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At least 271 records · Page 15

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DOE OSTI2020

Review: knots and other new topological effects in liquid crystals and colloids

Abstract Humankind has been obsessed with knots in religion, culture and daily life for millennia, while physicists like Gauss, Kelvin and Maxwell already involved them in models centuries ago. Nowadays, colloidal particles can be fabricated to have shapes of knots and links with arbitrary complexity. In liquid crystals, closed loops of singular vortex lines can be knotted by using colloidal particles and laser tweezers, as well as by confining nematic fluids into micrometer-sized droplets with complex topology. Knotted and linked colloidal particles induce knots and links of singular defects, which can be interlinked (or not) with colloidal particle knots, revealing the diversity of interactions between topologies of knotted fields and topologically nontrivial surfaces of colloidal objects. Even more diverse knotted structures emerge in nonsingular molecular alignment and magnetization fields in liquid crystals and colloidal ferromagnets. The topological solitons include hopfions, skyrmions, heliknotons, torons and other spatially localized continuous structures, which are classified based on homotopy theory, characterized by integer-valued topological invariants and often contain knotted or linked preimages, nonsingular regions of space corresponding to single points of the order parameter space. A zoo of topological solitons in liquid crystals, colloids and ferromagnets promises new breeds of information displays and a plethora of data storage, electro-optic and photonic applications. Their particle-like collective dynamics echoes coherent motions in active matter, ranging from crowds of people to schools of fish. This review discusses the state of the art in the field, as well as highlights recent developments and open questions in physics of knotted soft matter. We systematically overview knotted field configurations, the allowed transformations between them, their physical stability and how one can use one form of knotted fields to model, create and imprint other forms. The large variety of symmetries accessible to liquid crystals and colloids offer insights into stability, transformation and emergent dynamics of fully nonsingular and singular knotted fields of fundamental and applied importance. The common thread of this review is the ability to experimentally visualize these knots in real space. The review concludes with a discussion of how the studies of knots in liquid crystals and colloids can offer insights into topologically related structures in other branches of physics, with answers to many open questions, as well as how these experimentally observable knots hold a strong potential for providing new inspirations to the mathematical knot theory.

Physics↗

DOE OSTI2023

Spacetime foam: a review

More than 65 years ago, John Wheeler suggested that quantum uncertainties of the metric would be of order one at the Planck scale, leading to large fluctuations in spacetime geometry and topology, which he termed ‘spacetime foam.’ In this review I discuss various attempts to implement this idea and to test it, both theoretically and, to a lesser extent, observationally.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Searching for the QCD dark-matter axion

Proposed half a century ago, the quantum chromodynamics (QCD) axion explains the lack of charge and parity violation in the strong interactions and is a compelling candidate for cold dark matter. The last decade has seen the rapid improvement in the sensitivity and mass-range of axion experiments, as well as developments in theory regarding consequences of axion dark matter. In this review we cover the astrophysical searches and theoretical progress regarding the QCD axion. We then give a historical overview of axion searches, review the current status and future prospects of dark matter axion searches, and then discuss proposed dark matter axion techniques currently in development.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Overview of the recent experimental research on the J-TEXT tokamak

The J-TEXT capability is enhanced compared to two years ago with several upgrades of its diagnostics and the increase of electron cyclotron resonance heating (ECRH) power to 1 MW. With the application of electron cyclotron wave (ECW), the ECW assisted plasma startup is achieved; the tearing mode is suppressed; the toroidal injection of 300 kW ECW drives around 24 kA current; fast electrons are generated with toroidal injected ECW and the runaway current conversion efficiency increases with ECRH power. The mode coupling between 2/1 and 3/1 modes are extensively studied. The coupled 2/1 and 3/1 modes usually lead to major disruption. Their coupling can be either suppressed or avoided by external resonant magnetic perturbation fields and hence avoids the major disruption. It is also found that the 2/1 threshold of external field is significantly reduced by a pre-excited 3/1 mode, which can be either a locked island or an external kink mode. The disruption control is studied by developing prediction methods capable of cross tokamak application and by new mitigation methods, such as the biased electrode or electromagnetic pellet injector. The high-density operation and related disruptions are studied from various aspects. Approaching the density limit, the collapse of the edge shear layer is observed and such collapse can be prevented by applying edge biasing, leading to an increased density limit. The density limit is also observed to increase, if the plasma is operated in the poloidal divertor configuration or the plasma purity is increased by increasing the pre-filled gas pressure or ECRH power during the start-up phase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Cosmic Muon Veto for the mini-ICAL detector at IICHEP, Madurai

