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  • 1.
    Abrikosov, Alexei I.
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Topological analysis of density fields: An evaluation of segmentation methods2021In: Computers & graphics, ISSN 0097-8493, E-ISSN 1873-7684, Vol. 98, p. 231-241Article in journal (Refereed)
    Abstract [en]

    Topological and geometric segmentation methods provide powerful concepts for detailed field analysis and visualization. However, when it comes to a quantitative analysis that requires highly accurate geometric segmentation, there is a large discrepancy between the promising theory and the available computational approaches. In this paper, we compare and evaluate various segmentation methods with the aim to identify and quantify the extent of these discrepancies. Thereby, we focus on an application from quantum chemistry: the analysis of electron density fields. It is a scalar quantity that can be experimentally measured or theoretically computed. In the evaluation we consider methods originating from the domain of quantum chemistry and computational topology. We apply the methods to the charge density of a set of crystals and molecules. Therefore, we segment the volumes into atomic regions and derive and compare quantitative measures such as total charge and dipole moments from these regions. As a result, we conclude that an accurate geometry determination can be crucial for correctly segmenting and analyzing a scalar field, here demonstrated on the electron density field.

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  • 2.
    Bykov, Maxim
    et al.
    Carnegie Inst Sci, DC 20015 USA; Howard Univ, DC 20059 USA.
    Fedotenko, Timofey
    Univ Bayreuth, Germany.
    Chariton, Stella
    Univ Chicago, IL 60637 USA.
    Laniel, Dominique
    Univ Bayreuth, Germany.
    Glazyrin, Konstantin
    Deutsch Electronen Synchrotron DESY, Germany.
    Hanfland, Michael
    European Synchrotron Radiat Facil, France.
    Smith, Jesse S.
    Argonne Natl Lab, IL 60439 USA.
    Prakapenka, Vitali B.
    Univ Chicago, IL 60637 USA.
    Mahmood, Mohammad F.
    Howard Univ, DC 20059 USA.
    Goncharov, Alexander F.
    Carnegie Inst Sci, DC 20015 USA.
    Ponomareva, Alena V
    Natl Univ Sci & Technol MISIS, Russia.
    Tasnadi, Ferenc
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Abrikossov, Alexei
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Rudenko, Alexander N.
    Wuhan Univ, Peoples R China; Wuhan Univ, Peoples R China; Radboud Univ Nijmegen, Netherlands; Ural Fed Univ, Russia.
    Katsnelson, Mikhail I
    Radboud Univ Nijmegen, Netherlands; Ural Fed Univ, Russia.
    Doubrovinckaia, Natalia
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Univ Bayreuth, Germany.
    Dubrovinsky, Leonid
    Univ Bayreuth, Germany.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    High-Pressure Synthesis of Dirac Materials: Layered van der Waals Bonded BeN4 Polymorph2021In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 126, no 17, article id 175501Article in journal (Refereed)
    Abstract [en]

    High-pressure chemistry is known to inspire the creation of unexpected new classes of compounds with exceptional properties. Here, we employ the laser-heated diamond anvil cell technique for synthesis of a Dirac material BeN4. A triclinic phase of beryllium tetranitride tr-BeN4 was synthesized from elements at similar to 85 GPa. Upon decompression to ambient conditions, it transforms into a compound with atomic-thick BeN4 layers interconnected via weak van der Waals bonds and consisting of polyacetylene-like nitrogen chains with conjugated pi systems and Be atoms in square-planar coordination. Theoretical calculations for a single BeN4 layer show that its electronic lattice is described by a slightly distorted honeycomb structure reminiscent of the graphene lattice and the presence of Dirac points in the electronic band structure at the Fermi level. The BeN4 layer, i.e., beryllonitrene, represents a qualitatively new class of 2D materials that can be built of a metal atom and polymeric nitrogen chains and host anisotropic Dirac fermions.

  • 3.
    Engelke, Wito
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Beran, Jakob
    Department of Meteorology (MISU)Stockholm University, Stockholm, Sweden.
    Caballero, Rodrigo
    Department of Meteorology (MISU)Stockholm University, Stockholm, Sweden.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Topology-Based Feature Design and Tracking for Multi-center Cyclones2021In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 71-85Chapter in book (Refereed)
    Abstract [en]

    In this paper, we propose a concept to design, track, and compare application-specific feature definitions expressed as sets of critical points. Our work has been inspired by the observation that in many applications a large variety of different feature definitions for the same concept are used. Often, these definitions compete with each other and it is unclear which definition should be used in which context. A prominent example is the definition of cyclones in climate research. Despite the differences, frequently these feature definitions can be related to topological concepts.

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  • 4.
    Hotz, Ingrid
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha BinLinköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.Sadlo, FilipHeidelberg University, IWR, Heidelberg, Germany.Tierny, JulienCNRS, Department of Scientific Computing, Sorbonne Université, Paris, France.
    Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software2021Collection (editor) (Refereed)
    Abstract [en]

    This book is a result of a workshop, the 8th of the successful TopoInVis workshop series, held in 2019 in Nyköping, Sweden. The workshop regularly gathers some of the world’s leading experts in this field. Thereby, it provides a forum for discussions on the latest advances in the field with a focus on finding practical solutions to open problems in topological data analysis for visualization. The contributions provide introductory and novel research articles including new concepts for the analysis of multivariate and time-dependent data, robust computational approaches for the extraction and approximations of topological structures with theoretical guarantees, and applications of topological scalar and vector field analysis for visualization. The applications span a wide range of scientific areas comprising climate science, material sciences, fluid dynamics, and astronomy. In addition, community efforts with respect to joint software development are reported and discussed.  

  • 5.
    Kottravel, Sathish
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. SeRC, Sweden.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. SeRC, Sweden.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. SeRC, Sweden.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. SeRC, Sweden.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. SeRC, Sweden.
    Visual Analysis of Charge Flow Networks for Complex Morphologies2019In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 38, no 3, p. 479-489Article in journal (Refereed)
    Abstract [en]

    In the field of organic electronics, understanding complex material morphologies and their role in efficient charge transport in solar cells is extremely important. Related processes are studied using the Ising model and Kinetic Monte Carlo simulations resulting in large ensembles of stochastic trajectories. Naive visualization of these trajectories, individually or as a whole, does not lead to new knowledge discovery through exploration. In this paper, we present novel visualization and exploration methods to analyze this complex dynamic data, which provide succinct and meaningful abstractions leading to scientific insights. We propose a morphology abstraction yielding a network composed of material pockets and the interfaces, which serves as backbone for the visualization of the charge diffusion. The trajectory network is created using a novel way of implicitly attracting the trajectories to the skeleton of the morphology relying on a relaxation process. Each individual trajectory is then represented as a connected sequence of nodes in the skeleton. The final network summarizes all of these sequences in a single aggregated network. We apply our method to three different morphologies and demonstrate its suitability for exploring this kind of data.

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  • 6.
    Laniel, Dominique
    et al.
    Univ Bayreuth, Germany; Univ Edinburgh, Scotland.
    Trybel, Florian
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Yin, Yuqing
    Univ Bayreuth, Germany; Shandong Univ, Peoples R China.
    Fedotenko, Timofey
    Univ Bayreuth, Germany.
    Khandarkhaeva, Saiana
    Univ Bayreuth, Germany.
    Aslandukov, Andrey
    Univ Bayreuth, Germany.
    Aprilis, Georgios
    European Synchrotron Radiat Facil, France.
    Abrikosov, Alexei I.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Giacobbe, Carlotta
    European Synchrotron Radiat Facil, France.
    Bright, Eleanor Lawrence
    European Synchrotron Radiat Facil, France.
    Glazyrin, Konstantin
    Photon Sci, Germany.
    Hanfland, Michael
    European Synchrotron Radiat Facil, France.
    Wright, Jonathan
    European Synchrotron Radiat Facil, France.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Igor A.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Dubrovinsky, Leonid
    Shandong Univ, Peoples R China.
    Doubrovinckaia, Natalia
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Aromatic hexazine [N6]4− anion featured in the complex structure of the high-pressure potassium nitrogen compound K9N562023In: Nature Chemistry, ISSN 1755-4330, E-ISSN 1755-4349, Vol. 15, no 5, p. 641-646Article in journal (Refereed)
    Abstract [en]

