281 research outputs found

    Structure‚ÄďProperty Relationship of Geopolymers for Aqueous Pb Removal

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    The geopolymer -- an inorganic polymeric material synthesized from the reaction of aluminosilicate precursors and alkaline activating solutions -- has gained wide research attention in recent decades as a promising adsorbent for the removal of aqueous heavy metals. However, the high variability of the material and several unanswered questions have limited its development and general adoption in the industry. This study evaluates the impacts of composition and microstructure on the performance of geopolymers for aqueous lead (Pb) removal to elucidate the composition-structure-property relationship. The Pb sorption kinetics and efficiency of four geopolymers, prepared using different fly ash precursors and activating solutions, were investigated. Although all the four geopolymer compositions studied displayed a high Pb removal efficiency of over 99.5%, with a slight decrease in efficiency with increasing Ca/(Si + Al) and Al/Si contents, the results show that the sorption kinetics decreases exponentially with increasing Ca/(Si + Al) and Al/Si molar ratios. The performance of the geopolymers also shows strong correlation to the microstructure, wherein the sorption kinetics increases exponentially, while the efficiency increases slightly, with increasing mass fraction of the amorphous phase in the geopolymer\u27s phase assemblage. The results of this research indicate that using appropriate precursor formulation and curing conditions to evoke the best microstructures, geopolymer materials can be optimized for high performance in removing heavy metals, thereby improving the chances of the material\u27s general acceptability in the adsorbent industry

    Biodiversity, Disparity and Evolvability

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    A key problem in conservation biology is how to measure biological diversity. Taxic diversity (the number of species in a community or in a local biota) is not necessarily the most important aspect, if what most matters is to evaluate how the loss of the different species may impact on the future of the surviving species and communities. Alternative approaches focus on functional diversity (a measure of the distribution of the species among the different 'jobs' in the ecosystem), others on morphological disparity, still others on phylogenetic diversity. There are three major reasons to prioritize the survival of species which provide the largest contributions to the overall phylogenetic diversity. First, evolutionarily isolated lineages are frequently characterized by unique traits. Second, conserving phylogenetically diverse sets of taxa is valuable because it conserves some sort of trait diversity, itself important in so far as it helps maintain ecosystem functioning, although a strict relationships between phylogenetic diversity and functional diversity cannot be taken for granted. Third, in this way we maximize the "evolutionary potential" depending on the evolvability of the survivors. This suggests an approach to conservation problems focussed on evolvability, robustness and phenotypic plasticity of developmental systems in the face of natural selection: in other terms, an approach based on evolutionary developmental biology

    Conformality in atomic layer deposition

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    Atomic layer deposition (ALD) relies on alternated, self-limiting reactions between gaseous reactants and an exposed solid surface to deposit highly conformal coatings with a thickness controlled at the submonolayer level. These advantages have rendered ALD a mainstream technique in microelectronics and have triggered growing interest in ALD for a variety of nanotechnology applications, including energy technologies. Often, the choice for ALD is related to the need for a conformal coating on a 3D nanostructured surface, making the conformality of ALD processes a key factor in actual applications. In this work, we aim to review the current status of knowledge about the conformality of ALD processes. We describe the basic concepts related to the conformality of ALD, including an overview of relevant gas transport regimes, definitions of exposure and sticking probability, and a distinction between different ALD growth types observed in high aspect ratio structures. In addition, aiming for a more standardized anddirect comparison of reported results concerning the conformality of ALD processes, we propose a new concept, Equivalent Aspect Ratio (EAR), to describe 3D substrates and introduce standard ways to express thin film conformality. Other than the conventional aspect ratio, the EAR provides a measure for the ease of coatability by referring to a cylindrical hole as the reference structure. The different types of high aspect ratio structures and characterization approaches that have been used for quantifying the conformality of ALD processes are reviewed. The published experimental data on the conformality of thermal, plasma-enhanced, and ozone-based ALD processes are tabulated and discussed. Besides discussing the experimental results of conformality of ALD, we will also give an overview of the reported models for simulating the conformality of ALD. The different classes of models are discussed with special attention for the key assumptions typically used in the different modelling approaches. The influence of certain assumptions on simulated deposition thickness profiles is illustrated and discussed with the aim of shedding light on how deposition thickness profiles can provide insights into factors governing the surface chemistry of ALD processes. We hope that this review can serve as a starting point and reference work for new and expert researchers interested in the conformality of ALD and, at the same time, will trigger new research to further improve our understanding of this famous characteristic of ALD processes.Peer reviewe

    The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling

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    Stochastic loss and gain of symmetric divisions in the C. elegans epidermis perturbs robustness of stem cell number

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    Biological systems are subject to inherent stochasticity. Nevertheless, development is remarkably robust, ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue. It is currently unclear which genes modulate phenotypic variability, what their relationship is to core components of developmental gene networks, and what is the developmental basis of variable phenotypes. Here, we start addressing these questions using the robust number of Caenorhabditis elegans epidermal stem cells, known as seam cells, as a readout. We employ genetics, cell lineage tracing, and single molecule imaging to show that mutations in lin-22, a Hes-related basic helix-loop-helix (bHLH) transcription factor, increase seam cell number variability. We show that the increase in phenotypic variability is due to stochastic conversion of normally symmetric cell divisions to asymmetric and vice versa during development, which affect the terminal seam cell number in opposing directions. We demonstrate that LIN-22 acts within the epidermal gene network to antagonise the Wnt signalling pathway. However, lin-22 mutants exhibit cell-to-cell variability in Wnt pathway activation, which correlates with and may drive phenotypic variability. Our study demonstrates the feasibility to study phenotypic trait variance in tractable model organisms using unbiased mutagenesis screens

    Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

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    Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks

    Critical mutation rate has an exponential dependence on population size for eukaryotic-length genomes with crossover

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    The critical mutation rate (CMR) determines the shift between survival-of-the-fittest and survival of individuals with greater mutational robustness (‚Äúflattest‚ÄĚ). We identify an inverse relationship between CMR and sequence length in an in silico system with a two-peak fitness landscape; CMR decreases to no more than five orders of magnitude above estimates of eukaryotic per base mutation rate. We confirm the CMR reduces exponentially at low population sizes, irrespective of peak radius and distance, and increases with the number of genetic crossovers. We also identify an inverse relationship between CMR and the number of genes, confirming that, for a similar number of genes to that for the plant Arabidopsis thaliana (25,000), the CMR is close to its known wild-type mutation rate; mutation rates for additional organisms were also found to be within one order of magnitude of the CMR. This is the first time such a simulation model has been assigned input and produced output within range for a given biological organism. The decrease in CMR with population size previously observed is maintained; there is potential for the model to influence understanding of populations undergoing bottleneck, stress, and conservation strategy for populations near extinction

    Extending Epigenesis: From Phenotypic Plasticity to the Bio-Cultural Feedback

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    The paper aims at proposing an extended notion of epigenesis acknowledging an actual causal import to the phenotypic dimension for the evolutionary diversification of life forms. Section 1 offers introductory remarks on the issue of epigenesis contrasting it with ancient and modern preformationist views. In Section 2 we propose to intend epigenesis as a process of phenotypic formation and diversification a) dependent on environmental influences, b) independent of changes in the genomic nucleotide sequence, and c) occurring during the whole life span. Then, Section 3 focuses on phenotypic plasticity and offers an overview of basic properties (like robustness, modularity and degeneracy) that allows biological systems to be evolvable ‚Äď i.e. to have the potentiality of producing phenotypic variation. Successively (Section 4), the emphasis is put on environmentally-induced modification in the regulation of gene expression giving rise to phenotypic variation and diversification. After some brief considerations on the debated issue of epigenetic inheritance (Section 5), the issue of culture (kept in the background of the preceding sections) is considered. The key point is that, in the case of humans and of the evolutionary history of the genus Homo at least, the environment is also, importantly, the cultural environment. Thus, Section 6 argues that a bio-cultural feedback should be acknowledged in the ‚Äúepigenic‚ÄĚ processes leading to phenotypic diversification and innovation in Homo evolution. Finally, Section 7 introduces the notion of ‚Äúcultural neural reuse‚ÄĚ, which refers to phenotypic/neural modifications induced by specific features of the cultural environment that are effective in human cultural evolution without involving genetic changes. Therefore, cultural neural reuse may be regarded as a key instance of the bio-cultural feedback and ultimately of the extended notion of epigenesis proposed in this work

    Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing <i>In Vivo</i>

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    <div><p>Prions are a group of proteins that can adopt a spectrum of metastable conformations <i>in vivo</i>. These alternative states change protein function and are self-replicating and transmissible, creating protein-based elements of inheritance and infectivity. Prion conformational flexibility is encoded in the amino acid composition and sequence of the protein, which dictate its ability not only to form an ordered aggregate known as amyloid but also to maintain and transmit this structure <i>in vivo</i>. But, while we can effectively predict amyloid propensity <i>in vitro</i>, the mechanism by which sequence elements promote prion propagation <i>in vivo</i> remains unclear. In yeast, propagation of the [<i>PSI</i><sup><i>+</i></sup>] prion, the amyloid form of the Sup35 protein, has been linked to an oligopeptide repeat region of the protein. Here, we demonstrate that this region is composed of separable functional elements, the repeats themselves and a repeat proximal region, which are both required for efficient prion propagation. Changes in the numbers of these elements do not alter the physical properties of Sup35 amyloid, but their presence promotes amyloid fragmentation, and therefore maintenance, by molecular chaperones. Rather than acting redundantly, our observations suggest that these sequence elements make complementary contributions to prion propagation, with the repeat proximal region promoting chaperone binding to and the repeats promoting chaperone processing of Sup35 amyloid.</p></div

    Understanding the Role of Hyponitrite in Nitric Oxide Reduction

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    Herein, we review the preparation and coordination chemistry of cis and trans isomers of hyponitrite, [N2O2](2-). Hyponitrite is known to bind to metals via a variety of bonding modes. In fact, at least eight different bonding modes have been observed, which is remarkable for such a simple ligand. More importantly, it is apparent that the cis isomer of hyponitrite is more reactive than the trans isomer because the barrier of N2O elimination from cis-hyponitrite is lower than that of trans-hyponitrite. This observation may have important mechanistic implications for both heterogeneous NOx reduction catalysts and NO reductase. However, our understanding of the hyponitrite ligand has been limited by the lack of a general route to this fragment, and most instances of its formation have been serendipitous
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