A 51-kiloton magnetised Iron Calorimeter (ICAL) detector, using Resistive Plate Chambers (RPCs) as active detector elements, aims to study atmospheric neutrinos. A prototype - 1/600 of the weight of ICAL, called mini-ICAL was installed in the INO transit campus at Madurai. A modest proof-of-principle cosmic muon veto detector of about 1 m × 1 m × 0.3 m dimensions was setup a few years ago, using scintillator paddles. The measured cosmic muon veto efficiency of 99.98% and simulation studies of muon-induced background events in the ICAL detector surrounded by an efficient veto detector were promising. This led to the idea of constructing a bigger cosmic muon veto around the mini-ICAL detector. Details of the design and construction of the detector including the electronics, trigger and DAQ systems planned will be briefly presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Performance of PMTs for the JSNS 2 experiment

The JSNS 2 (J-PARC Sterile Neutrino Search at J-PARC Spallation Neutron Source) experiment aims to search for neutrino oscillations over a 24 m short baseline at J-PARC. The JSNS 2 inner detector is filled with 17 tons of gadolinium-loaded liquid scintillator (LS) and both the intermediate γ-catcher and the optically separated outer veto are filled with un-loaded LS. Optical photons from scintillation are observed by 120 Photomultiplier Tubes (PMTs). A total of 130 PMTs for the JSNS 2 experiment were both donated by other experiments and purchased from Hamamatsu. Donated PMTs were purchased around 10 years ago, therefore JSNS 2 did pre-calibration of the PMTs including the purchased PMTs. 123 PMTs demonstrated acceptable performance for the JSNS 2 experiment, and 120 PMTs were installed in the detector.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

The design, construction, and commissioning of the KATRIN experiment

The KArlsruhe TRItium Neutrino (KATRIN) experiment, which aims to make a direct and model-independent determination of the absolute neutrino mass scale, is a complex experiment with many components. More than 15 years ago, we published a technical design report (TDR) to describe the hardware design and requirements to achieve our sensitivity goal of 0.2 eV at 90%C.L. on the neutrino mass. Since then there has been considerable progress, culminating in the publication of first neutrino mass results with the entire beamline operating. In this paper, we document the current state of all completed beamline components (as of the first neutrino mass measurement campaign), demonstrate our ability to reliably and stably control them over long times,and present details on their respective commissioning campaigns.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Simulation of hydropower at subcontinental to global scales: a state-of-the-art review

Abstract Hydroelectric power is playing a new and often expanded role in the world’s major power grids, offering low carbon generating capacity in industrializing, dam-building economies while providing reserve and flexibility to co-manage fledgling wind and solar resources in high income countries. Driven by river flows, conventional hydropower is exposed to the vagaries of weather and climate, motivating drought and climate change hydropower impact studies at large spatial scales. Here we review methods of climate-driven hydropower simulation at large spatial scales, specifically multi-basin regions to global. We identify four types of approach based on complexity of tools and richness of data applied to the problem. Since the earliest attempts to model climate-driven hydropower at continental scale almost two decades ago, the field has transitioned from one of scientific curiosity to practical application, with studies increasingly motivated by the need to inform power grid expansion planning and operation. As the hydrological and water management models used in large-scale hydropower studies become more sophisticated, new opportunities will emerge to study the impacts of changing hydropower on power system reliability and performance at large power grid scale. To grasp these opportunities, the water resources community must continue to enhance data and models for representing river flows and anthropogenic water use and management at subcontinental to global scales.

