Biological Physics

Authors and titles for physics.bio-ph in Jun 2023

[1]  arXiv:2306.00537 [pdf, other]

Title: Stable developmental patterns of gene expression without morphogen gradients

Authors: Maciej Majka, Nils B. Becker, Pieter Rein ten Wolde, Marcin Zagorski, Thomas R. Sokolowski

Comments: Final version, ready for submission to PLCB. Significantly extended part containing analytical models, updated figures and general overhaul of text

Subjects: Biological Physics (physics.bio-ph); Statistical Mechanics (cond-mat.stat-mech); Pattern Formation and Solitons (nlin.PS); Cell Behavior (q-bio.CB); Molecular Networks (q-bio.MN)

[2]  arXiv:2306.01515 [pdf, other]

Title: Variational formulation of active nematics: theory and simulation

Authors: Waleed Mirza, Alejandro Torres-Sánchez, Guillermo Vilanova, Marino Arroyo

Comments: 37 pages, 5 figures, 3 supplementary movies

Subjects: Biological Physics (physics.bio-ph)

[3]  arXiv:2306.01803 [pdf, other]

Title: The central dogma of biological homochirality: How does chiral information propagate in a prebiotic network?

Authors: S. Furkan Ozturk, Dimitar D. Sasselov, John D. Sutherland

Comments: 8 pages, 4 figures

Subjects: Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph)

[4]  arXiv:2306.04229 [pdf, ps, other]

Title: On concepts of mathematical physics for modelling signals in axons

Authors: Tanel Peets, Kert Tamm, Jüri Engelbrecht

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

[5]  arXiv:2306.04260 [pdf, ps, other]

Title: Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand

Authors: Valérie Gabelica (ARNA, IECB)

Journal-ref: Accounts of Chemical Research, 2021, 54 (19), pp.3691-3699

Subjects: Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph); Biomolecules (q-bio.BM)

[6]  arXiv:2306.04331 [pdf, other]

Title: Towards a Benchmark for Markov State Models: The Folding of HP35

Authors: Daniel Nagel (1), Sofia Sartore (1), Gerhard Stock (1) ((1) Albert-Ludwigs-Universität Freiburg)

Comments: arXiv admin note: text overlap with arXiv:2303.03814

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Biomolecules (q-bio.BM)

[7]  arXiv:2306.04882 [pdf, other]

Title: Influence of physical interactions on spatiotemporal patterns

Authors: Chengjie Luo, David Zwicker

Comments: 9 pages, 4 figures, and appendix

Subjects: Biological Physics (physics.bio-ph); Pattern Formation and Solitons (nlin.PS)

[8]  arXiv:2306.05653 [pdf, ps, other]

Title: Rapid, antibiotic incubation-free determination of tuberculosis drug resistance using machine learning and Raman spectroscopy

Authors: Babatunde Ogunlade, Loza F. Tadesse, Hongquan Li, Nhat Vu, Niaz Banaei, Amy K. Barczak, Amr. A. E. Saleh, Manu Prakash, Jennifer A. Dionne

Subjects: Biological Physics (physics.bio-ph); Optics (physics.optics); Quantitative Methods (q-bio.QM)

[9]  arXiv:2306.06560 [pdf, other]

Title: The Mechanism of Pattern Transitions between Formation and Dispersion

Authors: Shin Nishihara, Toru Ohira

Comments: a) Short version submitted for a publication, b) Supplementary Videos in <this https URL>

Journal-ref: Journal of Theoretical Biology. 581, 111736 (2024)

Subjects: Biological Physics (physics.bio-ph)

[10]  arXiv:2306.07256 [pdf, other]

Title: An interpenetrating-network theory of cytoplasm

Authors: Haiqian Yang, Thomas Henzel, Eric M. Stewart, Lallit Anand, Ming Guo

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

[11]  arXiv:2306.07676 [pdf, other]

Title: Maximization of the olfactory receptor neuron selectivity in the sub-threshold regime

Authors: Alexander Vidybida

Comments: 13 pages, 4 figures, 29 references

Journal-ref: Ukr.J. Phys.68, No. 4, 266 (2023)

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

[12]  arXiv:2306.08070 [pdf, other]

Title: Entanglement in living systems

Authors: Thomas C. Day, S. Alireza Zamani-Dahaj, G. Ozan Bozdag, Anthony J. Burnetti, Emma P. Bingham, Peter L. Conlin, William C. Ratcliff, Peter J. Yunker

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

[13]  arXiv:2306.08077 [pdf, other]

Title: Phase synchronization in a sparse network of randomly connected neurons under the effect of Poissonian spike inputs

