arXiv - PHYS - Biological Physics最新文献_第2页

Ordering, spontaneous flows and aging in active fluids depositing tracks 活性流体沉积轨道的有序、自发流动和老化

arXiv - PHYS - Biological Physics Pub Date : 2024-09-08 DOI: arxiv-2409.05195

Samuel Bell, Joseph Ackermann, Ananyo Maitra, Raphael Voituriez

{"title":"Ordering, spontaneous flows and aging in active fluids depositing tracks","authors":"Samuel Bell, Joseph Ackermann, Ananyo Maitra, Raphael Voituriez","doi":"arxiv-2409.05195","DOIUrl":"https://doi.org/arxiv-2409.05195","url":null,"abstract":"Growing experimental evidence shows that cell monolayers can induce\u0000long-lived perturbations to their environment, akin to footprints, which in\u0000turn influence the global dynamics of the system. Inspired by these\u0000observations, we propose a comprehensive theoretical framework to describe\u0000systems where an active field dynamically interacts with a non-advected\u0000footprint field, deposited by the active field. We derive the corresponding\u0000general hydrodynamics for both polar and nematic fields. Our findings reveal\u0000that the dynamic coupling to a footprint field induces remarkable effects\u0000absent in classical active hydrodynamics, such as symmetry-dependent\u0000modifications to the isotropic-ordered transition, which may manifest as either\u0000second-order or first-order, alterations in spontaneous flow transitions,\u0000potentially resulting in oscillating flows and rotating fields, and initial\u0000condition-dependent aging dynamics characterized by long-lived transient\u0000states. Our results suggest that footprint deposition could be a key mechanism\u0000determining the dynamical phases of cellular systems, or more generally active\u0000systems inducing long-lived perturbations to their environment.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Origin of yield stress and mechanical plasticity in biological tissues 生物组织中屈服应力和机械塑性的起源

arXiv - PHYS - Biological Physics Pub Date : 2024-09-06 DOI: arxiv-2409.04383

Anh Q. Nguyen, Junxiang Huang, Dapeng Bi

{"title":"Origin of yield stress and mechanical plasticity in biological tissues","authors":"Anh Q. Nguyen, Junxiang Huang, Dapeng Bi","doi":"arxiv-2409.04383","DOIUrl":"https://doi.org/arxiv-2409.04383","url":null,"abstract":"During development and under normal physiological conditions, biological\u0000tissues are continuously subjected to substantial mechanical stresses. In\u0000response to large deformations cells in a tissue must undergo multicellular\u0000rearrangements in order to maintain integrity and robustness. However, how\u0000these events are connected in time and space remains unknown. Here, using\u0000computational and theoretical modeling, we studied the mechanical plasticity of\u0000epithelial monolayers under large deformations. Our results demonstrate that\u0000the jamming-unjamming (solid-fluid) transition in tissues can vary\u0000significantly depending on the degree of deformation, implying that tissues are\u0000highly unconventional materials. Using analytical modeling, we elucidate the\u0000origins of this behavior. We also demonstrate how a tissue accommodates large\u0000deformations through a collective series of rearrangements, which behave\u0000similarly to avalanches in non-living materials. We find that these tissue\u0000avalanches are governed by stress redistribution and the spatial distribution\u0000of vulnerable spots. Finally, we propose a simple and experimentally accessible\u0000framework to predict avalanches and infer tissue mechanical stress based on\u0000static images.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantum features of the transport through ion channels in the soft knock-on model 软敲击模型中离子通道传输的量子特征

arXiv - PHYS - Biological Physics Pub Date : 2024-09-05 DOI: arxiv-2409.03497

Mateusz Polakowski, Miłosz Panfil

引用次数: 0

Critical transition between intensive and extensive active droplets 密集型和广泛型活性液滴之间的临界过渡

arXiv - PHYS - Biological Physics Pub Date : 2024-09-05 DOI: arxiv-2409.03629

Jonathan Bauermann, Giacomo Bartolucci, Job Boekhoven, Frank Jülicher, Christoph A. Weber