    The recent high-pressure synthesis of pentazolates and the subsequent stabilization of the aromatic [N-5](-) anion at atmospheric pressure have had an immense impact on nitrogen chemistry. Other aromatic nitrogen species have also been actively sought, including the hexaazabenzene N-6 ring. Although a variety of configurations and geometries have been proposed based on ab initio calculations, one that stands out as a likely candidate is the aromatic hexazine anion [N-6](4-). Here we present the synthesis of this species, realized in the high-pressure potassium nitrogen compound K9N56 formed at high pressures (46 and 61 GPa) and high temperature (estimated to be above 2,000 K) by direct reaction between nitrogen and KN3 in a laser-heated diamond anvil cell. The complex structure of K9N56-composed of 520 atoms per unit cell-was solved based on synchrotron single-crystal X-ray diffraction and corroborated by density functional theory calculations. The observed hexazine anion [N-6](4-) is planar and proposed to be aromatic.

  • 7.
    Lukasczyk, Jonas
    et al.
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Beran, Jakob
    Stockholm University, Stockholm, Sweden.
    Engelke, Wito
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Friederici, Anke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Garth, Christoph
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Köpp, Wiebke
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Olejniczak, Małgorzata
    University of Warsaw, Warsaw, Poland.
    Rosen, Paul
    University of South Florida, Tampa, USA.
    Sohns, Jan-Tobias
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Weinkauf, Tino
    KTH Royal Institute of Technology, Stockholm, Sweden.
    Werner, Kilian
    Technische Universität Kaiserslautern, Kaiserslautern, Germany.
    Tierny, Julien
    CNRS, Sorbonne Universite, Paris, France.
    Report of the TopoInVis TTK Hackathon: Experiences, Lessons Learned, and Perspectives2021In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 359-373Chapter in book (Refereed)
    Abstract [en]

    This paper documents the organization, the execution, and the results of the Topology ToolKit (TTK) hackathon that took place at the TopoInVis 2019 conference. The primary goal of the hackathon was to promote TTK in our research community as a unified software development platform for topology-based data analysis algorithms. To this end, participants were first introduced to the structure and capabilities of TTK, and then worked on their own TTK-related projects while being mentored by senior TTK developers. Notable outcomes of the hackathon were first steps towards Python and Docker packages, further integration of TTK in Inviwo, the extension of TTK with new algorithms, and the discovery of current limitations of TTK as well as future development directions.

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  • 8.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Budin, Joseph
    Sorbonne Université, Paris, France.
    Falk, Martin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Favelier, Guillaume
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Garth, Christoph
    TU Kaiserslautern, Kaiserslautern, Germany.
    Gueunet, Charles
    Kitware, New York, USA.
    Guillou, Pierre
    Sorbonne Université, Paris, France.
    Hofmann, Lutz
    Heidelberg University, Heidelberg, Germany.
    Hristov, Petar
    University of Leeds, Leeds, UK.
    Kamakshidasan, Adhitya
    INRIA Saclay - Île-de-France, Palaiseau, France.
    Kappe, Christopher
    TU Kaiserslautern, Kaiserslautern, Germany.
    Klacansky, Pavol
    SCI Institute, University of Utah, Salt Lake City, USA.
    Laurin, Patrick
    ShapeShift3D, Montreal, Canada.
    Levine, Joshua A.
    University of Arizona, Tucson, USA.
    Lukasczyk, Jonas
    Arizona State University, Phoenix, USA.
    Sakurai, Daisuke
    Kyushu University, Fukuoka, Japan.
    Soler, Maxime
    Total / Sorbonne Université, Paris, France.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Tierny, Julien
    CNRS / Sorbonne Université, Paris, France.
    Usher, Will
    SCI Institute, University of Utah, Salt Lake City, USA.
    Vidal, Jules
    Sorbonne Université, Paris, France.
    Wozniak, Michal
    ShapeShift3D, Montreal, Canada.
    An Overview of the Topology ToolKit2021In: Topological Methods in Data Analysis and Visualization VI: Theory, Applications, and Software / [ed] Ingrid Hotz, Talha Bin Masood, Filip Sadlo and Julien Tierny, Springer, 2021, p. 327-342Chapter in book (Refereed)
    Abstract [en]

