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The application of network techniques to the analysis of neural data has greatly improved our ability to quantify and describe these rich interacting systems. Among many important contributions, networks have proven useful in identifying…

Quantitative Methods · Quantitative Biology 2018-06-14 Ann E. Sizemore , Jennifer Phillips-Cremins , Robert Ghrist , Danielle S. Bassett

It is well-known that in two dimensions Turing systems produce spots, stripes and labyrinthine patterns, and in three dimensions lamellar and spherical structures or their combinations are observed. We study transitions between these states…

Statistical Mechanics · Physics 2007-05-23 Teemu Leppanen , Mikko Karttunen , R. A. Barrio , Kimmo Kaski

We study the topology of reionization using accurate three-dimensional radiative transfer calculations post-processed on outputs from cosmological hydrodynamic simulations. In our simulations, reionization begins in overdense regions and…

Cosmology and Nongalactic Astrophysics · Physics 2015-05-13 K. Finlator , F. Ozel , R. Dave , B. D. Oppenheimer

In this work, we study the evolution of Betti curves obtained by persistent-homological analysis of point clouds formed by halos in different cosmological $N$-body simulations. We show that they can be approximated with a scaled log-normal…

Cosmology and Nongalactic Astrophysics · Physics 2024-12-20 Vitalii Tymchyshyn , Maksym Tsizh , Franco Vazza , Marco Baldi

Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…

Disordered Systems and Neural Networks · Physics 2009-11-10 A. Vazquez , R. Dobrin , D. Sergi , J. -P. Eckmann , Z. N. Oltvai , A. -L. Barabasi

The effectiveness of Spatio-temporal Graph Neural Networks (STGNNs) in time-series applications is often limited by their dependence on fixed, hand-crafted input graph structures. Motivated by insights from the Topological Data Analysis…

Machine Learning · Computer Science 2025-03-20 Viet The Nguyen , Duy Anh Pham , An Thai Le , Jans Peter , Gunther Gust

Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology.…

Biomolecules · Quantitative Biology 2014-12-25 Kelin Xia , Guo-Wei Wei

Phenomenological (P-type) bifurcations are qualitative changes in stochastic dynamical systems whereby the stationary probability density function (PDF) changes its topology. The current state of the art for detecting these bifurcations…

Algebraic Topology · Mathematics 2024-06-10 Sunia Tanweer , Firas A. Khasawneh

Persistent homology has recently emerged as a powerful technique in topological data analysis for analyzing the emergence and disappearance of topological features throughout a filtered space, shown via persistence diagrams. Additionally,…

Algebraic Topology · Mathematics 2016-12-16 Nicholas A. Scoville , Karthik Yegnesh

We apply the quantum renormalization group to construct a holographic dual for the U(N) vector model for complex bosons defined on a lattice. The bulk geometry becomes dynamical as the hopping amplitudes which determine connectivity of…

High Energy Physics - Theory · Physics 2015-08-31 Peter Lunts , Subhro Bhattacharjee , Jonah Miller , Erik Schnetter , Yong Baek Kim , Sung-Sik Lee

The description of the Internet topology is an important open problem, recently tackled with the introduction of scale-free networks. In this paper we focus on the topological and dynamical properties of real Internet maps in a three years…

Statistical Mechanics · Physics 2009-11-07 Romualdo Pastor-Satorras , Alexei Vazquez , Alessandro Vespignani

The present paper reports on our effort to characterize vortical interactions in complex fluid flows through the use of network analysis. In particular, we examine the vortex interactions in two-dimensional decaying isotropic turbulence and…

Fluid Dynamics · Physics 2017-05-23 Kunihiko Taira , Aditya G. Nair , Steven L. Brunton

Higher-order topological crystalline phases in low-dimensional interacting quantum systems represent a challenging and largely unexplored research topic. Here, we derive a Hamiltonian describing fermions interacting through correlated…

Strongly Correlated Electrons · Physics 2023-01-04 A. Montorsi , U. Bhattacharya , Daniel González-Cuadra , M. Lewenstein , G. Palumbo , L. Barbiero

The analysis of network dynamics is oftentimes restricted to networks with one-dimensional internal dynamics. Here, we show how symmetry explains the relation between behavior of systems with one-dimensional internal dynamics and with…

Dynamical Systems · Mathematics 2026-03-25 Sören von der Gracht , Eddie Nijholt , Bob Rink

An important characteristic of cosmic hydrogen reionization is the growth of ionized gas bubbles surrounding early luminous objects. Ionized bubble sizes are beginning to be probed using Lyman-$\alpha$ emission from high-redshift galaxies,…

Most real-world networks are embedded in latent geometries. If a node in a network is found in the vicinity of another node in the latent geometry, the two nodes have a disproportionately high probability of being connected by a link. The…

Physics and Society · Physics 2024-06-19 Bukyoung Jhun

Complex systems in the real world can be modeled as a network of connected components. The human brain, as a network of neurons among which the interactions cause perception, is a complex network. Synchronization is a dynamical phenomenon…

Biological Physics · Physics 2019-04-30 Arefeh Mazarei , Mohammad Amirian Matlob , Gholamhossein Riazi , Yousef Jamali

Persistent homology encodes the evolution of homological features of a multifiltered cell complex in the form of a multigraded module over a polynomial ring, called a multiparameter persistence module, and quantifies it through invariants…

Algebraic Topology · Mathematics 2026-03-24 Andrea Guidolin , Claudia Landi

We use synthetic sightlines drawn through snapshots of the Technicolor Dawn simulations to explore how the statistics of neutral oxygen OI absorbers respond to hydrogen reionization. The ionization state of the circumgalactic medium (CGM)…

Cosmology and Nongalactic Astrophysics · Physics 2019-08-26 Caitlin Doughty , Kristian Finlator

In this paper, we explore the higher- and lower-order connectivity aspects of the visibility graph representation of sandpile models, focusing on the Bak-Tang-Wiesenfeld (BTW) model. By converting the time series of avalanche events into…

Statistical Mechanics · Physics 2026-02-23 Vadood Adami , Hosseing Masoomy , Morteza Nattagh-Najafi