exascale Earth System Model (E3SM), we identified physically unrealistic wind gust and surface flux responses to secondary circulations, diagnosed a systematic overestimation of wind shear in convective cold pools, and uncovered a multivariate relationship between land surface fluxes and the scales of updrafts that form shallow cumulus clouds. These findings provide observation-based recommendations for improving parameterizations of surface fluxes and wind gusts in high-resolution Earth system models, thereby reducing uncertainty in convective storm prediction and land-atmosphere feedbacks.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Probing the mesoscopic size limit of quantum anomalous Hall insulators

The inelastic scattering length (L s ) is a length scale of fundamental importance in condensed matters due to the relationship between inelastic scattering and quantum dephasing. In quantum anomalous Hall (QAH) materials, the mesoscopic length scale L s plays an instrumental role in determining transport properties. Here we examine L s in three regimes of the QAH system with distinct transport behaviors: the QAH, quantum critical, and insulating regimes. Although the resistance changes by five orders of magnitude when tuning between these distinct electronic phases, scaling analyses indicate a universal L s among all regimes. Finally, mesoscopic scaled devices with sizes on the order of L s were fabricated, enabling the direct detection of the value of L s in QAH samples. Our results unveil the fundamental length scale that governs the transport behavior of QAH materials.

42 ENGINEERING↗

DOE OSTI2026

Sensing Plant Photosynthesis Using Solar-Induced Chlorophyll Fluorescence: From Chloroplasts to the Globe

Photosynthesis is the fundamental biological process that introduced oxygen into Earth's atmosphere and continues to power life, from the earliest single-celled organisms to entire global ecosystems. Yet, measuring photosynthesis across scales has been challenging because traditional techniques have not transcended scales. The emergence of remote-sensing techniques to measure solar-induced chlorophyll fluorescence (SIF) provides a unique approach to estimate photosynthesis across spatiotemporal scales, representing a new age for optical remote sensing to study photosynthesis and shaping the decades of satellite SIF research. Here, focusing on spatiotemporal scales, we review the mechanisms that drive the relationship between SIF and photosynthesis. Remotely sensed SIF is modulated by biological drivers, environmental drivers, the interaction between biological and environmental drivers, and the viewing geometry. Studying fluorescence at small scales provides the ecophysiological understanding needed to disentangle the biological and environmental drivers of SIF at larger scales. Leveraging progress in satellite SIF, future research should focus on cross-scale mechanistic understanding of the drivers of SIF and using SIF as a metric for plant function beyond photosynthesis.

ecophysiology↗

DOE OSTI2021

Detecting forest response to droughts with global observations of vegetation water content

Droughts in a warming climate have become more common and more extreme, making understanding forest responses to water stress increasingly pressing. Analysis of water stress in trees has long focused on water potential in xylem and leaves, which influences stomatal closure and water flow through the soil-plant-atmosphere continuum. At the same time, changes of vegetation water content (VWC) are linked to a range of tree responses, including fluxes of water and carbon, mortality, flammability, and more. Unlike water potential, which requires demanding in situ measurements, VWC can be retrieved from remote sensing measurements, particularly at microwave frequencies using radar and radiometry. Here, we highlight key frontiers through which VWC has the potential to significantly increase our understanding of forest responses to water stress. To validate remote sensing observations of VWC at landscape scale and to better relate them to data assimilation model parameters, we introduce an ecosystem-scale analogue of the pressure-volume curve, the non-linear relationship between 44 average leaf or branch water potential and water content commonly used in plant hydraulics. The 45 sources of variability in these ecosystem-scale pressure-volume curves and their relationship to 46 forest response to water stress are discussed. We further show to what extent diel, seasonal, and 47 decadal dynamics of VWC reflect variations in different processes relating the tree response to 48 water stress. VWC can also be used for inferring belowground conditions – which are difficult to 49 impossible to observe directly. Lastly, we discuss how a dedicated geostationary spaceborne 50 observational system for VWC, when combined with existing datasets, can capture diel and 51 seasonal water dynamics to advance the science and applications of global forest vulnerability to 52 future droughts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