    This software paper gives an overview of the features supported by the Topology ToolKitTopology ToolKit (TTK), which is an  Open-sourceopen-source library for  Topological data analysistopological data analysis (TDA). TTK implements, in a generic and efficient way, a substantial collection of reference algorithms in TDA. Since its initial public release in 2017, both its user and developer bases have grown, resulting in a significant increase in the number of supported features. In contrast to the original paper introducing TTK [40] (which detailed the core algorithms and data structures of TTK), the purpose of this Softwaresoftware paper is to describe the list of features currently supported by TTK, ranging from image segmentation tools to advanced topological analysis of high-dimensional data, with concrete usage examples available on the TTK website [42].

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  • 9.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Continuous Histograms for Anisotropy of 2D Symmetric Piece-wise Linear Tensor Fields2021In: Anisotropy Across Fields and Scales / [ed] Evren Özarslan, Thomas Schultz, Eugene Zhang, and Andrea Fuster, Cham: Springer, 2021, p. 39-70Chapter in book (Refereed)
    Abstract [en]

    In this chapter we present an accurate derivation of the distribution of scalar invariants with quadratic behavior represented as continuous histograms. The anisotropy field, computed from a two-dimensional piece-wise linear tensor field, is used as an example and is discussed in all details. Histograms visualizing an approximation of the distribution of scalar values play an important role in visualization. They are used as an interface for the design of transfer-functions for volume rendering or feature selection in interactive interfaces. While there are standard algorithms to compute continuous histograms for piece-wise linear scalar fields, they are not directly applicable to tensor invariants with non-linear, often even non-convex behavior in cells when applying linear tensor interpolation. Our derivation is based on a sub-division of the mesh in triangles that exhibit a monotonic behavior. We compare the results to a naïve approach based on linear interpolation on the original mesh or the subdivision.

  • 10.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ray, Tathagata
    BITS Pilani, India.
    Natarajan, Vijay
    Indian Institute of Science, Bangalore, India.
    Parallel Computation of Alpha Complexes for Biomolecules2020In: 36th International Symposium on Computational Geometry (SoCG 2020) / [ed] Sergio Cabello and Danny Z. Chen, Dagstuhl, Germany, 2020, Vol. 164, p. 1-16, article id 17Conference paper (Refereed)
    Abstract [en]

    The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which exploits the knowledge of typical spatial distribution and sizes of atoms in a biomolecule. Unlike existing methods, this algorithm does not require prior construction of the Delaunay triangulation. The algorithm computes the alpha complex in two stages. The first stage proceeds in a bottom-up fashion and computes a superset of the edges, triangles, and tetrahedra belonging to the alpha complex. The false positives from this estimation stage are removed in a subsequent pruning stage to obtain the correct alpha complex. Computational experiments on several biomolecules demonstrate the superior performance of the algorithm, up to a factor of 50 when compared to existing methods that are optimized for biomolecules.