{"title":"Critical transition between intensive and extensive active droplets","authors":"Jonathan Bauermann, Giacomo Bartolucci, Job Boekhoven, Frank Jülicher, Christoph A. Weber","doi":"arxiv-2409.03629","DOIUrl":"https://doi.org/arxiv-2409.03629","url":null,"abstract":"Emulsions ripen with an average droplet size increasing in time. In\u0000chemically active emulsions, coarsening can be absent, leading to a\u0000non-equilibrium steady state with mono-disperse droplet sizes. By considering a\u0000minimal model for phase separation and chemical reactions maintained away from\u0000equilibrium, we show that there is a critical transition in the conserved\u0000quantity between two classes of chemically active droplets: intensive and\u0000extensive ones. Single intensive active droplets reach a stationary size mainly\u0000controlled by the reaction-diffusion length scales. Intensive droplets in an\u0000emulsion interact only weakly, and the stationary size of a single droplet\u0000approximately sets the size of each droplet. On the contrary, the size of a\u0000single extensive active droplet scales with the system size, similar to passive\u0000phases. In an emulsion of many extensive droplets, their sizes become\u0000stationary only due to interactions among them. We discuss how the critical\u0000transition between intensive and extensive active droplets affects shape\u0000instabilities, including the division of active droplets, paving the way for\u0000the observation of successive division events in chemically active emulsions","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alpha helices are more evolutionarily robust to environmental perturbations than beta sheets: Bayesian learning and statistical mechanics to protein evolution 与β片相比，α螺旋对环境扰动的进化更为稳健：蛋白质进化的贝叶斯学习和统计力学

arXiv - PHYS - Biological Physics Pub Date : 2024-09-05 DOI: arxiv-2409.03297

Tomoei Takahashi, George Chikenji, Kei Tokita, Yoshiyuki Kabashima

{"title":"Alpha helices are more evolutionarily robust to environmental perturbations than beta sheets: Bayesian learning and statistical mechanics to protein evolution","authors":"Tomoei Takahashi, George Chikenji, Kei Tokita, Yoshiyuki Kabashima","doi":"arxiv-2409.03297","DOIUrl":"https://doi.org/arxiv-2409.03297","url":null,"abstract":"How typical elements that shape organisms, such as protein secondary\u0000structures, have evolved, or how evolutionarily susceptible/resistant they are\u0000to environmental changes, are significant issues in evolutionary biology,\u0000structural biology, and biophysics. According to Darwinian evolution, natural\u0000selection and genetic mutations are the primary drivers of biological\u0000evolution. However, the concept of ``robustness of the phenotype to\u0000environmental perturbations across successive generations,'' which seems\u0000crucial from the perspective of natural selection, has not been formalized or\u0000analyzed. In this study, through Bayesian learning and statistical mechanics we\u0000formalize the stability of the free energy in the space of amino acid sequences\u0000that can design particular protein structure against perturbations of the\u0000chemical potential of water surrounding a protein as such robustness. This\u0000evolutionary stability is defined as a decreasing function of a quantity\u0000analogous to the susceptibility in the statistical mechanics of magnetic bodies\u0000specific to the amino acid sequence of a protein. Consequently, in a\u0000two-dimensional square lattice protein model composed of 36 residues, we found\u0000that as we increase the stability of the free energy against perturbations in\u0000environmental conditions, the structural space shows a steep step-like\u0000reduction. Furthermore, lattice protein structures with higher stability\u0000against perturbations in environmental conditions tend to have a higher\u0000proportion of $alpha$-helices and a lower proportion of $beta$-sheets. The\u0000latter result shows that protein structures rich in $alpha$-helices are more\u0000robust to environmental perturbations through successive generations than those\u0000rich in $beta$-sheets.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fluctuating Hydrodynamics Describes Transport in Cellular Aggregates 波动流体力学描述了细胞聚集体的运输过程

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.03039

Subhadip Chakraborti, Vasily Zaburdaev

引用次数: 0

UNC-104 transport properties are robust and independent of changes in its cargo binding UNC-104 的运输特性非常稳定，不受货物结合变化的影响

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.02655

Amir Shee, Vidur Sabharwal, Sandhya P. Koushika, Amitabha Nandi, Debasish Chaudhuri

