Demonstration of a parity-time symmetry breaking phase transition using superconducting and trapped-ion qutrits

Scalable quantum computers hold the promise to solve hard computational problems, such as prime factorization, combinatorial optimization, simulation of many-body physics, and quantum chemistry. While being key to understanding many real-world phenomena, simulation of non-conservative quantum dynamics presents a challenge for unitary quantum computation. In this work, we focus on simulating non-unitary parity-time symmetric systems, which exhibit a distinctive symmetry-breaking phase transition as well as other unique features that have no counterpart in closed systems. We show that a qutrit, a three-level quantum system, is capable of realizing this non-equilibrium phase transition. By using two physical platforms - an array of trapped ions and a superconducting transmon - and by controlling their three energy levels in a digital manner, we experimentally simulate the parity-time symmetry-breaking phase transition. Our results indicate the potential advantage of multi-level (qudit) processors in simulating physical effects, where additional accessible levels can play the role of a controlled environment.Comment: 14 pages, 9 figure

A pan-metazoan concept for adult stem cells : the wobbling Penrose landscape

Funding: EU COST action MARISTEM. Grant Number: 16203 Marie Skłodowska-Curie COFUND program ARDRE. Grant Number: 847681 National Research Agency, ANR. Grant Numbers: ANR-15-IDEX-01, ANR-19-PRC United States-Israel Binational Science Foundation. Grant Number: 2015012Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long-lived, lineage-restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ-restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by ‘stemness’ gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ-cell markers, but often lack germ-line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole-body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the ‘wobbling Penrose’ landscape. Here, totipotent ASCs adopt ascending/descending courses of an ‘Escherian stairwell’, in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.Publisher PDFPeer reviewe

Expression of Wnt and TGF-Beta Pathway Components during Whole-Body Regeneration from Cell Aggregates in Demosponge Halisarca dujardinii

The phenomenon of whole-body regeneration means rebuilding of the whole body of an animal from a small fragment or even a group of cells. In this process, the old axial relationships are often lost, and new ones are established. An amazing model for studying this process is sponges, some of which are able to regenerate into a definitive organism after dissociation into cells. We hypothesized that during the development of cell aggregates, primmorphs, new axes are established due to the activation of the Wnt and TGF-beta signaling pathways. Using in silico analysis, RNA-seq, and whole-mount in situ hybridization, we identified the participants in these signaling pathways and determined the spatiotemporal changes in their expression in demosponge Halisarca dujardinii. It was shown that Wnt and TGF-beta ligands are differentially expressed during primmorph development, and transcripts of several genes are localized at the poles of primmorphs, in the form of a gradient. We suppose that the Wnt and TGF-beta signaling cascades are involved in the initial axial patterning of the sponge body, which develops from cells after dissociation

У ОБЫКНОВЕННЫХ ГУБОК ТОЖЕ ЕСТЬ PARAHOX, ИЛИ СИСТЕМА ГОМЕОБОКСНЫХ ГЕНОВ HALISARCA DUJARDINI (DEMOSPONGIAE)

International audienceГомеобокс-содержащие гены кодируют транскрипционные факторы с ультраконсервативным гомеодоменом, отвечающим за связывание с ДНК-мишенью. Они обнаружены у всех животных и подразделяются не менее, чем на 19 классов. Представители как минимум одного суперсемейства – Antennapedia – участвуют в регуляции многих процессов в развитии, в паттернировании осей тела и дифференцировке клеточных типов. В суперсемейство Antennapedia входят классы Hox, ParaHox и NK, притом у губок не обнаружены Hox-гены, а репертуар ParaHox и NK сильно разнится у исследованных видов. Кластерная организация NKгенов, характерная для Bilateria, наблюдается и у губок, а у Amphimedon queenslandica были обнаружены т.н. «призрачные локусы» Hox-генов – участки геномной ДНК, фланкирующие данные гены, однако кодирующие регионы найдены не были. С помощью биоинформатических методов в транскриптоме демоспонгии Halisarca dujardini был осуществлен поиск гомеобокссодержащих генов, выполнен филогенетический анализ с использованием репрезентативной выборки ортологов из разных классов гомеобоксов Metazoa. Последовательности из суперсемейства Antennapedia клонированы, паттерны экспрессии исследованы методом WMISH (whole mount in situ hybridization) на разных стадиях развития. Нами были идентифицированы более 70 гомеобокс-содержащих генов. С помощью предсказания доменной организации и филогенетическими методами показано распределение их по классам, описанным для Bilateria. В составе суперсемейства Antennapedia не обнаружено Hox-генов, однако присутствует один ParaHox – ортолог гена cdx (caudal). Идентичный набор наблюдается у кальциевой губки Sycon ciliatum (один ParaHox и нет Hoх), тогда как у Amphimedon из того же класса Demospongiae гены класса ParaHox отсутствуют, вероятно, в силу вторичной утраты. NK-гены широко представлены в геноме H. dujardini. Многие из Antennapedia экспрессируются в ходе развития H. dujardini. Предполагается их участие в спецификации осей зародыша и типов клеток, получено новое подтверждение наличия ParaHox у общего предка Metazoa

Tentacular apparatus ultrastructure in the larva of Bolinopsis infundibulum (Lobata: Ctenophora)

