323 research outputs found

    Selected problems of materials science. Vol. 2. Nano-dielectrics metals in electronics. Mеtamaterials. Multiferroics. Nano-magnetics

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    The textbook examines physical foundations and practical application of current electronics materials. Modern theories are presented, more important experimental data and specifications of basic materials necessary for practical application are given. Contemporary research in the field of microelectronics and nanophysics is taken into account, while special attention is paid to the influence of the internal structure on the physical properties of materials and the prospects for their use. English-language lectures and other classes on the subject of the book are held at Igor Sikorsky Kyiv Polytechnic Institute at the departments of “Applied Physics” and “Microelectronics” on the subject of materials science, which is necessary for students of higher educational institutions when performing scientific works. For master’s degree applicants in specialty 105 “Applied physics and nanomaterials”.Розглянуто фізичні основи та практичне застосування актуальних матеріалів електроніки. Подано сучасні теорії, наведено найважливіші експериментальні дані та специфікації основних матеріалів, які потрібні для практичного застосування. Враховано сучасні дослідження у галузі мікроелектроніки та нанофізики, при цьому особливу увагу приділено впливу внутрішньої структури на фізичні властивості матеріалів і на перспективи їх використання. Англомовні лекції та інші види занять за тематикою книги проводяться в КПІ ім. Ігоря Сікорського на кафедрах «Прикладна фізика» та «Мікро-електроніка» за напрямом матеріалознавство, що необхідно студентам вищих навчальних закладів при виконанні наукових робіт. Для здобувачів магістратури за спеціальністю 105 «Прикладна фізика та наноматеріали»

    Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids

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    Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T=3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose 3D geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case, and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures

    Cryo-Electron Microscopy to Investigate Molecular Dynamics and Conformational Changes in Protein Complexes

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    Stress can be considered as one of the most fundamental aspects in life, and all living organisms are constantly exposed to a variety of different stress situations. Thus, efficient stress sensing and reaction mechanisms are crucial for their survival. Stress response mechanisms are as diverse as the causative stimuli and oftentimes cross-linked forming a versatile reaction network, to ensure the cells’ survival under critical situations. Notably, stress response mechanisms play a major role in pathogenicity, virulence and disease. Pathogenic Bacteria are permanently facing environmental pressure originating from the host’s defense systems or drug treatments, while mutations in eukaryotic stress response systems have been shown to cause a large number of severe human diseases such as diabetes, cancer or Parkinson’s and Alzheimer’s disease. A profound molecular knowledge on the respective mechanisms is thus the inevitable prerequisite towards a global understanding of this fundamental aspect of life, paving the way for the development of new drugs or therapeutic approaches. Within this thesis, various aspects of stress response mechanisms in three different systems were investigated using state-of-the-art electron microscopy techniques. First, I set out to solve the structure of the Vibrio vulnificus stressosome complex, a key player in the bacterial environmental stress response. Currently, there is no structural data available for any gram-negative stressosome. A medium-resolution cryo-electron microscopy (cryo-EM) structure of the minimal complex could be obtained, which features an exceptional symmetry break originating from its unique, regulatory stoichiometry. Based on the structural data, it was possible to propose an activation mechanism and to pinpoint a number of significant differences in comparison to gram-positive stressosome complexes. Undoubtedly, the structure contributes a major piece of information necessary to understand stress sensing and signal transduction in this human pathogen. This study was complemented by a number of physiological and phylogenetic experiments contributed by our co-workers, and published recently (VIII. PUBLICATION 1). The second project focused on the gram-positive soil bacterium Corynebacterium glutamicum, a prime model organism for investigations of the bacterial osmostress response. Sensing of hyper-osmotic stress and regulation of the respective stress response in C. glutamicum are simultaneously performed by BetP, a conformationally asymmetric-trimeric secondary active transporter able to import the compatible solute betaine. Two stimuli are identified to initiate the full osmostress response in BetP, namely an elevated cytoplasmic K+ concentration and a loosely defined ‘membrane stimulus’. Despite the availability of functional data on BetP regulation, structural information especially of the down-regulated state and the subsequent transition events are absent. Using single particle cryo-EM analysis, I was able to provide high-resolution structures of the down-regulated and a transition state, which elucidated a number of important structural features not described so far. It could be shown that down-regulated BetP adopts a symmetric arrangement stabilized by antight cytoplasmic interaction network of the sensory domain, further strengthened by Cardiolipin molecules located at regulatory lipid binding sites. These constraints are released upon stress sensing, as demonstrated by fourier transform infrared (FTIR) spectroscopy and molecular dynamics simulation (MD) data contributed by our co-workers, resulting in the well-established, asymmetric-trimeric structures previously known. The wealth of new data on the down-regulated state allowed to propose a detailed regulation mechanism and to further sharpen the previously vague picture of the membrane stimulus. The data are summarized and presented in IX. PREPRINT 1. A third topic of this thesis was the three dimensional investigation via dual-axis scanning transmission electron microscopy (STEM) tomography of crystalloid-ER structures we identified before in human embryonic kidney (HEK) cells upon over-expression of polycystin-2 (PC-2). In this study presented in X. MANUSCRIPT 1, I was further able to proof the presence of ER whorls, and to obtain high-resolution three-dimensional (3D) reconstructions of the two different ER morphotypes. These data provided unmatched insights into the cellular ER interaction partners and clearly demonstrated the dynamic nature of the organelle even under stress situations. A detailed discussion of the identified morphological features in their respective cellular context finally allowed for the description of the organellar membrane architecture at a high level of detail. Lastly, the discussion addresses the electron microscopy techniques and instruments used and contains an outlook on further perspectives for the projects. Overall, this thesis yielded intriguing mechanistic insights into the versatile bacterial and eukaryotic stress response mechanisms, reflecting their manifold nature ultimately converging to a common outcome

    Writing Science for Diverse Audiences: A Corpus-based Discourse Analysis of the Language of Science News and Research Articles

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    Despite the historic prevalence of the research article (RA) genre in the English for Academic Purposes (ESP) literature, work examining the ways that academic research is communicated with broader audiences—sometimes referred to as ‘popularization’ or ‘popular science’ (Gotti, 2014)—is on the rise. Scholars from diverse fields have shown interest in contexts of popular science in part because they represent a meeting point between the general public and academia. However, much of the research examining the language of popular science has adopted a rhetorical rather than linguistic lens (Pérez-Llantada, 2021). In addition, the recent interest in digital multi-modal genres (e.g., Luzón, 2023; Xia, 2023) has left the linguistic features of written discourse comparatively under-examined, and studies adopting corpus approaches have often included texts which are out-of-date, few in number, or under-described with regard to their place under the umbrella of popular science. This dissertation applies a mixed methods design to a new corpus representative of one variety of popular science writing, namely online science news articles (SNAs). It uses computer programs to compare the linguistic profiles of 400 SNAs with a matching corpus of the 400 RAs. Specifically, this dissertation investigates features of the verb phrase, namely short verb phrase variation, long verb phrase variation, and attribution of knowledge via reporting clauses. These features offer a useful contrast to the current noun-focused approach to grammatical complexity research (see Lan, Liu, & Staples, 2019). To inform interpretation of corpus findings, discourse- based interviews (Conrad, 2014) with seven SNA writers were also employed. Findings from the linguistic analyses, analyses of the registers’ situational characteristics, and informant interviews highlight the many differences between the registers, differences motivated especially by characteristics of audience, textual layout, and purpose. SNAs are short texts which function to inform and entertain an audience of mixed expertise. As a result, they utilize more verbs overall, as well as features of short and long verb phrases which allow writers to report research activities as stories involving researchers, their beliefs, and their words. Implications relating to contexts of science communication and pedagogical applications are discussed