The impact of the fiducial cosmology assumption on BAO distance scale measurements

ABSTRACT Standard analysis pipelines for measurements of Baryon Acoustic Oscillations (BAO) in galaxy surveys make use of a fiducial cosmological model to guide the data compression required to transform from observed redshifts and angles to the measured angular and radial BAO peak positions. In order to remove any dependence on the fiducial cosmology from the results, all models compared to the data should mimic the compression and its dependence on the fiducial model. In practice, approximations are made when testing models: (1) There is assumed to be no residual dependence on the fiducial cosmology after reconstruction, (2) differences in the distance–redshift relationship are assumed to match a linear scaling, and (3) differences in clustering between true and fiducial models are assumed to be removed by the free parameters used to null the non-BAO signal. We test these approximations using the current standard measurement procedure with a set of halo catalogues from the aemulus suite of N-body simulations, which span a range of wCDM cosmological models. We focus on reconstruction of the primordial BAO and locating the BAO. For the range of wCDM cosmologies covered by the aemulus suite, we find no evidence for systematic errors in the measured BAO shift parameters α∥ and α⊥ to $\lt 0.1\%$. However, the measured errors $\sigma _{\alpha _{\parallel }}$ and $\sigma _{\alpha _{\bot }}$ show a notable absolute increase by up to +0.001 and +0.002, respectively, in the case that the fiducial cosmology does not match the truth. These effects on the inferred BAO scale will be important, given the precision of measurements expected from future surveys including DESI, Euclid, and WFIRST.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Relationships between summertime surface albedo and melt pond fraction in the central Arctic Ocean: The aggregate scale of albedo obtained on the MOSAiC floe

As part of the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC), the HELiX uncrewed aircraft system (UAS) was deployed over the sea ice in the central Arctic Ocean during summer 2020. Albedo measurements were obtained with stabilized pyranometers, and melt pond fraction was calculated from orthomosaic imagery from a surface-imaging multispectral camera. This study analyzed HELiX flight data to provide insights on the temporal and spatial evolution of albedo and melt pond fraction of the MOSAiC floe during the melt season as it drifted south through Fram Strait. The surface albedo distributions showed peak values changing from high albedo (0.55–0.6) to lower values (0.3) as the season advanced. Inspired by methods developed for satellite data, an algorithm was established to retrieve melt pond fraction from the orthomosaic images. We demonstrate that the near-surface observations of melt pond fraction were highly dependent on sample area, offering insight into the influence of subgrid scale features and spatial heterogeneity in satellite observations. Vertical observations conducted with the HELiX were used to quantify the influence of melt pond scales on observed surface albedo as a function of sensor footprint. These scaling results were used to link surface-based measurements collected during MOSAiC to broader-scale satellite data to investigate the influence of surface features on observed albedo. Albedo values blend underlying features within the sensor footprint, as determined by the melt pond size and concentration. This study framed the downscaling (upscaling) problem related to the airborne (surface) observations of surface albedo across a variety of spatial scales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Integrating in situ environmental covariates in an American lobster catch model to improve impact assessment

The installation and operation of floating offshore wind power is an integral component of societal transition to renewable energy generation where fixed bottom offshore wind is not possible. However, it will cause unique ecosystem changes. To disentangle the effects of offshore wind installations from the concurrent effects of climate change and the fishing practices on commercially significant resources, we must develop detailed characterizations of the resources before development occurs. In the Gulf of Maine, American lobster is the most commercially and culturally important fishery. At the time of writing, this is the largest fishery by value in North America. Our understanding of baseline localized parameters (such as catch per trap at the spatial scale of individual turbines) should be informed by relationships to environmental, biological, and survey-specific functional drivers of catch. A more mechanistic understanding of catch will allow for strategic adjustments to Post- Deployment fishery responses and ultimately, the development of research- and commercial-scale floating offshore wind development. Here, we used survey data from the New England Aqua Ventus Pre-Construction Commercial Trapping Survey to develop Generalized Additive Models describing seasonal catch per trap for legal and sublegal lobsters. We found fall catch to be nearly twice that of spring. Bottom temperature dynamics could be used to predict catch, and the Fall survey was associated with a warmer temperature regime. By using analytical tools that incorporate environmental heterogeneity, we developed monitoring methods from preconstruction baseline data that will be applicable over the post-construction operating period of an offshore wind farm.

BACI↗

DOE OSTI2025

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Dual X-ray computed tomography-aided classification of melt pool boundaries and flaws in crept additively manufactured parts

In metal additive manufacturing (AM), understanding the process-structure-performance relationships requires a combination of multi-scale characterization techniques that allows for the measurement of the melt pool shape and boundary and classifying various defects and flaws in the AM parts. Such approaches can be destructive, only 2D in nature, or have a small field of view and can be complex to co-register and analyze. Here, in this work, we present a non-destructive 3D inspection technique that employs dual-energy X-ray computed tomography (XCT) along with a model-based iterative reconstruction (MBIR) and a new segmentation algorithm. The proposed approach and algorithm are not only capable of classifying and quantifying flaws such as pores, cracks, and inclusions, but they also allow for the extraction of microstructural features such as melt pool boundaries (MPB) and melt pool regions (MPR), that can help understand process-structure-performance relationships for alloys under study. As an exemplar application, we employed the method for characterization of an additively manufactured aluminum alloy crept under tensile stress at 300 °C for 1064 h. Our results demonstrate high quality segmentation and classification of various flaws and MPB and MPR, for the first time, using 3D X-ray CT inspection. The delineated MPB and MPR in the crept samples reveal the preferential growth paths of cracks that formed during creep deformation. The technique was used for successfully quantifying the characteristics (number of defects, their density, volume fraction, etc.) of the manufacturing-induced pores and creep-induced cracks, which is necessary to better understand the creep failure mechanisms of the material.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Seasonal changes in GPP/SIF ratios and their climatic determinants across the Northern Hemisphere

Satellite-derived sun-induced chlorophyll fluorescence (SIF) has been increasingly used for estimating gross primary production (GPP). However, the relationship between SIF and GPP has not been well defined, impeding the translation of satellite observed SIF to GPP. Previous studies have generally assumed a linear relationship between SIF and GPP at daily and longer time scales, but support for this assumption is lacking. Here, we used the GPP/SIF ratio to investigate seasonal variations in the relationship between SIF and GPP over the Northern Hemisphere (NH). Based on multiple SIF products and MODIS and FLUXCOM GPP data, we found strong seasonal hump-shaped patterns for the GPP/SIF ratio over northern latitudes, with higher values in the summer than in the spring or autumn. This hump-shaped GPP/SIF seasonal variation was confirmed by examining different SIF products and was evident for most vegetation types except evergreen broadleaf forests. The seasonal amplitude of the GPP/SIF ratio decreased from the boreal/arctic region to drylands and the tropics. For most of the NH, the lowest GPP/SIF values occurred in October or September, while the maximum GPP/SIF values were evident in June and July. The most pronounced seasonal amplitude of GPP/SIF occurred in intermediate temperature and precipitation ranges. GPP/SIF was positively related to temperature in the early and late parts of the growing season, but not during the peak growing months. These shifting relationships between temperature and GPP/SIF across different months appeared to play a key role in the seasonal dynamics of GPP/SIF. Several mechanisms may explain the patterns we observed, and future research encompassing a broad range of climate and vegetation settings is needed to improve our understanding of the spatial and temporal relationships between SIF and GPP. Nonetheless, the strong seasonal variation in GPP/SIF we identified highlights the importance of incorporating this behavior into SIF-based GPP estimations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Galaxy Zoo DESI: large-scale bars as a secular mechanism for triggering AGNs

