Biological Physics

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New submissions for Fri, 10 May 24

[1]  arXiv:2405.05425 [pdf, other]

Title: Identifying stable communities in Hi-C data using a multifractal null model

Authors: Lucas Hedström, Antón Carcedo Martínez, Ludvig Lizana

Subjects: Biological Physics (physics.bio-ph); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

Chromosome capture techniques like Hi-C have expanded our understanding of mammalian genome 3D architecture and how it influences gene activity. To analyze Hi-C data sets, researchers increasingly treat them as DNA-contact networks and use standard community detection techniques to identify mesoscale 3D communities. However, there are considerable challenges in finding significant communities because the Hi-C networks have cross-scale interactions and are almost fully connected. This paper presents a pipeline to distil 3D communities that remain intact under experimental noise. To this end, we bootstrap an ensemble of Hi-C datasets representing noisy data and extract 3D communities that we compare with the unperturbed dataset. Notably, we extract the communities by maximizing local modularity (using the Generalized Louvain method), which considers the multifractal spectrum recently discovered in Hi-C maps. Our pipeline finds that stable communities (under noise) typically have above-average internal contact frequencies and tend to be enriched in active chromatin marks. We also find they fold into more nested cross-scale hierarchies than less stable ones. Apart from presenting how to systematically extract robust communities in Hi-C data, our paper offers new ways to generate null models that take advantage of the network's multifractal properties. We anticipate this has a broad applicability to several network applications.

Cross-lists for Fri, 10 May 24

[2]  arXiv:2405.05494 (cross-list from physics.flu-dyn) [pdf, other]

Title: Localization and bistability of bioconvection in a doubly periodic domain

Authors: Yoshiki Hiruta, Kenta Ishimoto

Comments: 10 pages, 9 figures

Subjects: Fluid Dynamics (physics.flu-dyn); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

A suspension of swimming microorganisms often generates a large-scale convective pattern known as bioconvection. In contrast to the thermal Rayleigh-Benard system, recent experimental studies report an emergence of steady localized convection patterns and bistability near the onset of instability in bioconvection systems. In this study, to understand the underlying mechanisms and identify the roles of particle self-propulsion in pattern formation, we theoretically and numerically investigate a model bioconvection system in a two-dimensional periodic boundary domain. In doing so, we extend a standard bioconvection model by introducing the equilibrium density profile as an independent parameter, for which the particle self-propulsion is treated as an independent dimensional parameter. Since the large-scale vertical structure dominates in this system, we are able to simplify the model by truncating the higher vertical modes. With this truncated model, we analytically derived the neutrally stable curve and found that the particle motility stabilizes the system. We then numerically analyzed the bifurcation diagram and found the bistable structure at the onset of instability. These findings, localization and bistability, are consistent with experimental observations. We further examined the global structure of the bistable dynamical system and found that the non-trivial unstable steady solution behaves as an edge state that separates the basins of attractors. These results highlight the importance of particle self-propulsion in bioconvection, and more generally our methodology based on the dynamical systems theory is useful in understanding complex flow patterns in nature.

Replacements for Fri, 10 May 24

[3]  arXiv:2309.02708 (replaced) [pdf, ps, other]

Title: Cooling down and waking up: feedback cooling switches an unconscious neural computer into a conscious quantum computer

Authors: Andrew Bell

Comments: 37 pages, 3 figures. Fixed typo

Subjects: Neurons and Cognition (q-bio.NC); Biological Physics (physics.bio-ph)

[4]  arXiv:2405.04201 (replaced) [pdf, other]

Title: Exact calculation of the probabilities of rare events in cluster-cluster aggregation

Authors: R. Rajesh, V. Subashri, Oleg Zaboronski

Subjects: Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph); Classical Physics (physics.class-ph); Data Analysis, Statistics and Probability (physics.data-an)

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