{"title":"UNC-104 transport properties are robust and independent of changes in its cargo binding","authors":"Amir Shee, Vidur Sabharwal, Sandhya P. Koushika, Amitabha Nandi, Debasish Chaudhuri","doi":"arxiv-2409.02655","DOIUrl":"https://doi.org/arxiv-2409.02655","url":null,"abstract":"Cargo distribution within eukaryotic cells relies on the active transport\u0000mechanisms driven by molecular motors. Despite their critical role, the\u0000intricate relationship between motor transport properties and cargo binding -\u0000and its impact on motor distribution - remains inadequately understood.\u0000Additionally, improper regulation of ubiquitination, a pivotal\u0000post-translational modification that affects protein degradation, activation,\u0000and localization, is associated with several neurodegenerative diseases. Recent\u0000data showed that ubiquitination can alter motor-cargo binding of the Kinesin-3\u0000motor UNC-104 / KIF1A that transports synaptic vesicles. To investigate how\u0000ubiquitin-like modifications affect motor protein function, particularly cargo\u0000binding, transport properties, and distribution, we utilize the PLM neuron of\u0000C. elegans as a model system. Using fluorescent microscopy, we assess the\u0000distribution of cargo-bound UNC-104 motors along the axon and probe their\u0000dynamics using FRAP experiments. We model cargo binding kinetics with a Master\u0000equation and motor density dynamics using a Fokker-Planck approach. Our\u0000combined experimental and theoretical analysis reveals that ubiquitin-like\u0000knockdowns enhance UNC-104's cooperative binding to its cargo. However, these\u0000modifications do not affect UNC-104's transport properties, such as\u0000processivity and diffusivity. Thus, while ubiquitin-like modifications\u0000significantly impact the cargo-binding of UNC-104, they do not alter its\u0000transport dynamics, keeping the homeostatic distribution of UNC-104 unchanged.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Margination of artificially stiffened red blood cells 人工硬化红细胞的边缘化

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.02776

Revaz D. Chachanidze, Othmane Aouane, Jens Harting, Christian Wagner, Marc Leonetti

引用次数: 0

Hydromechanical field theory of plant morphogenesis 植物形态发生的水力机械场理论

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.02775

Hadrien Oliveri, Ibrahim Cheddadi

{"title":"Hydromechanical field theory of plant morphogenesis","authors":"Hadrien Oliveri, Ibrahim Cheddadi","doi":"arxiv-2409.02775","DOIUrl":"https://doi.org/arxiv-2409.02775","url":null,"abstract":"The growth of plants is a hydromechanical phenomenon in which cells enlarge\u0000by absorbing water, while their walls expand and remodel under turgor-induced\u0000tension. In multicellular tissues, where cells are mechanically interconnected,\u0000morphogenesis results from the combined effect of local cell growths, which\u0000reflects the action of heterogeneous mechanical, physical, and chemical fields,\u0000each exerting varying degrees of nonlocal influence within the tissue. To\u0000describe this process, we propose a physical field theory of plant growth. This\u0000theory treats the tissue as a poromorphoelastic body, namely a growing\u0000poroelastic medium, where growth arises from pressure-induced deformations and\u0000osmotically-driven imbibition of the tissue. From this perspective, growing\u0000regions correspond to hydraulic sinks, leading to the possibility of complex\u0000non-local regulations, such as water competition and growth-induced water\u0000potential gradients. More in general, this work aims to establish foundations\u0000for a mechanistic, mechanical field theory of morphogenesis in plants, where\u0000growth arises from the interplay of multiple physical fields, and where\u0000biochemical regulations are integrated through specific physical parameters.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Elephant trunk wrinkles: A mathematical model of function and form 象鼻皱纹功能与形态的数学模型

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.03075

Yang Liu, Alain Goriely, L. Angela Mihai

{"title":"Elephant trunk wrinkles: A mathematical model of function and form","authors":"Yang Liu, Alain Goriely, L. Angela Mihai","doi":"arxiv-2409.03075","DOIUrl":"https://doi.org/arxiv-2409.03075","url":null,"abstract":"A remarkable feature of the elephant trunk is the pronounced wrinkling that\u0000enables its great flexibility. Here, we devise a general mathematical model\u0000that accounts for characteristic skin wrinkles formed during morphogenesis in\u0000elephant trunk. Using physically realistic parameters and operating within the\u0000theoretical framework of nonlinear morphoelasticity, we elucidate analytically\u0000and numerically the effect of skin thickness, relative stiffness and\u0000differential growth on the physiological pattern of transverse wrinkles\u0000distributed along the trunk. We conclude that, since the skin and muscle\u0000components have similar material properties, geometric parameters, such as\u0000curvature, play important roles. In particular, our model predicts that, in the\u0000proximal region close to the skull, where curvature is lower, fewer wrinkles\u0000form and sooner than in the distal narrower region where more wrinkles develop.\u0000Similarly, less wrinkling is found on the ventral side, which is flatter,\u0000compared to the dorsal side. In summary, the mechanical compatibility between\u0000the skin and the muscle enables them to grow seamlessly, while the wrinkled\u0000skin acts as a protective barrier that is both thicker and more flexible than\u0000the unwrinkled skin.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"280 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0