  • 11.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ray, Tathagata
    BITS Pilani, India.
    Natarajan, Vijay
    Indian Institute of Science, Bangalore, India.
    Parallel computation of alpha complexes for biomolecules2020In: Computational geometry, ISSN 0925-7721, E-ISSN 1879-081X, Vol. 90, article id UNSP 101651Article in journal (Refereed)
    Abstract [en]

    The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which exploits the knowledge of typical spatial distribution and sizes of atoms in a biomolecule. Unlike existing methods, this algorithm does not require prior construction of the Delaunay triangulation. The algorithm computes the alpha complex in two stages. The first stage proceeds in a bottom-up fashion and computes a superset of the edges, triangles, and tetrahedra belonging to the alpha complex. The false positives from this estimation stage are removed in a subsequent pruning stage to obtain the correct alpha complex. Computational experiments on several biomolecules demonstrate the superior performance of the algorithm, up to a factor of 50 when compared to existing methods that are optimized for biomolecules. (C) 2020 Elsevier B.V. All rights reserved.

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  • 12.
    Masood, Talha Bin
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sidwall Thygesen, Signe
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Alexei I.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Indian Institute of Science, Bangalore.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Visual Analysis of Electronic Densities and Transitions in Molecules2021In: Computer Graphics Forum, ISSN 0167-7055, Vol. 40, no 3, p. 287-298Article in journal (Refereed)
    Abstract [en]

    The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials. The transitions are complex quantum mechanical processes and a detailed analysis requires a breakdown of these processes into components that can be interpreted via characteristic chemical properties. We approach these tasks by providing a detailed analysis of the electron density field. This entails methods to quantify and visualize electron localization and transfer from molecular subgroups combining spatial and abstract representations. The core of our method uses geometric segmentation of the electronic density field coupled with a graph-theoretic formulation of charge transfer between molecular subgroups. The design of the methods has been guided by the goal of providing a generic and objective analysis following fundamental concepts. We illustrate the proposed approach using several case studies involving the study of electronic transitions in different molecular systems.

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  • 13.
    Nilsson, Emma
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Lukasczyk, Jonas
    TU Kaiserslautern, Germany.
    Engelke, Wito
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Svensson, Gunilla
    Stockholm Univ, Sweden.
    Caballero, Rodrigo
    Stockholm Univ, Sweden.
    Garth, Christoph
    TU Kaiserslautern, Germany.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Exploring Cyclone Evolution with Hierarchical Features2022In: 2022 IEEE WORKSHOP ON TOPOLOGICAL DATA ANALYSIS AND VISUALIZATION (TOPOINVIS 2022), IEEE , 2022, p. 92-102Conference paper (Refereed)
    Abstract [en]

    The problem of tracking and visualizing cyclones is still an active area of climate research, since the nature of cyclones varies depending on geospatial location and temporal season, resulting in no clear mathematical definition. Thus, many cyclone tracking methods are tailored to specific datasets and therefore do not support general cyclone extraction across the globe. To address this challenge, we present a conceptual application for exploring cyclone evolution by organizing the extracted cyclone tracks into hierarchical groups. Our approach is based on extrema tracking, and the resulting tracks can be defined in a multi-scale structure by grouping the points based on a novel feature descriptor defined on the merge tree, so-called crown features. Consequently, multiple parameter settings can be visualized and explored in a level-of-detail approach, supporting experts to quickly gain insights on cyclonic formation and evolution. We describe a general cyclone exploration pipeline that consists of four modular building blocks: (1) an extrema tracking method, (2) multiple definitions of cyclones as groups of extrema, including crown features, (3) the correlation of cyclones based on the underlying tracking information, and (4) a hierarchical visualization of the resulting feature tracks and their spatial embedding, allowing exploration on a global and local scale. In order to be as flexible as possible, our pipeline allows for exchanging every module with different techniques, such as other tracking methods and cyclone definitions.

