arXiv subjects

Talha Bin Masood

Publications and source records attributed to Talha Bin Masood.

27 records · Page 2Linked to original sources

arXiv2021

Segmentation Driven Peeling for Visual Analysis of Electronic Transitions

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 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.

physics.chem-ph↗

arXiv2021

Geometry-Aware Merge Tree Comparisons for Time-Varying Data with Interleaving Distances

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 using labeled interleaving distances. 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 time-varying datasets, as well as to diagnose and highlight the topological changes between adjacent data instances.

cs.HC↗

arXiv2021

Visual Analysis of Electronic Densities and Transitions in Molecules

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.

cs.HC↗

arXiv2021

Scalar Field Comparison with Topological Descriptors: Properties and Applications for Scientific Visualization

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.

cs.HC↗

arXiv2021

High-pressure synthesis of Dirac materials: layered van der Waals bonded BeN$_4$ polymorph

High pressure chemistry is known to inspire the creation of unexpected new classes of compounds with exceptional properties. Here we report the synthesis at ~90 GPa of novel beryllium polynitrides, monoclinic and triclinic BeN4. The triclinic phase, upon decompression to ambient conditions, transforms into a compound with atomic-thick BeN4 layers interconnected via weak van der Waals bonds consisting of polyacetylene-like nitrogen chains with conjugated π-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.

cond-mat.mtrl-sci↗

arXiv2020

Topology-Based Feature Design and Tracking for Multi-Center Cyclones

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. In our approach, we provide a cyclone tracking framework that supports interactive feature definition and comparison based on a precomputed tracking graph that stores all extremal points as well as their temporal correspondents. The framework combines a set of independent building blocks: critical point extraction, critical point tracking, feature definition, and track exploration. One of the major advantages of such an approach is the flexibility it provides, that is, each block is exchangeable. Moreover, it also enables us to perform the most expensive analysis, the construction of a full tracking graph, as a prepossessing step, while keeping the feature definition interactive. Different feature definitions can be explored and compared interactively based on this tracking graph. Features are specified by rules for grouping critical points, while feature tracking corresponds to filtering and querying the full tracking graph by specific requests. We demonstrate this method for cyclone identification and tracking in the context of climate research.

cs.LG↗

arXiv2020

Parallel Computation of Alpha Complex for Biomolecules

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.

cs.CG↗

arXiv2019

Continuous Histograms for Anisotropy of 2D Symmetric Piece-wise Linear Tensor Fields

The analysis of contours of scalar fields plays an important role in visualization. For example the contour tree and contour statistics can be used as a means for interaction and filtering or as signatures. In the context of tensor field analysis, such methods are also interesting for the analysis of derived scalar invariants. While there are standard algorithms to compute and analyze contours, they are not directly applicable to tensor invariants when using component-wise tensor interpolation. In this chapter we present an accurate derivation of the contour spectrum for invariants with quadratic behavior computed from two-dimensional piece-wise linear tensor fields. For this work, we are mostly motivated by a consistent treatment of the anisotropy field, which plays an important role as stability measure for tensor field topology. We show that it is possible to derive an analytical expression for the distribution of the invariant values in this setting, which is exemplary given for the anisotropy in all details. Our derivation is based on a topological sub-division of the mesh in triangles that exhibit a monotonic behavior. This triangulation can also directly be used to compute the accurate contour tree with standard algorithms. We compare the results to a naïve approach based on linear interpolation on the original mesh or the subdivision.

cs.GR↗

arXiv2016

Approximation Algorithms for Max-Morse Matching

In this paper, we prove that the Max-Morse Matching Problem is approximable, thus resolving an open problem posed by Joswig and Pfetsch. We describe two different approximation algorithms for the Max-Morse Matching Problem. For $D$-dimensional simplicial complexes, we obtain a $\frac{(D+1)}{(D^2+D+1)}$-factor approximation ratio using a simple edge reorientation algorithm that removes cycles. Our second result is an algorithm that provides a $\frac{2}{D}$-factor approximation for simplicial manifolds by processing the simplices in increasing order of dimension. One application of these algorithms is towards efficient homology computation of simplicial complexes. Experiments using a prototype implementation on several datasets indicate that the algorithm computes near optimal results.

cs.CG↗