    CERNAS: Current Evolution and Research Novelty in Agricultural Sustainability

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    Climate changes pose overwhelming impacts on primary production and, consequently, on agricultural and animal farming. Additionally, at present, agriculture still depends strongly on fossil fuels both for energy and production factors ,such as synthetized inorganic fertilizers and harmful chemicals such as pesticides. The need to feed the growing world population poses many challenges. The need to reduce environmental impacts to a minimum, maintain healthy ecosystems, and improve soil microbiota are central to ensuring a promising future for coming generations. Livestock production under cover crop systems helps to alleviate compaction so that oxygen and water can sufficiently flow in the soil, add organic matter, and help hold soil in place, reducing crusting and protecting against erosion. The use of organic plant production practices allied to the control of substances used in agriculture also decisively contributes to alleviating the pressure on ecosystems. Some of the goals of this new decade are to use enhanced sustainable production methodologies to improve the input/output ratios of primary production, reduce environmental impacts, and rely on new innovative technologies. This reprint addresses original studies and reviews focused on the current evolution and research novelty in agricultural sustainability. New developments are discussed on issues related to quality of soil, natural fertilizers, or the sustainable use of land and water. Also, crop protection techniques are pivotal for sustainable food production under the challenges of the Sustainable Development Goals of the United Nations, allied to innovative weed control methodologies as a way to reduce the utilization of pesticides. The role of precision and smart agriculture is becoming more pertinent as communication technologies improve at a rapid rate. Waste management, reuse of agro-industrial residues, extension of shelf life, and use of new technologies are ways to reduce food waste, all contributing to higher sustainability in food supply chains, leading to a more rational use of natural resources. The unquestionable role of bees as pollinators and contributors to biodiversity is adjacent to characterizing beekeeping activities, which in turn contributes, together with the valorization of endemic varieties of plant foods, to the development of local communities. Finally, the short circuits and local food markets have a decisive role in the preservation and enhancement of rural economies.info:eu-repo/semantics/publishedVersio

    Understanding the Structure-Function Relationship in Peptide-Enabled High Entropy Alloy Nanocatalysts

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    The structural complexity in high entropy alloy nanocatalysts (HEAs), afforded by the homogeneous mixing of five or more elements, has resulted in a limited understanding about the origin of their promising electrocatalytic properties. This thesis investigates the structure-function relationship in HEAs using advanced material characterization techniques. At first, a methodology for resolving the atomic-scale structure of peptide-enabled HEAs was developed using high-energy X-ray diffraction (HE-XRD) coupled with atomic pair distribution function (PDF) and reverse Monte Carlo (RMC) simulations, yielding structure models over the length scale of HEAs. Coordination analysis of the structure models revealed a multifunctional interplay of geometric and electronic attributes of surface atoms in HEAs that was responsible for the catalytic activity enhancement during the methanol electrooxidation reaction. Using the methodology for resolving the atomic scale structure of HEAs and peptide sequence engineering, the structure-function relationship of model PtPdAuCoSn HEAs during ethanol electrooxidation reaction (EOR) was studied. Compositional analysis of the PtPdAuCoSn HEA structure models revealed distinct miscibility characteristics that were attributed to the unique biotic-abiotic interactions. Analysis of the structure models identified the rapid dehydrogenation of CH3CHO intermediate into CH3COads in an optimized adsorption configuration as the contributing factor for the high selectivity towards CH3COO- in PtPdAuCoSn HEAs. Armed with these insights, a study was designed for understanding the effect of changing the concentration of Pt in the structure-function relationship of PtPdAuCoSn HEAs using spatiotemporal structural insights from in-situ PDF. The structure models demonstrated a degree of metastability as a function of their corresponding configurational entropy. Analysis of the structure models revealed that high selectivity towards CH3COO- in PtPdAuCoSn HEAs during EOR originates from the enhanced distribution of Pd and Co surface atoms. In summary, this thesis uses atomic PDF and RMC simulations to draw structure-function correlations in HEAs, presenting a path forward for developing strategies for the rational design of HEAs. Through collaborative efforts from theoreticians and experimentalists, the methodology presented here can form the basis for accelerating the discovery of promising HEA configurations for emerging electrocatalytic applications