ABSTRACT Despite the evidence that supermassive black holes (SMBHs) co-evolve with their host galaxy, and that most of the growth of these SMBHs occurs via merger-free processes, the underlying mechanisms which drive this secular co-evolution are poorly understood. We investigate the role that both strong and weak large-scale galactic bars play in mediating this relationship. Using 48 871 disc galaxies in a volume-limited sample from Galaxy Zoo DESI, we analyse the active galactic nucleus (AGN) fraction in strongly barred, weakly barred, and unbarred galaxies up to $z = 0.1$ over a range of stellar masses and colours. After controlling for stellar mass and colour, we find that the optically selected AGN fraction is $31.6 \pm 0.9$ per cent in strongly barred galaxies, $23.3 \pm 0.8$ per cent in weakly barred galaxies, and $14.2 \pm 0.6$ per cent in unbarred disc galaxies. These are highly statistically robust results, strengthening the tantalizing results in earlier works. Strongly barred galaxies have a higher fraction of AGNs than weakly barred galaxies, which in turn have a higher fraction than unbarred galaxies. Thus, while bars are not required in order to grow an SMBH in a disc galaxy, large-scale galactic bars appear to facilitate AGN fuelling, and the presence of a strong bar makes a disc galaxy more than twice as likely to host an AGN than an unbarred galaxy at all galaxy stellar masses and colours.

Astronomy & Astrophysics↗

DOE OSTI2021

On the use of air temperature and precipitation as surrogate predictors in soil respiration modelling

Soil respiration (R S ), the soil-to-atmosphere CO 2 flux that is a major component of the global carbon cycle, is strongly influenced by local soil temperature (T soil ) and water content (SWC). Regional to global-scale R S modelling thus requires this information at local scales, but few high-quality, wall-to-wall (global) T soil and SWC data exist. As a result, such modelling efforts commonly use air temperature (T air ) and monthly precipitation (P m ) as surrogate predictors, but their site-scale accuracy and potential bias are unknown. In this report we used monthly data from 880 sites across a wide variety of different environmental conditions (i.e., climate, ecosystem type, elevation, vegetation leaf habit and drainage conditions) to determine the suitability of T air as a surrogate for T soil , and data from 507 sites to examine the suitability of P m as a surrogate for SWC. Site-specific linear and second-order exponential non-linear models were compared using model evaluation metrics (i.e., slope, p-value of slope, root mean square error [RMSE], index of agreement and model efficiency). We found that T soil and T air are highly correlated and explain similar R S variability. In contrast, P m is not a good surrogate for SWC, even though P m explains a similar amount of R S variability to SWC. The wide variability in the site-specific relationships between R S and SWC means that no single relationship can be used for large-scale modelling. The results from this study support the use of T air in continental-to-global scale R S models, and highlight the urgent need for continental-to-global scale SWC datasets for the modelling and evaluation of future soil carbon dynamics under global climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Kinetic simulations underestimate the effects of waves during magnetic reconnection

Collisionless plasma systems are often studied using fully kinetic simulations, where protons and electrons are treated as particles. Due to their computational expense, it is necessary to reduce the ion-to-electron mass ratio $m_i/m_e$ or the ratio between plasma and cyclotron frequencies in simulations of large systems. In this Letter we show that when electron-scale waves are present in larger-scale systems, numerical parameters affect their amplitudes and effects on the larger system. Using lower-hybrid drift waves during magnetic reconnection as an example, we find that the ratio between the wave electric field and the reconnection electric field scales as $\sqrt{m_i/m_e}$, while the phase relationship is also affected. The combination of these effects means that the anomalous drag that contributes to momentum balance in the reconnection region can be underestimated by an order of magnitude. The results are relevant to the coupling of electron-scale waves to ion-scale reconnection regions, and other systems such as collisionless shocks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