Authors: Bruno R. R. Boaretto, Paulo R. Protachevicz, Matheus Hansen, Jonas Oliveira, Alexandre C. Andreani, Elbert E. N. Macau

Comments: 10 pages, 9 figures

Subjects: Biological Physics (physics.bio-ph)

[14]  arXiv:2306.08957 [pdf, other]

Title: Deformability and collision-induced reorientation enhance cell topotaxis in dense microenvironments

Authors: Leonie van Steijn, Joeri A. J. Wondergem, Koen Schakenraad, Doris Heinrich, Roeland M. H. Merks

Subjects: Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

[15]  arXiv:2306.09063 [pdf, other]

Title: Physarum polycephalum: Smart network adaptation

Authors: Mathieu Le Verge-Serandour, Karen Alim

Comments: Manuscript for Annual Reviews in Condensed Matters, no peer-reviewed. 29 pages, 5 figures

Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Tissues and Organs (q-bio.TO)

[16]  arXiv:2306.10949 [pdf, ps, other]

Title: Cooperation of myosin II in muscle contraction through nonlinear elasticity

Authors: Beibei Shen, Yunxin Zhang

Comments: 10 pages, 7 figures

Subjects: Biological Physics (physics.bio-ph); Subcellular Processes (q-bio.SC)

[17]  arXiv:2306.11012 [pdf, other]

Title: Trapping and Scattering of a Multiflagellated Bacterium by a Hard Surface

Authors: Alexander P Petroff, Schuyler McDonough

Subjects: Biological Physics (physics.bio-ph)

[18]  arXiv:2306.11931 [pdf, ps, other]

Title: The Noise Within: Signal-to-Noise Enhancement via Coherent Wave Amplification in the Mammalian Cochlea

Authors: Alessandro Altoè, Christopher A Shera

Subjects: Biological Physics (physics.bio-ph)

[19]  arXiv:2306.13435 [pdf, other]

Title: High-throughput design of cultured tissue moulds using a biophysical model

Authors: James P. Hague, Allison E. Andrews, Hugh Dickinson

Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Tissues and Organs (q-bio.TO)

[20]  arXiv:2306.13622 [pdf, other]

Title: Kinetics of the xanthophyll cycle and its role in photoprotective memory and response

Authors: Audrey Short, Thomas P. Fay, Thien Crisanto, Ratul Mangal, Krishna K. Niyogi, David T. Limmer, Graham R. Fleming

Comments: NCOMMS-23-25582, DOI : 10.1038/s41467-023-42281-8

Subjects: Biological Physics (physics.bio-ph); Chemical Physics (physics.chem-ph)

[21]  arXiv:2306.14059 [pdf, other]

Title: Universal Casimir attraction between filaments at the cell scale

Authors: Benjamin Spreng, Hélène Berthoumieux, Astrid Lambrecht, Anne-Florence Bitbol, Paulo A. Maia Neto, Serge Reynaud

Comments: 15 pages, 9 figures. This paper extends the unpublished short report arXiv:2304.06006

Journal-ref: 2024 New J. Phys. 26 013009

Subjects: Biological Physics (physics.bio-ph); Statistical Mechanics (cond-mat.stat-mech)

[22]  arXiv:2306.14900 [pdf, other]

Title: A numerical model of the human cornea accounting for the fiber-distributed collagen microstructure

Authors: Maria Laura De Bellis, Marcello Vasta, Alessio Gizzi, Anna Pandolfi

Comments: 18 pages, 6 figures

Subjects: Biological Physics (physics.bio-ph)

[23]  arXiv:2306.15352 [pdf, other]

Title: Theory of active self-organization of dense nematic structures in the actin cytoskeleton

Authors: Waleed Mirza, Marco De Corato, Marco Pensalfini, Guillermo Vilanova, Alejandro Torres-Sánchez, Marino Arroyo

Comments: 11 pages, 4 figures, 1 supplementary PDF, 8 supplementary videos

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

[24]  arXiv:2306.15459 [pdf, other]

Title: Permanent magnet systems to study the interaction between magnetic nanoparticles and cells in microslide channels

Authors: Leon Abelmann, Eunheui Gwag, Baeckkyoung Sung

Comments: 14 pages, 15 figures

Subjects: Biological Physics (physics.bio-ph); Applied Physics (physics.app-ph)

[25]  arXiv:2306.16885 [pdf, other]

Title: Optimality in superselective surface binding by multivalent DNA nanostars

Authors: Christine Linne, Eva Heemskerk, Jos Zwanikken, Daniela J. Kraft, Liedewij Laan

Comments: 14 pages, 4 figures

Subjects: Biological Physics (physics.bio-ph)