Multivariate Topology Simplification

Topological simplification of scalar and vector fields is well-established as an effective method for analysing and visualising complex data sets. For multivariate (alternatively, multi-field) data, topological analysis requires simultaneous advances both mathematically and computationally. We propose a robust multivariate topology simplification method based on “lip”-pruning from the Reeb space. Mathematically, we show that the projection of the Jacobi set of multivariate data into the Reeb space produces a Jacobi structure that separates the Reeb space into simple components. We also show that the dual graph of these components gives rise to a Reeb skeleton that has properties similar to the scalar contour tree and Reeb graph, for topologically simple domains. We then introduce a range measure to give a scaling-invariant total ordering of the components or features that can be used for simplification. Computationally, we show how to compute Jacobi structure, Reeb skeleton, range and geometric measures in the Joint Contour Net (an approximation of the Reeb space) and that these can be used for visualisation similar to the contour tree or Reeb graph

Time-convolutionless reduced-density-operator theory of a noisy quantum channel: a two-bit quantum gate for quantum information processing

An exact reduced-density-operator for the output quantum states in time-convolutionless form was derived by solving the quantum Liouville equation which governs the dynamics of a noisy quantum channel by using a projection operator method and both advanced and retarded propagators in time. The formalism developed in this work is general enough to model a noisy quantum channel provided specific forms of the Hamiltonians for the system, reservoir, and the mutual interaction between the system and the reservoir are given. Then, we apply the formulation to model a two-bit quantum gate composed of coupled spin systems in which the Heisenberg coupling is controlled by the tunneling barrier between neighboring quantum dots. Gate Characteristics including the entropy, fidelity, and purity are calculated numerically for both mixed and entangled initial states

Interactive Visualization for Singular Fibers of Functions f : R3 → R2

Scalar topology in the form of Morse theory has provided computational tools that analyze and visualize data from scientific and engineering tasks. Contracting isocontours to single points encapsulates variations in isocontour connectivity in the Reeb graph. For multivariate data, isocontours generalize to fibers—inverse images of points in the range, and this area is therefore known as fiber topology. However, fiber topology is less fully developed than Morse theory, and current efforts rely on manual visualizations. This paper presents how to accelerate and semi-automate this task through an interface for visualizing fiber singularities of multivariate functions R3 → R2. This interface exploits existing conventions of fiber topology, but also introduces a 3D view based on the extension of Reeb graphs to Reeb spaces. Using the Joint Contour Net, a quantized approximation of the Reeb space, this accelerates topological visualization and permits online perturbation to reduce or remove degeneracies in functions under study. Validation of the interface is performed by assessing whether the interface supports the mathematical workflow both of experts and of less experienced mathematicians

Mass-conserving tracer transport modelling on a reduced latitude-longitude grid with NIES-TM

The need to perform long-term simulations with reasonable accuracy has led to the development of mass-conservative and efficient numerical methods for solving the transport equation in forward and inverse models. We designed and implemented a flux-form (Eulerian) tracer transport algorithm in the National Institute for Environmental Studies Transport Model (NIES TM), which is used for simulating diurnal and synoptic-scale variations of tropospheric long-lived constituents, as well as their seasonal and inter-annual variability. Implementation of the flux-form method requires the mass conservative wind fields. However, the model is off-line and is driven by datasets from a global atmospheric model or data assimilation system, in which vertically integrated mass changes are not in balance with the surface pressure tendency and mass conservation is not achieved. To rectify the mass-imbalance, a flux-correction method is employed. To avoid a singularity near the poles, caused by the small grid size arising from the meridional convergence problem, the proposed model uses a reduced latitude–longitude grid scheme, in which the grid size is doubled several times approaching the poles. This approach overcomes the Courant condition in the Polar Regions, maintains a reasonably high integration time-step, and ensures adequate model performance during simulations. To assess the model performance, we performed global transport simulations for SF<sub>6</sub>, <sup>222</sup>Rn, and CO<sub>2</sub>. The results were compared with observations available from the World Data Centre for Greenhouse Gases, GLOBALVIEW, and the Hateruma monitoring station, Japan. Overall, the results show that the proposed flux-form version of NIES TM can produce tropospheric tracer transport more realistically than previously possible. The reasons for this improvement are discussed

A Conditional Yeast E1 Mutant Blocks the Ubiquitin–Proteasome Pathway and Reveals a Role for Ubiquitin Conjugates in Targeting Rad23 to the Proteasome

E1 ubiquitin activating enzyme catalyzes the initial step in all ubiquitin-dependent processes. We report the isolation of uba1-204, a temperature-sensitive allele of the essential Saccharomyces cerevisiae E1 gene, UBA1. Uba1-204 cells exhibit dramatic inhibition of the ubiquitin–proteasome system, resulting in rapid depletion of cellular ubiquitin conjugates and stabilization of multiple substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play in the dynamic interaction of the UbL/UBA adaptor proteins Rad23 and Dsk2 with the proteasome. Although proteasomes purified from mutant cells are intact and proteolytically active, they are depleted of ubiquitin conjugates, Rad23, and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo

Enabling Personalized Composition and Adaptive Provisioning of Web Services

The proliferation of interconnected computing devices is fostering the emergence of environments where Web services made available to mobile users are a commodity. Unfortunately, inherent limitations of mobile devices still hinder the seamless access to Web services, and their use in supporting complex user activities. In this paper, we describe the design and implementation of a distributed, adaptive, and context-aware framework for personalized service composition and provisioning adapted to mobile users. Users specify their preferences by annotating existing process templates, leading to personalized service-based processes. To cater for the possibility of low bandwidth communication channels and frequent disconnections, an execution model is proposed whereby the responsibility of orchestrating personalized processes is spread across the participating services and user agents. In addition, the execution model is adaptive in the sense that the runtime environment is able to detect exceptions and react to them according to a set of rules

Self-consistent non-Markovian theory of a quantum state evolution for quantum information processing

It is shown that the operator sum representation for non-Markovian dynamics and the Lindblad master equation in Markovian limit can be derived from a formal solution to quantum Liouville equation for a qubit system in the presence of decoherence processes self-consistently. Our formulation is the first principle theory based on projection-operator formalism to obtain an exact reduced density operator in time-convolutionless form starting from the quantum Liouville equation for a noisy quantum computer. The advantage of our approach is that it is general enough to describe a realistic quantum computer in the presence of decoherence provided details of the Hamiltonians are known.Comment: 5page

Natural dimethyl sulfide gradients would lead marine predators to higher prey biomass

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Owen, K., Saeki, K., Warren, J. D., Bocconcelli, A., Wiley, D. N., Ohira, S., Bombosch, A., Toda, K., & Zitterbart, D. P. Natural dimethyl sulfide gradients would lead marine predators to higher prey biomass. Communications Biology, 4(1), (2021): 149, https://doi.org/10.1038/s42003-021-01668-3.Finding prey is essential to survival, with marine predators hypothesised to track chemicals such as dimethyl sulfide (DMS) while foraging. Many predators are attracted to artificially released DMS, and laboratory experiments have shown that zooplankton grazing on phytoplankton accelerates DMS release. However, whether natural DMS concentrations are useful for predators and correlated to areas of high prey biomass remains a fundamental knowledge gap. Here, we used concurrent hydroacoustic surveys and in situ DMS measurements to present evidence that zooplankton biomass is spatially correlated to natural DMS concentration in air and seawater. Using agent simulations, we also show that following gradients of DMS would lead zooplankton predators to areas of higher prey biomass than swimming randomly. Further understanding of the conditions and scales over which these gradients occur, and how they are used by predators, is essential to predicting the impact of future changes in the ocean on predator foraging success.Open Access funding enabled and organized by Projekt DEAL. This study was funded by the Herrington Fitch Family Foundation, by the Woods Hole Oceanographic Institution Joint Initiative Awards Fund from the Andrew W. Mellon Foundation and The President’s Investment Fund, and by KAKENHI, Grants-in-Aid for Basic Research (B) (Grant no. 16H04168) and Bilateral Programs Joint Research Projects (open partnership), both from the Japan Society for the Promotion of Science. The authors thank Mrs. Norio Hayashi, Takanori Nagahata, and Ms. Mihoko Asano (Mitsubishi Chemical Analytech Co.) for their support with the SGV-CL device. The research was conducted under Scientific Research Permit number 18059, issued by the National Oceanic and Atmospheric Administration under the Marine Mammal Protection Act

CP violation and baryogenesis

In these lecture notes an introduction is given to some ideas and attempts to understand the origin of the matter-antimatter asymmetry of the universe. After the discussion of some basic issues of cosmology and particle theory the scenarios of electroweak baryogenesis, GUT baryogenesis, and leptogenesis are outlined.Comment: 57 pages, 17 figure