    CERNAS – Current Evolution and Research Novelty in Agricultural Sustainability

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    This book addresses original studies and reviews focused on the current evolution and research novelty in agricultural sustainability. New developments are discussed on issues related with quality of soil, natural fertilizers or the sustainable use of land and water. Also crop protection techniques are pivotal for the sustainable food production under the challenges of the Sustainable Development Goals of the United Nations, allied to innovative weed control methodologies, as a way to reduce the utilization of pesticides. The role of precision and smart agriculture is becoming more pertinent as the communication technologies improve at a high rate. Waste management, reuse of agro industrial residues, extension of shelf life and use of new technologies are ways to reduce food waste, all contributing to a higher sustainability of the food supply chains, leading to a more rational use of natural resources. The unquestionable role of bees as pollinators and contributors for biodiversity is subjacent to the work of characterization of beekeeping activities, which in turn contribute, together with the valorization of endemic varieties of plant foods, for the development of local communities. Finally, the short circuits and local food markets have a decisive role in the preservation and enhancement of rural economies.info:eu-repo/semantics/publishedVersio

    A review of commercialisation mechanisms for carbon dioxide removal

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    The deployment of carbon dioxide removal (CDR) needs to be scaled up to achieve net zero emission pledges. In this paper we survey the policy mechanisms currently in place globally to incentivise CDR, together with an estimate of what different mechanisms are paying per tonne of CDR, and how those costs are currently distributed. Incentive structures are grouped into three structures, market-based, public procurement, and fiscal mechanisms. We find the majority of mechanisms currently in operation are underresourced and pay too little to enable a portfolio of CDR that could support achievement of net zero. The majority of mechanisms are concentrated in market-based and fiscal structures, specifically carbon markets and subsidies. While not primarily motivated by CDR, mechanisms tend to support established afforestation and soil carbon sequestration methods. Mechanisms for geological CDR remain largely underdeveloped relative to the requirements of modelled net zero scenarios. Commercialisation pathways for CDR require suitable policies and markets throughout the projects development cycle. Discussion and investment in CDR has tended to focus on technology development. Our findings suggest that an equal or greater emphasis on policy innovation may be required if future requirements for CDR are to be met. This study can further support research and policy on the identification of incentive gaps and realistic potential for CDR globally

    Targeting Fusion Proteins of HIV-1 and SARS-CoV-2

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    Viruses are disease-causing pathogenic agents that require host cells to replicate. Fusion of host and viral membranes is critical for the lifecycle of enveloped viruses. Studying viral fusion proteins can allow us to better understand how they shape immune responses and inform the design of therapeutics such as drugs, monoclonal antibodies, and vaccines. This thesis discusses two approaches to targeting two fusion proteins: Env from HIV-1 and S from SARS-CoV-2. The first chapter of this thesis is an introduction to viruses with a specific focus on HIV-1 CD4 mimetic drugs and antibodies against SARS-CoV-2. It discusses the architecture of these viruses and fusion proteins and how small molecules, peptides, and antibodies can target these proteins successfully to treat and prevent disease. In addition, a brief overview is included of the techniques involved in structural biology and how it has informed the study of viruses. For the interested reader, chapter 2 contains a review article that serves as a more in-depth introduction for both viruses as well as how the use of structural biology has informed the study of viral surface proteins and neutralizing antibody responses to them. The subsequent chapters provide a body of work divided into two parts. The first part in chapter 3 involves a study on conformational changes induced in the HIV-1 Env protein by CD4-mimemtic drugs using single particle cryo-EM. The second part encompassing chapters 4 and 5 includes two studies on antibodies isolated from convalescent COVID-19 donors. The former involves classification of antibody responses to the SARS-CoV-2 S receptor-binding domain (RBD). The latter discusses an anti-RBD antibody class that binds to a conserved epitope on the RBD and shows cross-binding and cross-neutralization to other coronaviruses in the sarbecovirus subgenus.</p
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