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Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…

Quantitative Methods · Quantitative Biology 2025-05-15 Tiexin Qin , Mengxu Zhu , Chunyang Li , Terry Lyons , Hong Yan , Haoliang Li

Self-organization is the spontaneous formation of spatial, temporal, or spatiotemporal patterns in complex systems far from equilibrium. During such self-organization, energy distributed in a broadband of frequencies gets condensed into a…

Adaptation and Self-Organizing Systems · Physics 2020-12-08 Induja Pavithran , Vishnu R. Unni , Alan John Varghese , D. Premraj , R. I. Sujith , C. Vijayan , Abhishek Saha , Norbert Marwan , Jürgen Kurths

In the paper we present a description of complex systems in terms of self-organization processes of prime integer relations. A prime integer relation is an indivisible element made up of integers as the basic constituents following a single…

Adaptation and Self-Organizing Systems · Physics 2016-11-23 Victor Korotkikh , Galina Korotkikh

Extrinsic faulting has been discussed previously within the so called difference method and random walk calculation. In this contribution is revisited under the framework of computational mechanics, which allows to derive expressions for…

The TTE approach to Computable Analysis is the study of so-called representations (encodings for continuous objects such as reals, functions, and sets) with respect to the notions of computability they induce. A rich variety of such…

Computational Complexity · Computer Science 2023-06-22 Carsten Rösnick-Neugebauer

Many complex systems can be reduced to their key components through spectrally decomposing matrices that capture their dynamics. These matrices can in turn be constructed from data, often by least-squares fitting: examples of algorithms to…

Numerical Analysis · Mathematics 2026-05-18 Caroline Wormell

Computation is commonly defined as the execution of abstract algorithms over symbolic representations, with physical systems treated as substrates that realise predefined operations. While effective for engineered machines, this separation…

Physics and Society · Physics 2026-01-21 Kimia Witte

While there has been a keen interest in studying computation at the edge of chaos for dynamical systems undergoing a phase transition, this has come under question for cellular automata. We show that for continuously deformed cellular…

Cellular Automata and Lattice Gases · Physics 2019-04-15 E. Estevez-Rams , D. Estevez-Moya , K. Garcia-Medina , R. Lora-Serrano

Deep-inelastic scattering, in the laboratory and on the lattice, is most instructive for understanding how the nucleon is built from quarks and gluons. The long-term goal is to compute the associated structure functions from first…

High Energy Physics - Lattice · Physics 2017-06-21 A. J. Chambers , R. Horsley , Y. Nakamura , H. Perlt , P. E. L. Rakow , G. Schierholz , A. Schiller , K. Somfleth , R. D. Young , J. M. Zanotti

Self-organization in complex systems is a process in which randomness is reduced and emergent structures appear that allow the system to function in a more competitive way with other states of the system or with other systems. It occurs…

Adaptation and Self-Organizing Systems · Physics 2025-06-02 Matthew J Brouillet , Georgi Yordanov Georgiev

Large language models have achieved remarkable success but remain largely black boxes with poorly understood internal mechanisms. To address this limitation, many researchers have proposed various interpretability methods including…

Machine Learning · Computer Science 2025-10-17 Zihao Fu , Ming Liao , Chris Russell , Zhenguang G. Cai

We study the global hypoellipticity and solvability of strongly invariant operators and systems of strongly invariant operators on closed manifolds. Our approach is based on the Fourier analysis induced by an elliptic pseudo-differential…

Analysis of PDEs · Mathematics 2026-02-11 Alexandre Kirilov , Wagner Augusto Almeida de Moraes , Pedro Meyer Tokoro

We extend previously proposed measures of complexity, emergence, and self-organization to continuous distributions using differential entropy. This allows us to calculate the complexity of phenomena for which distributions are known. We…

Adaptation and Self-Organizing Systems · Physics 2016-04-01 Guillermo Santamaría-Bonfil , Nelson Fernández , Carlos Gershenson

The problem of reconstructing nonlinear and complex dynamical systems from measured data or time series is central to many scientific disciplines including physical, biological, computer, and social sciences, as well as engineering and…

Data Analysis, Statistics and Probability · Physics 2017-05-01 Wenxu Wang , Ying-Cheng Lai , Celso Grebogi

Identifying coherent spatiotemporal patterns generated by complex dynamical systems is a central problem in many science and engineering disciplines. Here, we combine ideas from the theory of operator-valued kernels with delay-embedding…

Data Analysis, Statistics and Probability · Physics 2018-05-24 Dimitrios Giannakis , Joanna Slawinska , Abbas Ourmazd , Zhizhen Zhao

The spectral density function describes the second-order properties of a stationary stochastic process on $\mathbb{R}^d$. This paper considers the nonparametric estimation of the spectral density of a continuous-time stochastic process…

Statistics Theory · Mathematics 2023-02-07 Rafail Kartsioukas , Stilian Stoev , Tailen Hsing

Existing permanental processes often impose constraints on kernel types or stationarity, limiting the model's expressiveness. To overcome these limitations, we propose a novel approach utilizing the sparse spectral representation of…

Machine Learning · Statistics 2024-12-20 Zicheng Sun , Yixuan Zhang , Zenan Ling , Xuhui Fan , Feng Zhou

Quantum mechanics, in principle, allows for processes with indefinite causal order. However, most of these causal anomalies have not yet been detected experimentally. We show that every such process can be simulated experimentally by means…

Quantum Physics · Physics 2018-04-04 Simon Milz , Felix A. Pollock , Thao P. Le , Giulio Chiribella , Kavan Modi

Different aspects of the predictability problem in dynamical systems are reviewed. The deep relation among Lyapunov exponents, Kolmogorov-Sinai entropy, Shannon entropy and algorithmic complexity is discussed. In particular, we emphasize…

Chaotic Dynamics · Physics 2009-11-07 G. Boffetta , M. Cencini , M. Falcioni , A. Vulpiani

In the context of functional data analysis, probability density functions as non-negative functions are characterized by specific properties of scale invariance and relative scale which enable to represent them with the unit integral…

Numerical Analysis · Mathematics 2019-12-19 Jitka Machalova , Renata Talska , Karel Hron , Ales Gaba