International audienceMost ctenophores have a tentacular apparatus, which plays some role in their feeding. Tentacle structure has been described in adults of only three ctenophore species, but the larval tentacles have remained completely unstudied. We made a light and electron microscopic study of the tentacular apparatus in the larvae of Bolinopsis infundibulum from the White Sea. The tentacular apparatus of B. infundibulum larvae consists of the tentacle proper and the tentacle root. The former contains terminally differentiated cells, while the latter contains stem cells and cells undergoing differentiation. The core of the tentacle is formed by myo-cytes, and its epidermis contains colloblasts (hunting cells), wall cells, degenerating cask cells, refractive vesicles, and ciliated sensory cells. Stem cells, colloblasts, and cask cells at various stages of differentiation and putative myo-cytes progenitors were revealed in the tentacle root. Two different populations of the stem cells in the tentacle root give rise to epidermal (colloblasts and cask cells) and mesogleal (myocytes) cell lines. Nervous elements, glandular cells, and basal lamina were not found. Step-by-step differentiation of colloblasts and cask cells is described

Proliferating activity in a bryozoan lophophore

Bryozoans are small benthic colonial animals; their colonies consist of zooids which are composed of a cystid and polypide. According to morphological and molecular data, three classes of bryozoans are recognized: Phylactolaemata, Gymnolaemata and Stenolaemata. Bryozoans are active suspension feeders and their feeding apparatus, the lophophore, is fringed with a single row of ciliated tentacles. In gymnolaemates, the lophophore is bell-shaped and its tentacles may be equal in length (equitentacled lophophores) or some tentacles may be longer than others (obliquely truncated lophophores). In encrusting colonies, polypides with obliquely truncated lophophores usually border specific sites of excurrent water outlets (colony periphery and chimneys) where depleted water has to be removed. It is known that during colony astogeny, colony-wide water currents rearrange: new chimneys are formed and/or location of the chimneys within a given colony changes with time. Such rearrangement requires remodeling of the lophophore shape and lengthening of some tentacles in polypides surrounding water outlets. However, proliferating activity has not been described for bryozoans. Here, we compared the distribution of S-phase and mitotic cells in young and adult polypides in three species of Gymnolaemata. We tested the hypothesis that tentacle growth/elongation is intercalary and cell proliferation takes place somewhere at the lophophore base because such pattern does not interfere with the feeding process. We also present a detailed description of ultrastructure of two parts of the lophophore base: the oral region and ciliated pits, and uncover the possible function of the latter. The presence of stem cells within the ciliated pits and the oral region of polypides provide evidence that both sites participate in tentacle elongation. This confirms the suggested hypothesis about intercalary tentacle growth which provides a potential to alter a lophophore shape in adult polypides according to rearrangement of colony wide water currents during colony astogeny. For the first time deuterosome-like structures were revealed during kinetosome biogenesis in the prospective multiciliated epithelial cells in invertebrates. Tentacle regeneration experiments in Electra pilosa demonstrated that among all epidermal cell types, only non-ciliated cells at the abfrontal tentacle surface are responsible for wound healing. Ciliated cells on the frontal and lateral tentacle surfaces are specialized and unable to proliferate, not even under wound healing. Tentacle regeneration in E. pilosa is very slow and similar to the morphallaxis type. We suggest that damaged tentacles recover their length by a mechanism similar to normal growth, powered by proliferation of cells both within ciliated pits and the oral region

Components of TGF-beta signaling pathway in the sponge Halisarca dujardini.

International audienceTGF-beta pathway is one of the major signaling mechanisms that orchestrate development of multicellular organisms. Axial patterning in embryo development is the brightest example of its role. Thus, asymmetric expression of TGF-betasuperfamily ligands determines of dorso-ventral axis in bilateral animals. Ligands from several families manage the different embryonic morphogenesis through regulation of proliferation, differentiation, apoptosis, cytoskeleton, adhesion and cell migration. Functions of TGF-beta pathway established early in evolution of multicellularity as ligands or receptors not found in Protista, whereas in Cnidaria this pathway determines the directive axis of body. At the same time, TGF-beta expression data from sponges’ development tell us about involvement of TGF-beta pathway in axialpatterning of Porifera embryo. Number of ligands may be as many as eight in demosponge Amphimedon queenslandica or twenty-two in calcisponge Sycon ciliatum so sponges are not simple in sense of ligand repertoire in comparison to Bilateria. In this study we search through transcriptome and analyze ligands, receptors and cytoplasmic messenger proteins of TGF-beta pathway in sponge Halisarca dujardini (Demospongiae). Eight ligand sequences wereidentified, and their primary structure and domain organization correspond to eumetazoan TGF-beta. Three of eight identified ligands can be classified as TGF-beta sensu stricto when next five are not fall into any of eumetazoan family of TGF-beta. With hybridization in situ and quantitative transcriptomics shown that expression of some ligands restricted to oscular tube similar to Wnt expression pattern. Similar situation described for Wnt pathway ligandsin sponges, and it shows independent involvement end lineage-specific expansion of some signaling pathways members inside Porifera phyla

Differential gene expression in regeneration of sponge Halisarca dujardinii

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