13 HYDRO ENERGY↗

DOE OSTI2020

Thermal and Electrical Properties of Isocyanate Derived Organic Aerogels for Cryogenic Insulation Applications

The use and storage of cryogens such as liquefied nitrogen, helium, hydrogen among others requires reliable and efficient thermal insulation systems. Passive insulation from high performance materials that are well-known for their inherent low thermal conductivity would reduce the overall costs involved in design, manufacture and maintenance of such systems. One such class of materials are referred to as aerogels. These materials are known for their low density, high mesoporosity, high surface areas, low thermal conductivity and high acoustic impedance. Aerogels were invented by S.S. Kistler in 1931 and the most common type are those made of silica. However, the inherent fragility of silica aerogels makes them hard to mass produce, and therefore applications have been limited. A major breakthrough was introduced by our team almost 20 years ago with the invention of polymer crosslinked silica aerogels. Those materials shifted attention to all-polymer aerogels that have overcome all fragility issues associated with their inorganic counterparts. This study focuses on such polymeric aerogels that can be mass produced as large monoliths while maintaining the low thermal conductivity of traditional silica aerogels over a wide temperature range. Manufacturing flexibility of polymeric aerogels allows fabrication of blocks and sheets that can be applied in various configurations to insulate cryogenic and superconducting devices. The thermal conductivity with 80 K and room temperature boundary are reported as well as other properties (electrical), that need to be considered when designing devices for cryogenic applications.

Churu, Gitogo↗

DOE OSTI2024

Infrastructure first principles for the Anthropocene

Abstract There appears to be a growing decoupling between the conditions that infrastructures were designed for and today’s rapidly changing environments. Infrastructures today are largely predicated on the technologies, goals, and governance structures from a century ago. While infrastructures continue to deliver untold value, there is growing evidence that these critical, basic, and lifeline systems appear ill-equipped to confront the volatility, uncertainty, accelerating conditions, and complexity that define them and their changing environments. Innovative and disruptive first principles are needed to guide infrastructures in the Anthropocene. Drawing from emerging infrastructure research and disciplines that appear better able to confront disruption and change, a novel set of first principles are identified: (1) Plan for complex conditions and surprise; (2) Recouple with agility and flexibility; (3) Govern for exploration and instability; (4) Build consensus as control decentralizes; (5) Restructure to engage with porous boundaries; and, (6) Cyberthreat planning is now mission critical. These principles should guide infrastructure planning recognizing the changing nature and increasingly obsolete boundaries that have defined engineered systems in the modern era.

Chester, Mikhail (ORCID:0000000293542102)↗

DOE OSTI2023

The tubulin structure, a quarter of a century later

This retrospective on the 25th anniversary of the publication of the first structure of tubulin is shaped by my own personal experiences rather than being a strict and complete historical account of the event. It is a reflection on how working in science felt many years ago, on the struggles and the joys of reaching for the high-hanging fruit, and, ultimately, on how relevant or not our personal scientific contributions are to the broader scientific community. Writing it brought back memories of my unique and sadly lost postdoctoral advisor Ken Downing, who dreamt of this structure and brought it to fruition against all odds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss)

Abstract Background and Aims New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. Methods We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. Key Results Using sliding-window population genetic analyses we find that differentiation is concentrated within ‘islands’ of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. Conclusions We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth’s climate rapidly changes.

58 GEOSCIENCES↗

DOE OSTI2025

Recent evolution of risk analyses in atomic bomb survivor studies: new methods and applications

Abstract Several decades ago a dramatic leap forward occurred in the development and application of statistical methods for modeling radiation risk at the Radiation Effects Research Foundation (RERF). Poisson regression analysis for grouped person-year cohort data and the linear excess relative risk model were introduced, and subsequently a devoted software system, Epicure® (https://www.hirosoft.com), was developed by researchers at RERF and at the U.S. National Cancer Institute. Numerous advancements in understanding radiation effects on humans were made possible with these methods, which are still the state-of-the-art for risk assessment at RERF and have remained part of the standard toolbox for radiation—and other environmental—epidemiological studies worldwide. Nevertheless, as our understanding of radiation risk has increased, so have the breadth and depth of questions that require answers based on emerging data that are not amenable to these conventional methods. This overview briefly recounts the conventional methods and then describes our recent diversification into the use or development of new statistical approaches to meet the challenges of burgeoning biological data and emerging mechanistic information. We briefly discuss the development and application of new methods, current and planned, that are part of the RERF Statistics Department’s role in supporting institution-wide research, especially in our collaborations involving the Life Span Study, Adult Health Study, and First-generation Offspring Clinical Study. Some approaches to modeling and assessing radiation risk with newer methods mentioned herein have already been published, while some are still in development or are only beginning at the proposal stage.

