arXiv - PHYS - Biological Physics最新文献_第10页

Nonequilibrium Membrane Dynamics Induced by Active Protein Interactions and Chemical Reactions: A Review 活性蛋白质相互作用和化学反应诱导的非平衡膜动力学：综述

arXiv - PHYS - Biological Physics Pub Date : 2024-07-22 DOI: arxiv-2407.15371

Hiroshi Noguchi

引用次数: 0

Binding and dimerization control phase separation in a compartment 结合和二聚化控制隔室中的相分离

arXiv - PHYS - Biological Physics Pub Date : 2024-07-21 DOI: arxiv-2407.15179

Riccardo Rossetto, Gerrit Wellecke, David Zwicker

引用次数: 0

Generalized Langevin equation for a tagged monomer in a Gaussian semiflexible polymer 高斯半柔性聚合物中标记单体的广义朗温方程

arXiv - PHYS - Biological Physics Pub Date : 2024-07-20 DOI: arxiv-2407.14886

Xavier Durang, Jae-Hyung Jeon

引用次数: 0

Growing tissue sheets on substrates: buds, buckles, and pores 在基质上生长组织片：芽、扣和孔

arXiv - PHYS - Biological Physics Pub Date : 2024-07-18 DOI: arxiv-2407.13187

Hiroshi Noguchi, Jens Elgeti

引用次数: 0

Dissipation at limited resolutions: Power law and detection of hidden dissipative scales 有限分辨率下的耗散：幂律和隐藏耗散尺度的检测

arXiv - PHYS - Biological Physics Pub Date : 2024-07-18 DOI: arxiv-2407.13707

Qiwei Yu, Pedro E. Harunari

{"title":"Dissipation at limited resolutions: Power law and detection of hidden dissipative scales","authors":"Qiwei Yu, Pedro E. Harunari","doi":"arxiv-2407.13707","DOIUrl":"https://doi.org/arxiv-2407.13707","url":null,"abstract":"Nonequilibrium systems, in particular living organisms, are maintained by\u0000irreversible transformations of energy that drive diverse functions.\u0000Quantifying their irreversibility, as measured by energy dissipation, is\u0000essential for understanding the underlying mechanisms. However, existing\u0000techniques usually overlook experimental limitations, either by assuming full\u0000information or by employing a coarse-graining method that requires knowledge of\u0000the structure behind hidden degrees of freedom. Here, we study the inference of\u0000dissipation from finite-resolution measurements by employing a recently\u0000developed model-free estimator that considers both the sequence of\u0000coarse-grained transitions and the waiting time distributions:\u0000$sigma_2=sigma_2^ell + sigma_2^t$. The dominant term $sigma_2^ell$\u0000originates from the sequence of observed transitions; we find that it scales\u0000with resolution following a power law. Comparing the scaling exponent with a\u0000previous estimator highlights the importance of accounting for flux\u0000correlations at lower resolutions. $sigma_2^t$ comes from asymmetries in\u0000waiting time distributions, with its peak revealing characteristic scales of\u0000the underlying dissipative process. Alternatively, the characteristic scale can\u0000be detected in a crossover of the scaling of $sigma_2^ell$. This provides a\u0000novel perspective for extracting otherwise hidden characteristic dissipative\u0000scales directly from dissipation measurements. We illustrate these results in\u0000biochemical models as well as complex networks. Overall, this study highlights\u0000the significance of resolution considerations in nonequilibrium systems,\u0000providing insights into the interplay between experimental resolution, entropy\u0000production, and underlying complexity.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745038","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

Encoding spatiotemporal asymmetry in artificial cilia with a ctenophore-inspired soft-robotic platform 用栉水母启发的软机器人平台编码人工纤毛的时空不对称性

arXiv - PHYS - Biological Physics Pub Date : 2024-07-18 DOI: arxiv-2407.13894

David J. Peterman, Margaret L. Byron

{"title":"Encoding spatiotemporal asymmetry in artificial cilia with a ctenophore-inspired soft-robotic platform","authors":"David J. Peterman, Margaret L. Byron","doi":"arxiv-2407.13894","DOIUrl":"https://doi.org/arxiv-2407.13894","url":null,"abstract":"A remarkable variety of organisms use metachronal coordination (i.e.,\u0000numerous neighboring appendages beating sequentially with a fixed phase lag) to\u0000swim or pump fluid. This coordination strategy is used by microorganisms to\u0000break symmetry at small scales where viscous effects dominate and flow is\u0000time-reversible. Some larger organisms use this swimming strategy at\u0000intermediate scales, where viscosity and inertia both play important roles.\u0000However, the role of individual propulsor kinematics - especially across\u0000hydrodynamic scales - is not well-understood, though the details of propulsor\u0000motion can be crucial for the efficient generation of flow. To investigate this\u0000behavior, we developed a new soft robotic platform using magnetoactive silicone\u0000elastomers to mimic the metachronally coordinated propulsors found in swimming\u0000organisms. Furthermore, we present a method to passively encode spatially\u0000asymmetric beating patterns in our artificial propulsors. We investigated the\u0000kinematics and hydrodynamics of three propulsor types, with varying degrees of\u0000asymmetry, using Particle Image Velocimetry and high-speed videography. We find\u0000that asymmetric beating patterns can move considerably more fluid relative to\u0000symmetric beating at the same frequency and phase lag, and that asymmetry can\u0000be passively encoded into propulsors via the interplay between elastic and\u0000magnetic torques. Our results demonstrate that nuanced differences in propulsor\u0000kinematics can substantially impact fluid pumping performance. Our soft robotic\u0000platform also provides an avenue to explore metachronal coordination at the\u0000meso-scale, which in turn can inform the design of future bioinspired pumping\u0000devices and swimming robots.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745174","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

A statistical mechanics investigation of Unfolded Protein Response across organisms 跨生物体的折叠蛋白反应统计力学研究

arXiv - PHYS - Biological Physics Pub Date : 2024-07-17 DOI: arxiv-2407.12464

Nicole Luchetti, Keith M. Smith, Margherita A. G. Matarrese, Alessandro Loppini, Simonetta Filippi, Letizia Chiodo

{"title":"A statistical mechanics investigation of Unfolded Protein Response across organisms","authors":"Nicole Luchetti, Keith M. Smith, Margherita A. G. Matarrese, Alessandro Loppini, Simonetta Filippi, Letizia Chiodo","doi":"arxiv-2407.12464","DOIUrl":"https://doi.org/arxiv-2407.12464","url":null,"abstract":"Living systems rely on coordinated molecular interactions, especially those\u0000related to gene expression and protein activity. The Unfolded Protein Response\u0000is a crucial mechanism in eukaryotic cells, activated when unfolded proteins\u0000exceed a critical threshold. It maintains cell homeostasis by enhancing protein\u0000folding, initiating quality control, and activating degradation pathways when\u0000damage is irreversible. This response functions as a dynamic signaling network,\u0000with proteins as nodes and their interactions as edges. We analyze these\u0000protein-protein networks across different organisms to understand their\u0000intricate intra-cellular interactions and behaviors. In this work, analyzing\u0000twelve organisms, we assess how fundamental measures in network theory can\u0000individuate seed-proteins and specific pathways across organisms. We employ\u0000network robustness to evaluate and compare the strength of the investigated PPI\u0000networks, and the structural controllability of complex networks to find and\u0000compare the sets of driver nodes necessary to control the overall networks. We\u0000find that network measures are related to phylogenetics, and advanced network\u0000methods can identify main pathways of significance in the complete Unfolded\u0000Protein Response mechanism.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745172","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

Metabolic activity controls the emergence of coherent flows in microbial suspensions 代谢活动控制着微生物悬浮液中相干流的出现

arXiv - PHYS - Biological Physics Pub Date : 2024-07-13 DOI: arxiv-2407.09884

Alexandros A. Fragkopoulos, Florian Böhme, Nicole Drewes, Oliver Bäumchen

{"title":"Metabolic activity controls the emergence of coherent flows in microbial suspensions","authors":"Alexandros A. Fragkopoulos, Florian Böhme, Nicole Drewes, Oliver Bäumchen","doi":"arxiv-2407.09884","DOIUrl":"https://doi.org/arxiv-2407.09884","url":null,"abstract":"Photosynthetic microbes have evolved and successfully adapted to the\u0000ever-changing environmental conditions in complex microhabitats throughout\u0000almost all ecosystems on Earth. In the absence of light, they can sustain their\u0000biological functionalities through aerobic respiration, and even in anoxic\u0000conditions through anaerobic metabolic activity. For a suspension of\u0000photosynthetic microbes in an anaerobic environment, individual cellular\u0000motility is directly controlled by its photosynthetic activity, i.e. the\u0000intensity of the incident light absorbed by chlorophyll. The effects of the\u0000metabolic activity on the collective motility on the population level, however,\u0000remain elusive so far. Here, we demonstrate that at high light intensities, a\u0000suspension of photosynthetically active microbes exhibits a stable reverse\u0000sedimentation profile of the cell density due to the microbes' natural bias to\u0000move against gravity. With decreasing photosynthetic activity, and therefore\u0000suppressed individual motility, the living suspension becomes unstable giving\u0000rise to coherent bioconvective flows. The collective motility is fully\u0000reversible and manifests as regular, three-dimensional plume structures, in\u0000which flow rates and cell distributions are directly controlled via the light\u0000intensity. The coherent flows emerge in the highly unfavourable condition of\u0000lacking both light and oxygen and, thus, might help the microbial collective to\u0000expand the exploration of their natural habitat in search for better survival\u0000conditions.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141720957","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

Modeling Ion-Specific Effects in Polyelectrolyte Brushes: A Modified Poisson-Nernst-Planck Model 聚电解质刷中的离子特异性效应建模：修正的泊松-纳斯特-普朗克模型

arXiv - PHYS - Biological Physics Pub Date : 2024-07-12 DOI: arxiv-2407.09633

William J Ceely, Marina Chugunova, Ali Nadim, James D Sterling

引用次数: 0

Directed Motion and Spatial Coherence in the Cell Nucleus 细胞核中的定向运动和空间一致性

arXiv - PHYS - Biological Physics Pub Date : 2024-07-12 DOI: arxiv-2407.08899

M. Hidalgo-Soria, Y. Haddad, E. Barkai, Y. Garini, S. Burov

引用次数: 0