  • 14.
    Nilsson, Emma
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Lukasczyk, Jonas
    TU Kaiserslautern, Germany.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Garth, Christoph
    TU Kaiserslautern, Germany.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Towards Benchmark Data Generation for Feature Tracking in Scalar Fields2022In: 2022 IEEE WORKSHOP ON TOPOLOGICAL DATA ANALYSIS AND VISUALIZATION (TOPOINVIS 2022), IEEE , 2022, p. 103-112Conference paper (Refereed)
    Abstract [en]

    We describe a benchmark data generator for tracking methods for two- and three-dimensional time-dependent scalar fields. More and more topology-based tracking methods are presented in the visualization community, but the validation and evaluation of the tracking results are currently limited to qualitative visual approaches. We present a pipeline for creating different ground truth features that support evaluating tracking methods based on quantitative measures. In short, our approach randomly simulates a temporal point cloud with birth, death, split, merge, and continuation events, where the points are then used to derive a scalar field whose topological features correspond to the points. These scalar fields can be used as the input for different tracking methods, where the computed tracks can be compared against the ground truth feature evolution. This approach facilitates directly comparing the results of different tracking methods, independent of the initial feature characterization.

  • 15.
    Pandey, Karran
    et al.
    Indian Inst Sci, India.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Singh, Saurabh
    Indian Inst Sci, India.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Indian Inst Sci, India.
    Murthy, Tejas G.
    Indian Inst Sci, India.
    Morse theory-based segmentation and fabric quantification of granular materials2022In: Granular Matter, ISSN 1434-5021, E-ISSN 1434-7636, Vol. 24, no 1, article id 27Article in journal (Refereed)
    Abstract [en]

    This article presents a robust Morse theory-based framework for segmenting 3D X-ray computed tomography image (CT) and computing the fabric, relative arrangement of particles, of granular ensembles. The framework includes an algorithm for computing the segmentation, a data structure for storing the segmentation and representing both individual particles and the connectivity network, and visualizations of topological descriptors of the CT image that enable interactive exploration. The Morse theory-based framework produces superior quality segmentation of a granular ensemble as compared to prior approaches based on the watershed transform. The accuracy of the connectivity network also improves. Further, the frame-work supports the efficient computation of various distribution statistics on the segmentation and the connectivity network. Such a comprehensive characterization and quantification of the fabric of granular ensembles is the first step towards a multiple length scale understanding of the behavior.

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  • 16.
    Rasheed, Farhan
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Jönsson, Daniel
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Nilsson, Emma
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Subject-Specific Brain Activity Analysis in fMRI Data Using Merge Trees2022In: 2022 IEEE WORKSHOP ON TOPOLOGICAL DATA ANALYSIS AND VISUALIZATION (TOPOINVIS 2022), IEEE , 2022, p. 113-123Conference paper (Refereed)
    Abstract [en]

    We present a method for detecting patterns in time-varying functional magnetic resonance imaging (fMRI) data based on topological analysis. The oxygenated blood flow measured by fMRI is widely used as an indicator of brain activity. The signal is, however, prone to noise from various sources. Random brain activity, physiological noise, and noise from the scanner can reach a strength comparable to the signal itself. Thus, extracting the underlying signal is a challenging process typically approached by applying statistical methods. The goal of this work is to investigate the possibilities of recovering information from the signal using topological feature vectors directly based on the raw signal without medical domain priors. We utilize merge trees to define a robust feature vector capturing key features within a time step of fMRI data. We demonstrate how such a concise feature vector representation can be utilized for exploring the temporal development of brain activations, connectivity between these activations, and their relation to cognitive tasks.

  • 17.
    Rasheed, Farhan
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Murthy, Tejas G.
    Indian Inst Sci, India.
    Natarajan, Vijay
    Indian Inst Sci, India.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Multi-scale visual analysis of cycle characteristics in spatially-embedded graphs2023In: VISUAL INFORMATICS, ISSN 2468-502X, Vol. 7, no 3, p. 49-58Article in journal (Refereed)
    Abstract [en]

    We present a visual analysis environment based on a multi-scale partitioning of a 2d domain into regions bounded by cycles in weighted planar embedded graphs. The work has been inspired by an application in granular materials research, where the question of scale plays a fundamental role in the analysis of material properties. We propose an efficient algorithm to extract the hierarchical cycle structure using persistent homology. The core of the algorithm is a filtration on a dual graph exploiting Alexander's duality. The resulting partitioning is the basis for the derivation of statistical properties that can be explored in a visual environment. We demonstrate the proposed pipeline on a few synthetic and one real-world dataset.

  • 18.
    Sharma, Mohit
    et al.
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sidwall Thygesen, Signe
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Media and Information Technology.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
    Continuous Scatterplot Operators for Bivariate Analysis and Study of Electronic Transitions2023In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506Article in journal (Refereed)
    Abstract [en]

    Electronic transitions in molecules due to the absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of electronic transitions, namely which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or conformations of the molecules. In this paper, we present a novel approach for the analysis of a bivariate field and show its applicability to the study of electronic transitions. This approach is based on two novel operators, the continuous scatterplot (CSP) lens operator and the CSP peel operator, that enable effective visual analysis of bivariate fields. Both operators can be applied independently or together to facilitate analysis. The operators motivate the design of control polygon inputs to extract fiber surfaces of interest in the spatial domain. The CSPs are annotated with a quantitative measure to further support the visual analysis. We study different molecular systems and demonstrate how the CSP peel and CSP lens operators help identify and study donor and acceptor characteristics in molecular systems.

  • 19.
    Sharma, Mohit
    et al.
    Indian Institute of Science, Bangalore, India.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sidwall Thygesen, Signe
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Indian Institute of Science, Bangalore, India.
    Segmentation Driven Peeling for Visual Analysis of Electronic Transitions2021In: 2021 IEEE Visualization Conference (VIS), IEEE, 2021, p. 96-100Conference paper (Refereed)
    Abstract [en]

    Electronic transitions in molecules due to absorption or emission of light is a complex quantum mechanical process. Their study plays an important role in the design of novel materials. A common yet challenging task in the study is to determine the nature of those electronic transitions, i.e. which subgroups of the molecule are involved in the transition by donating or accepting electrons, followed by an investigation of the variation in the donor-acceptor behavior for different transitions or conformations of the molecules. In this paper, we present a novel approach towards the study of electronic transitions based on the visual analysis of a bivariate field, namely the electron density in the hole and particle Natural Transition Orbital (NTO). The visual analysis focuses on the continuous scatter plots (CSPs) of the bivariate field linked to their spatial domain. The method supports selections in the CSP visualized as fiber surfaces in the spatial domain, the grouping of atoms, and the segmentation of the density fields to peel the CSP. This peeling operator is central to the visual analysis process and helps identify donors and acceptors. We study different molecular systems, identifying local excitation and charge transfer excitations to demonstrate the utility of the method.

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  • 20.
    Sidwall Thygesen, Signe
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Alexei I.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Level of Detail Visual Analysis of Structures in Solid-State Materials2023In: EuroVis 2023 - Short Papers / [ed] Thomas Hoellt, Wolfgang Aigner, and Bei Wang, The Eurographics Association , 2023Conference paper (Refereed)
    Abstract [en]

    We propose a visual analysis method for the comparison and evaluation of structures in solid-state materials based on the electron density field using topological analysis. The work has been motivated by a material science application, specifically looking for new so-called layered materials whose physical properties are required in many modern technological developments. Due to the incredibly large search space, this is a slow and tedious process, requiring efficient data analysis to characterize and understand the material properties. The core of our proposed analysis pipeline is an abstract bar representation that serves as a concise signature of the material, supporting direct comparison and also an exploration of different material candidates.

  • 21.
    Sidwall Thygesen, Signe
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Linares, Mathieu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Indian Inst Sci, India.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Level of Detail Exploration of Electronic Transition Ensembles using Hierarchical Clustering2022In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 41, no 3, p. 333-344Article in journal (Refereed)
    Abstract [en]

    We present a pipeline for the interactive visual analysis and exploration of molecular electronic transition ensembles. Each ensemble member is specified by a molecular configuration, the charge transfer between two molecular states, and a set of physical properties. The pipeline is targeted towards theoretical chemists, supporting them in comparing and characterizing electronic transitions by combining automatic and interactive visual analysis. A quantitative feature vector characterizing the electron charge transfer serves as the basis for hierarchical clustering as well as for the visual representations. The interface for the visual exploration consists of four components. A dendrogram provides an overview of the ensemble. It is augmented with a level of detail glyph for each cluster. A scatterplot using dimensionality reduction provides a second visualization, highlighting ensemble outliers. Parallel coordinates show the correlation with physical parameters. A spatial representation of selected ensemble members supports an in-depth inspection of transitions in a form that is familiar to chemists. All views are linked and can be used to filter and select ensemble members. The usefulness of the pipeline is shown in three different case studies.

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  • 22.
    Yan, Lin
    et al.
    University of Utah, Salt Lake City, Utah, United States.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Rasheed, Farhan
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Wang, Bei
    University of Utah, Salt Lake City, Utah, United States.
    Geometry Aware Merge Tree Comparisons for Time-Varying Data with Interleaving Distances2023In: IEEE Transactions on Visualization and Computer Graphics, ISSN 1077-2626, E-ISSN 1941-0506, Vol. 29, no 8, p. 3489-3506Article in journal (Refereed)
    Abstract [en]

    Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First, they give compressed and topology-preserving representations of data instances. Second, their comparisons provide a basis for studying the relations among data instances, such as their distributions, clusters, outliers, and periodicities. A number of comparative measures have been developed for merge trees. However, these measures are often computationally expensive since they implicitly consider all possible correspondences between critical points of the merge trees. In this paper, we perform geometry-aware comparisons of merge trees. The main idea is to decouple the computation of a comparative measure into two steps: a labeling step that generates a correspondence between the critical points of two merge trees, and a comparison step that computes distances between a pair of labeled merge trees by encoding them as matrices. We show that our approach is general, computationally efficient, and practically useful. Our general framework makes it possible to integrate geometric information of the data domain in the labeling process. At the same time, it reduces the computational complexity since not all possible correspondences have to be considered. We demonstrate via experiments that such geometry-aware merge tree comparisons help to detect transitions, clusters, and periodicities of a time-varying dataset, as well as to diagnose and highlight the topological changes between adjacent data instances.

  • 23.
    Yan, Lin
    et al.
    Scientific Computing and Imaging Institute, University of Utah, USA.
    Masood, Talha Bin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Sridharamurthy, Raghavendra
    Department of Computer Science and Automation, Indian Institute of Science Bangalore, India.
    Rasheed, Farhan
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Natarajan, Vijay
    Department of Computer Science and Automation, Indian Institute of Science Bangalore, India.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Wang, Bei
    Scientific Computing and Imaging Institute, University of Utah, USA.
    Scalar Field Comparison with Topological Descriptors: Properties and Applications for Scientific Visualization2021In: Computer graphics forum (Print), ISSN 0167-7055, E-ISSN 1467-8659, Vol. 40, no 3, p. 599-633Article in journal (Refereed)
    Abstract [en]

    In topological data analysis and visualization, topological descriptors such as persistence diagrams, merge trees, contour trees, Reeb graphs, and Morse–Smale complexes play an essential role in capturing the shape of scalar field data. We present a state-of-the-art report on scalar field comparison using topological descriptors. We provide a taxonomy of existing approaches based on visualization tasks associated with three categories of data: single fields, time-varying fields, and ensembles. These tasks include symmetry detection, periodicity detection, key event/feature detection, feature tracking, clustering, and structure statistics. Our main contributions include the formulation of a set of desirable mathematical and computational properties of comparative measures, and the classification of visualization tasks and applications that are enabled by these measures.

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