Oncology↗

DOE OSTI2024

Shared governance in the plant holobiont and implications for one health

Abstract The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Phage display and other peptide display technologies

ABSTRACT Phage display technology, which is based on the presentation of peptide sequences on the surface of bacteriophage virions, was developed over 30 years ago. Improvements in phage display systems have allowed us to employ this method in numerous fields of biotechnology, as diverse as immunological and biomedical applications, the formation of novel materials and many others. The importance of phage display platforms was recognized by awarding the Nobel Prize in 2018 ‘for the phage display of peptides and antibodies’. In contrast to many review articles concerning specific applications of phage display systems published in recent years, we present an overview of this technology, including a comparison of various display systems, their advantages and disadvantages, and examples of applications in various fields of science, medicine and the broad sense of biotechnology. Other peptide display technologies, which employ bacterial, yeast and mammalian cells, as well as eukaryotic viruses and cell-free systems, are also discussed. These powerful methods are still being developed and improved; thus, novel sophisticated tools based on phage display and other peptide display systems are constantly emerging, and new opportunities to solve various scientific, medical and technological problems can be expected to become available in the near future.

Jaroszewicz, Weronika (ORCID:0000000302948682)↗

DOE OSTI2021

Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea

Abstract Neonectria faginata and Neonectria coccinea are the causal agents of the insect-fungus disease complex known as beech bark disease (BBD), known to cause mortality in beech forest stands in North America and Europe. These fungal species have been the focus of extensive ecological and disease management studies, yet less progress has been made toward generating genomic resources for both micro- and macro-evolutionary studies. Here, we report a 42.1 and 42.7 mb highly contiguous genome assemblies of N. faginata and N. coccinea, respectively, obtained using Illumina technology. These species share similar gene number counts (12,941 and 12,991) and percentages of predicted genes with assigned functional categories (64 and 65%). Approximately 32% of the predicted proteomes of both species are homologous to proteins involved in pathogenicity, yet N. coccinea shows a higher number of predicted mitogen-activated protein kinase genes, virulence determinants possibly contributing to differences in disease severity between N. faginata and N. coccinea. A wide range of genes encoding for carbohydrate-active enzymes capable of degradation of complex plant polysaccharides and a small number of predicted secretory effector proteins, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 genes were also found. This arsenal of enzymes and effectors correlates with, and reflects, the hemibiotrophic lifestyle of these two fungal pathogens. Phylogenomic analysis and timetree estimations indicated that the N. faginata and N. coccinea species divergence may have occurred at ∼4.1 million years ago. Differences were also observed in the annotated mitochondrial genomes as they were found to be 81.7 kb (N. faginata) and 43.2 kb (N. coccinea) in size. The mitochondrial DNA expansion observed in N. faginata is attributed to the invasion of introns into diverse intra- and intergenic locations. These first draft genomes of N. faginata and N. coccinea serve as valuable tools to increase our understanding of basic genetics, evolutionary mechanisms and molecular physiology of these two nectriaceous plant pathogenic species.

Salgado-Salazar, Catalina↗

DOE OSTI2023

Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant

Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.

(sub)stoichiometric shifting↗

DOE OSTI2020

Rapid Shifts in the Temperature Dependence of Locomotor Performance in an Invasive Frog, Xenopus laevis , Implications for Conservation

Abstract Temperature is a critical abiotic factor impacting all aspects of the biology of organisms, especially in ectotherms. As such, it is an important determinant of the potential invasive ability of organisms and may limit population expansion unless organisms can physiologically respond to changes in temperature either through plasticity or by adapting to their novel environment. Here, we studied the African clawed frog, Xenopus laevis, which has become invasive on a global scale. We compared adults from an invasive population of western France with individuals from two populations in the native range in South Africa. We measured the thermal dependence of locomotor performance in adults given its relevance to dispersal, predator escape, and prey capture. Our results show significant differences in the limits of the 80% performance breadth interval for endurance with the French population showing a left shift in its limits congruent with the colder climate experienced in France. The French invasive population was introduced only about 40 years ago suggesting a rapid shift in the thermal physiology. Given that all individuals were acclimated under laboratory conditions at 23°C for 2 months this suggests that the invasive frogs have adapted to their new environment. These data may allow the refinement of physiologically informed species distribution models permitting better estimates of future ranges at risk of invasion.

Araspin, Laurie↗