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Motivated by a question about the sensitivity of knots' diffusive motion to the actual sequence of nucleotides placed on a given DNA, here we study a simple model of a sequence-reading diffusion on a stretched chain with a frozen sequence…

Statistical Mechanics · Physics 2025-01-17 Silvio Kalaj , Enzo Marinari , Gleb Oshanin , Luca Peliti

We have studied the collective behavior of a population of integrate-and-fire oscillators. We show that diversity, introduced in terms of a random distribution of natural periods, is the mechanism that permits to observe self-organized…

Condensed Matter · Physics 2009-10-30 Alvaro Corral , Conrad J. Perez , Albert Diaz-Guilera

In stark contrast to the jamming of frictionless hard-sphere (hard-disk if in two dimensions) packings, the critical jamming of frictional packings is much more elusive and still under intense debate. Here we show that frictional hard-disk…

Soft Condensed Matter · Physics 2021-10-15 Aile Sun , Yinqiao Wang , Yangrui Chen , Jin Shang , Xulai Sun , Jie Zheng , Yujie Wang , Jie Zhang

Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…

Biomolecules · Quantitative Biology 2020-01-28 Fatemeh Khodabandeh , Hashem Fatemi , Farshid Mohammad-Rafiee1

Cracks, the major vehicle for material failure, tend to accelerate to high velocities in brittle materials. In three-dimensions, cracks generically undergo a micro-branching instability at about 40% of their sonic limiting velocity. Recent…

Soft Condensed Matter · Physics 2017-12-06 Chih-Hung Chen , Eran Bouchbinder , Alain Karma

This paper is devoted to the statistics of the quantum eigenfunctions in an ensemble of finite disordered systems (metallic grains). We focus on moments of inverse participation ratio. In the universal random matrix limit that corresponds…

Mesoscale and Nanoscale Physics · Physics 2009-10-30 V. Prigodin , B. L. Altshuler

We numerically analyse quantum survival probability fluctuations in an open, classically chaotic system. In a quasi-classical regime, and in the presence of classical mixed phase space, such fluctuations are believed to exhibit a fractal…

Condensed Matter · Physics 2009-11-07 Giuliano Benenti , Giulio Casati , Italo Guarneri , Marcello Terraneo

Magnetic storms constitute the most remarkable large-scale phenomena of nonlinear magnetospheric dynamics. Studying the dynamical organization of macroscopic variability in terms of geomagnetic activity index data by means of complexity…

The spatiotemporal organization of bacterial cells is crucial for the active segregation of replicating chromosomes. In several species, including Caulobacter crescentus, the ATPase ParA binds to DNA and forms a gradient along the long cell…

Biological Physics · Physics 2021-09-29 Christian Hanauer , Silke Bergeler , Erwin Frey , Chase P. Broedersz

The article reviews recent developments in the theory of fluctuations and correlations of energy levels and eigenfunction amplitudes in diffusive mesoscopic samples. Various spatial geometries are considered, with emphasis on…

Disordered Systems and Neural Networks · Physics 2009-10-31 Alexander D. Mirlin

We have studied experimentally transport properties in a slowly driven granular system which recently was shown to display self-organized criticality [Frette {\em et al., Nature} {\bf 379}, 49 (1996)]. Tracer particles were added to a pile…

Condensed Matter · Physics 2016-08-15 Kim Christensen , Álvaro Corral , Vidar Frette , Jens Feder , Torstein Jøssang

Driven diffusive systems may undergo phase transitions to sustain atypical values of the current. This leads in some cases to symmetry-broken space-time trajectories which enhance the probability of such fluctuations. Here we shed light on…

Statistical Mechanics · Physics 2018-12-19 Carlos Pérez-Espigares , Federico Carollo , Juan P. Garrahan , Pablo I. Hurtado

The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…

Mesoscale and Nanoscale Physics · Physics 2010-09-20 Michael J. Harrison

We propose a dynamical model in which a network structure evolves in a self-organized critical (SOC) manner and explain a possible origin of the emergence of fractal and small-world networks. Our model combines a network growth and its…

Physics and Society · Physics 2015-07-22 Akitomo Watanabe , Shogo Mizutaka , Kousuke Yakubo

We study a simple model of spin network evolution motivated by the hypothesis that the emergence of classical space-time from a discrete microscopic dynamics may be a self-organized critical process. Self organized critical systems are…

High Energy Physics - Theory · Physics 2008-11-26 Mohammad H. Ansari , Lee Smolin

The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…

Quantitative Methods · Quantitative Biology 2023-10-04 Thomas Heinis , Roman Sokolovskii , Jamie J. Alnasir

Spatial self-similarity is a hallmark of critical phenomena. We investigate the dynamic process of percolation, in which bonds are incrementally inserted to an empty lattice until fully occupied, and track the gaps describing the changes in…

Statistical Mechanics · Physics 2024-11-08 Mingzhong Lu , Yu-Feng Song , Ming Li , Youjin Deng

The quantum dynamics of atoms subjected to pairs of closely-spaced $\delta$-kicks from optical potentials are shown to be quite different from the well-known paradigm of quantum chaos, the singly-$\delta$-kicked system. We find the unitary…

Atomic Physics · Physics 2009-11-11 C. E. Creffield , G. Hur , T. S. Monteiro

This is a short letter summarizing the long paper cond-mat/0106047 in which we present a simple two-dimensional dynamical system reaching a singularity in finite time decorated by accelerating oscillations due to the interplay between…

Statistical Mechanics · Physics 2009-11-07 D. Sornette , K. Ide

We consider a quasi one-dimensional chain of N chaotic scattering elements with periodic boundary conditions. The classical dynamics of this system is dominated by diffusion. The quantum theory, on the other hand, depends crucially on…

chao-dyn · Physics 2015-06-24 T. Dittrich , B. Mehlig , H. Schanz , U. Smilansky