Invertibility Conditions for Floating-Point Formulae

Automated reasoning procedures are essential for a number of applications that involve bit-exact floating-point computations. This paper presents conditions that characterize when a variable in a floating-point constraint has a solution, which we call invertibility conditions. We describe a novel workflow that combines human interaction and a syntax-guided synthesis (SyGuS) solver that was used for discovering these conditions. We verify our conditions for several floating-point formats. One implication of this result is that a fragment of floating-point arithmetic admits compact quantifier elimination. We implement our invertibility conditions in a prototype extension of our solver CVC4, showing their usefulness for solving quantified constraints over floating-points

Catalysts, autocatalysis and the origin of metabolism

If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO2, N2 and H2. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H2-CO2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins

Validity-Guided Synthesis of Reactive Systems from Assume-Guarantee Contracts

Automated synthesis of reactive systems from specifications has been a topic of research for decades. Recently, a variety of approaches have been proposed to extend synthesis of reactive systems from proposi- tional specifications towards specifications over rich theories. We propose a novel, completely automated approach to program synthesis which reduces the problem to deciding the validity of a set of forall-exists formulas. In spirit of IC3 / PDR, our problem space is recursively refined by blocking out regions of unsafe states, aiming to discover a fixpoint that describes safe reactions. If such a fixpoint is found, we construct a witness that is directly translated into an implementation. We implemented the algorithm on top of the JKind model checker, and exercised it against contracts written using the Lustre specification language. Experimental results show how the new algorithm outperforms JKinds already existing synthesis procedure based on k-induction and addresses soundness issues in the k-inductive approach with respect to unrealizable results.Comment: 18 pages, 5 figures, 2 table

Ampelographic and genetic characterization of Croatian grapevine varieties

Before the Phylloxera (Daktulosphaira vitifoliae) crisis in Croatia more than 400 grape varieties were under cultivation. Today their number is drastically decreased. Recently, many efforts in the preservation of grapevine biodiversity were undertaken: detailed inventory of varieties in different wine-growing regions, establishing of national and regional collections and their systematic ampelographic and genetic characterisation. This paper shows results of multiannual ampelographic and genetic research concerning Croatian grapevines considered as autochthonous varieties. After identification, many synonyms and homonyms were detected and unique genotypes were selected. Basic data of them are shown: description (according to OIV descriptors) and genetic profiles (9 SSR loci), growing area and status of vulnerability. Also, genetic relationship based on the shared allele distance is computed from SSR data. Results show certain level of similarity among varieties, and classify Croatia as important gene-pool in Europe. Some additional accessions which were detected and introduced into collections recently are still being investigated and characterized so that the here presented list of Croatian native grapevine cultivars is not final

PUGeo-Net: A Geometry-centric Network for 3D Point Cloud Upsampling

This paper addresses the problem of generating uniform dense point clouds to describe the underlying geometric structures from given sparse point clouds. Due to the irregular and unordered nature, point cloud densification as a generative task is challenging. To tackle the challenge, we propose a novel deep neural network based method, called PUGeo-Net, that learns a $3\times 3$ linear transformation matrix $\bf T$ for each input point. Matrix $\mathbf T$ approximates the augmented Jacobian matrix of a local parameterization and builds a one-to-one correspondence between the 2D parametric domain and the 3D tangent plane so that we can lift the adaptively distributed 2D samples (which are also learned from data) to 3D space. After that, we project the samples to the curved surface by computing a displacement along the normal of the tangent plane. PUGeo-Net is fundamentally different from the existing deep learning methods that are largely motivated by the image super-resolution techniques and generate new points in the abstract feature space. Thanks to its geometry-centric nature, PUGeo-Net works well for both CAD models with sharp features and scanned models with rich geometric details. Moreover, PUGeo-Net can compute the normal for the original and generated points, which is highly desired by the surface reconstruction algorithms. Computational results show that PUGeo-Net, the first neural network that can jointly generate vertex coordinates and normals, consistently outperforms the state-of-the-art in terms of accuracy and efficiency for upsampling factor $4\sim 16$.Comment: 17 pages, 10 figure

Serpentinization: Connecting geochemistry, ancient metabolism and industrial hydrogenation

Rock–water–carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe3O4) plus H2. The hydrogen can generate native metals such as awaruite (Ni3Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H2 and CO2 under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate—intermediates of the acetyl-CoA pathway, the most ancient pathway of CO2 fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni0 in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO2-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase—the only enzyme on Earth that reduces N2—is probably also a relic, a biological reconstruction of the naturally occurring inorganic catalyst that generated primordial organic nitrogen. Serpentinization generates Fe3O4 and H2, the catalyst and reductant for industrial CO2 hydrogenation and for N2 reduction via the Haber–Bosch process. In both industrial processes, an Fe3O4 catalyst is matured via H2-dependent reduction to generate Fe5C2 and Fe2N respectively. Whether serpentinization entails similar catalyst maturation is not known. We suggest that at the onset of life, essential reactions leading to reduced carbon and reduced nitrogen occurred with catalysts that were synthesized during the serpentinization process, connecting the chemistry of life and Earth to industrial chemistry in unexpected ways

Molecular characterization of old local grapevine varieties from South East European countries

South East European (SEE) viticulture partially relies on native grapevine varieties, previously scarcely described. In order to characterize old local grapevine varieties and assess the level of synonymy and genetic diversity from SEE countries, we described and genotyped 122 accessions from Albania, Federation of Bosnia and Herzegovina (B&H), Croatia, Macedonia, Moldova, Montenegro, Republika Srpska (Bosnia and Herzegovina) and Romania on nine most commonly used microsatellite loci. As a result of the study a total of 86 different genotypes were identified. All loci were very polymorphic and a total of 96 alleles were detected, ranging from 8 to 14 alleles per locus, with an average allele number of 10.67. Overall observed heterozygosity was 0.759 and slightly lower than expected (0.789) while gene diversity per locus varied between 0.600 (VVMD27) and 0.906 (VVMD28). Eleven cases of synonymy and three of homonymy have been recorded for samples harvested from different countries. Cultivars with identical genotypes were mostly detected between neighboring countries. No clear differentiation between countries was detected although several specific alleles were detected. The integration of the obtained genetic data with ampelographic ones is very important for accurate identification of the SEE cultivars and provides a significant tool in cultivar preservation and utilization.

The Future of Origin of Life Research: Bridging Decades-Old Divisions.

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research

A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism

Hydrogen gas, H2, is generated by alkaline hydrothermal vents through an ancient geochemical process called serpentinization in which water reacts with iron containing minerals deep within the Earth's crust. H2 is the electron donor for the most ancient and the only energy releasing route of biological CO2 fixation, the acetyl-CoA pathway. At the origin of metabolism, CO2 fixation by hydrothermal H2 within serpentinizing systems could have preceded and patterned biotic pathways. Here we show that three hydrothermal minerals—greigite (Fe3S4), magnetite (Fe3O4) and awaruite (Ni3Fe)—catalyse the fixation of CO2 with H2 at 100°C under alkaline aqueous conditions. The product spectrum includes formate (up to 200 mM), acetate (up to 100 µM), pyruvate (up to 10 µM), methanol (up to 100 µM), and methane. The results shed light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents